# Patent

## Title
Isolated nucleic acid molecules which encode peptides that bind to HLA molecules, and uses thereof

## Abstract

Nucleic acid molecules which encode decapeptides which are defined by an HLA-A2 binding motif are disclosed. Also disclosed are expression vectors which include these nucleic acid molecules.

## Background
RELATED APPLICATION
This application is a divisional application of application Ser. No. 09/099,543, filed Jun. 18, 1998, now U.S. Pat. No. 6,326,200, which is a continuation-in-part of application Ser. No. 09/061.388, filed Apr. 16, 1998, now U.S. Pat. No. 6,277,956, which is a continuation-in-part of application Ser. No. 08/880,963, filed Jun. 23, 1997, now U.S. Pat. No. 6,025,470, incorporated by reference in their entireties. A portion of the invention was published by the inventors, less than one year before the filing date of the first continuation-in-part application. See Romero et al., J. Immunol. 159:2366 (1997) incorporated by reference.


FIELD OF THE INVENTION
This invention relates to peptides which are useful in the context of cellular immunology. More particularly, the invention relates to peptides which bind to HLA molecules on the surface of cells. At least some of these peptides also induce the activation of cytolytic T cells, when they are complexed with their partner HLA molecule. Also a part of the invention are the uses of these peptides in areas such as identifying HLA-A2 positive cells, provoking T cells, determining presence of particular T cells, as well as cytolytic T cells themselves.
BACKGROUND AND PRIOR ART
The study of the recognition or lack of recognition of cancer cells by a host organism has proceeded in many different directions. Understanding of the field presumes some understanding of both basic immunology and oncology.
Early research on mouse tumors revealed that these displayed molecules which led to rejection of tumor cells when transplanted into syngeneic animals. These molecules are “recognized” by T-cells in the recipient animal, and provoke a cytolytic T-cell response with lysis of the transplanted cells. This evidence was first obtained with tumors induced in vitro by chemical carcinogens, such as methylcholanthrene. The antigens expressed by the tumors and which elicited the T-cell response were found to be different for each tumor. See Prehn, et al., J. Natl. Canc. Inst. 18: 769-778 (1957); Klein et al., Cancer Res. 20: 1561-1572 (1960); Gross, Cancer Res. 3: 326-333 (1943), Basombrio, Cancer Res. 30: 2458-2462 (1970) for general teachings on inducing tumors with chemical carcinogens and differences in cell surface antigens. This class of antigens has come to be known as “tumor specific transplantation antigens” or “TSTAs.” Following the observation of the presentation of such antigens when induced by chemical carcinogens, similar results were obtained when tumors were induced in vitro via ultraviolet radiation. See Kripke, J. Natl. Canc. Inst. 53: 333-1336 (1974).
While T-cell mediated immune responses were observed for the types of tumor described supra, spontaneous tumors were thought to be generally non-immunogenic. These were therefore believed not to present antigens which provoked a response to the tumor in the tumor carrying subject. See Hewitt, et al., Brit. J. Cancer 33: 241-259 (1976).
The family of tum− antigen presenting cell lines are immunogenic variants obtained by mutagenesis of mouse tumor cells or cell lines, as described by Boon et al., J. Exp. Med. 152:1184-1193 (1980), the disclosure of which is incorporated by reference. To elaborate, tum31  antigens are obtained by mutating tumor cells which is incorporated by reference. To elaborate, tum− syngeneic mice and will form tumors (i.e., “tum+” cells). When these tum+ cells are mutagenized, they are rejected by syngeneic mice, and fail to form tumors (thus “tum− ”). See Boon et al., Proc. Natl. Acad. Sci. USA 74: 272 (1977), the disclosure of which is incorporated by reference. Many tumor types have been shown to exhibit this phenomenon. See, e.g., Frost et al., Cancer Res. 43: 125 (1983).
It appears that tum− variants fail to form progressive tumors because they initiate an inmmune rejection process. The evidence in favor of this hypothesis includes the ability of “tum−” variants of tumors, i.e., those which do not normally form tumors, to do so in mice with immune systems suppressed by sublethal irradiation, Van Pel et al., Proc. Natl. Acad. Sci. USA 76:5282-5285 (1979); and the observation that intraperitoneally injected tum cells of mastocytoma P815 multiply exponentially for 12-15 days, and then are eliminated in only a few days in the midst of an influx of lymphocytes and macrophages (Uyttenhove et al., J. Exp. Med. 152: 1175-1183 (1980)). Further evidence includes the observation that mice acquire an immune memory which permits them to resist subsequent challenge to the same turn variant, even when immunosuppressive amounts of radiation are administered with the following challenge of cells (Boon et al., Proc. Natl. Acad. Sci. USA 74: 272-275 (1977); Van Pel et al., supra; Uyttenhove et al., supra). Later research found that when spontaneous tumors were subjected to mutagenesis, immunogenic variants were produced which did generate a response. Indeed, these variants were able to elicit an immune protective response against the original tumor. See Van Pel et al., J. Exp. Med. 157: 1992-2001 (1983). Thus, it has been shown that it is possible to elicit presentation of a so-called “tumor rejection antigen” in a tumor which is a target for a syngeneic rejection response. Similar results have been obtained when foreign genes have been transfected into spontaneous tumors. See Fearon et al., Cancer Res. 48: 2975-1980 (1988) in this regard.
A class of antigens has been recognized which are presented on the surface of tumor cells and are recognized by cytolytic T cells, leading to lysis. This class of antigens will be referred to as “tumor rejection antigens” or “TRAs” hereafter. TRAs may or may not elicit antibody responses. The extent to which these antigens have been studied, has been via cytolytic T cell characterization studies, in vitro, i.e., the study of the identification of the antigen by a particular cytolytic T cell (“CTL” hereafter) subset. The subset proliferates upon recognition of the presented tumor rejection antigen, and the cells presenting the tumor rejection antigens are lysed. Characterization studies have identified CTL clones which specifically lyse cells expressing the tumor rejection antigens. Examples of this work may be found in Levy et al., Adv. Cancer Res. 24: 1-59 (1977); Boon et al., J. Exp. Med. 152: 1184-1193 (1980); Brunner et al., J. Immunol. 124: 1627-1634 (1980); Maryanski et al., Eur. J. Immunol. 124: 1627-1634 (1980); Maryanski et al., Eur. J. Immunol. 12: 406-412 (1982); Palladino et al., Cancer. Res. 47: 5074-5079 (1987). This type of analysis is required for other types of antigens recognized by CTLs, including minor histocompatibility antigens, the male specific H-Y antigens, and the class of antigens referred to as “tum-” antigens, and discussed herein.
A tumor exemplary of the subject matter described supra is known as P815. See De Plaen et al., Proc. Natl. Acad. Sci. USA 85: 2274-2278 (1988); Szikora et al., EMBO J 9: 1041-1050 (1990), and Sibille et al., J. Exp. Med. 172: 35-45 (1990), the disclosures of which are incorporated by reference. The P815 tumor is a mastocytoma, induced in a DBA/2 mouse with methylcholanthrene and cultured as both an in vitro tumor and a cell line. The P815 line has generated many turn variants following mutagenesis, including variants referred to as P91A (DePlaen, supra), 35B (Szikora, supra), and P198 (Sibille, supra). In contrast to tumor rejection antigens—and this is a key distinction—the turn antigens are only present after the tumor cells are mutagenized. Tumor rejection antigens are present on cells of a given tumor without mutagenesis. Hence, with reference to the literature, a cell line can be tum+, such as the line referred to as “P1”, and can be provoked to produce tum− variants. Since the turn phenotype differs from that of the parent cell line, one expects a difference in the DNA of tum− cell lines as compared to their tum+ parental lines, and this difference can be exploited to locate the gene of interest in tum− cells. As a result, it was found that genes of tun variants such as P91A, 35B and P198 differ from their normal alleles by point mutations in the coding regions of the gene. See Szikora and Sibille, supra, and Lurquin et al., Cell 58: 293-303 (1989). This has proved not to be the case with the TRAs of this invention. These papers also demonstrated that peptides derived from the tug antigen are presented by H-2d Class I molecules for recognition by CTLs. P91A is presented by Ld, P35 by Dd and P198 by Kd.
PCT application PCT/US92/04354, filed on May 22, 1992 assigned to the same assignee as the subject application, teaches a family of human tumor rejection antigen precursor coding genes, referred to as the MAGE family. Several of these genes are also discussed in van der Bruggen et al., Science 254: 1643 (1991). It is now clear that the various genes of the MAGE family are expressed in tumor cells, and can serve as markers for the diagnosis of such tumors, as well as for other purposes discussed therein. See also Traversari et al., Immunogenetics 35: 145 (1992); van der Bruggen et al., Science 254: 1643 (1991) and De Plaen, et al., Immnunogenetics 40: 360(1994). The mechanism by which a protein is processed and presented on a cell surface has now been fairly well documented. A cursory review of the development of the field may be found in Barinaga, “Getting Some ‘Backbone’: How MHC Binds Peptides,” Science 257: 880 (1992); also, see Fremont et al., Science 257: 919 (1992); Matsumura et al., Science 257: 927 (1992); Engelhard, Ann. Rev. Immunol. 12:181-207 (1994); Madden, et al, Cell 75:693-708 (1993); Ramensee, et al, Ann. Rev. Immunol. 11:213-244 (1993); Germain, Cell 76: 287-299 (1994). These papers generally point to a requirement that the peptide which binds to an MHC/HLA molecule be nine amino acids long (a “nonapeptide”), and to the importance of the second and ninth residues of the nonapeptide. For H-2Kb, the anchor residues are positions 5 and 8 of an octamer, for H-2Db, they are positions 5 and 9 of a nonapeptide while the anchor residues for HLA-A1 are positions 3 and 9 of a nonamer. Generally, for HLA molecules, positions 2 and 9 are anchors.
Studies on the MAGE family of genes have now revealed that a particular nonapeptide is in fact presented on the surface of some tumor cells, and that the presentation of the nonapeptide requires that the presenting molecule be HLA-A1. Complexes of the MAGE-1 tumor rejection antigen (the “TRA” or “nonapeptide”) leads to lysis of the cell presenting it by cytolytic T cells (“CTLs”).
Research presented in, e.g., U.S. Pat. No. 5,405,940 filed Aug. 31, 1992, and in U.S. Pat. No. 5,571,711, found that when comparing homologous regions of various MAGE genes to the region of the MAGE-1 gene coding for the relevant nonapeptide, there is a great deal of homology. Indeed, these observations lead to one of the aspects of the invention disclosed and claimed therein, which is a family of nonapeptides all of which have the same N-terminal and C-terminal amino acids. These nonapeptides were described as being useful for various purposes which includes their use as imnmunogens, either alone or coupled to carrier peptides. Nonapeptides are of sufficient size to constitute an antigenic epitope, and the antibodies generated thereto were described as being useful for identifying the nonapeptide, either as it exists alone, or as part of a larger polypeptide.
The preceding survey of the relevant literature shows that various peptides, usually eight, nine, or ten amino acids in length, complex with MHC molecules and present targets for recognition by cytolytic T cells. A great deal of study has been carried out on melanoma, and melanoma antigens which are recognized by cytolytic T cells are now divided into three broad categories. The first, which includes many of the antigens discussed, supra, (e.g., MAGE), are expressed in some melanomas, as well as other tumor types, and normal testis and placenta. The antigens are the expression product of normal genes which are usually silent in normal tissues.
A second family of melanoma antigens includes antigens which are derived from mutant forms of normal proteins. Examples of this family are MUM-1 (Coulie, et al, Proc. Natl. Acad. Sci. USA 92:7976-7980 (1955)); CDK4 (Wölfel, et al, Science 269:1281-1284(1955)); Bcate (Robbins, et al, J. Exp. Med. 183:1185-1192 (1996)); and HLA-A2 (Brandel, et al, J. Exp. Med. 183:2501-2508 (1996)). A third category, also discussed, supra, includes the differentiation antigens which are expressed by both melanoma and melanocytes. Exemplary are tyrosinase, gp100, gp75, and Melan A/Mart-1. See U.S. Pat. No. 5,620,886 incorporated by reference, with respect to Melan-A. See Wölfel, et al., Eur. J. Immunol. 24: 759 (1994) and Brichard, et al., Eur. J. Immunol. 26: 224 (1996) for tyrosinase; Kang, et al., J. Immunol. 155: 1343 (1995); Cox, et al., Science 264: 716 (1994); Kawakami, et al., J. Immunol. 154: 3961 (1995) for gp 100; Wang, et al., J. Exp. Med. 183: 1131 (1996) for gp 75.
Cytolytic T cells (“CTLs” hereafter) have been identified in peripheral blood lymphocytes, and tumor infiltrating lymphocytes, of melanoma patients who are HLA-A*0201 positive. See Kawakami, et al, Proc. Natl. Acad. Sci. USA 91:3515 (1994); Coulie, et al, J. Exp. Med. 180:35 (1994). When ten HLA-A*0201 restricted Melan-A specific CTLs derived from different patients were tested, nine of them were found to recognize and react with the peptide Ala Ala Gly Ile Gly Ile Leu Thr Val, (SEQ ID NO: 2), which consists of amino acids 27-35 of Melan-A. (Kawakami, et al, J. Exp. Med. 180:347-352 (1994)). Rivoltini, et al, J. Immunol. 154:2257 (1995), showed that Melan-A specific CTLs could be induced by stimulating PBLs from HLA-A*0201 positive normal donors, and melanoma patients, using SEQ ID NO: 2. The strength of this response has led to SEQ ID NO: 2 being proposed as a target for vaccine development. It has now been found, however, that a decapeptide, i.e.,
Glu Ala Ala Gly Ile Gly Ile Leu Thr Val (SEQ ID NO: 1), is actually a better target than SEQ ID NO: 2. This recognition has led to work set forth herein, which is part of the invention.
The majority of peptides which have been identified as binding to HLA-A*0201 are 9 or 10 amino acids in length, and are characterized by two anchor residues. The first is Leu or Met at position 2, and the second is Leu or Val at position 9. See Falk, et al, Nature 351:290 (1991). Ruppert, et al, in Cell 74:929 (1993), show that amino acids found at other positions within a nona- or decapeptide may also have a role in the peptide-HLA-A*0201 interaction. They show, e.g., that a negatively charged residue or proline at position 1 was associated with poor HLA-A*0201 binding.
What is interesting about this work is that the two peptides represented by SEQ ID NOS: 1 and 2 do not possess the major anchor residue at position 2 and, the strong binder SEQ ID NO: 1 has a negatively charged residue at position 1.
A strong binder is not necessarily a stable binder, meaning that the interaction between peptide and HLA molecule may be, and is, brief When it is desired to induce CTLs, to identify them or to carry out other types of experiments, it would be desirable to have a peptide with the ability to bind to an MHC Class I molecule which binds with high affinity and forms stable complexes. See Van der Burg et al., J. Immunol, 156:3308 (1996).
The invention involves, inter alia, the development of new nonamers and decamers which are surprisingly good HLA binders and CTL stimulators. These molecules, as well as their uses, are among the features of the invention which are set forth in the disclosure which follows.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows results of experiments carried out to determine if tumor infiltrating lymphocyte populations would lyse cells presenting complexes of HLA-A*020 1 and various peptides on their surfaces.
FIGS. 2a-2d show stability studies comparing various peptides (SEQ ID NOS: 1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17).
FIG. 3 shows antigenic activity of various peptides when tested with TILNs.
FIG. 4 parallels FIG. 3, but uses CTLs generated from PBLs by stimulation of PBMCs with various peptides (SEQ ID NOS: 1, 2, 9).
FIGS. 5a-5r show results of flow cytometry studies, following stimulation of PBMCs with various peptides (SEQ ID NOS. 1, 2, 9, 15, 16, 17).
FIGS. 6a-6e depict results of cytolytic activity assays on PBMCs which have been stimulated with various peptides (SEQ ID NOS: 1, 2, 9, 15, 16).
FIGS. 7a-7e present data on Melan-A specific lytic activity of fluorescently sorted lymphocytes positive for tetramers containing SEQ ID NO: 1, following stimulation with other peptides (1, 2, 9, 15, 16).
FIG. 8 shows quantitative assessment of peptide dependent lytic activity of Melan-A monospecific CTL line. (SEQ ID NO: 1, 2, 9, 15, 16).



DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
EXAMPLE 1
In these experiments tumor infiltrating lymphocytes (“TILs” hereafter), were generated from tumor invaded lymph nodes of patients who were HLA-A*0201 positive. The experiments were designed so as to avoid antigen specific selection in vitro, and the methodology is now set forth.
Biopsies of tumor infiltrated lymph nodes (“TILNs” hereafter) were lysed to single cell suspensions, and then cultured in 24 well culture plates. A total of 3×106 cells were added to 2 mls of Iscove's Dulbecco medium which had been supplemented with Asn (0.24 mM), Arg (0.55 mM), and Gln (1.5 mM), and 10% pooled human A+ serum (serum obtained from type A blood donors), together with recombinant human IL-2 (100 u/ml), and IL-7 (10 ng/ml). These were the only cytokines used to culture the cell suspensions, so as to avoid antigen specific selection in vitro. The suspensions were cultured for 2-3 weeks, and the cells were then characterized for cell surface phenotype. Only populations with greater than 75% CD8+T cells, and of desired cytolytic activity were used. This second property was determined by combining the TILN populations with autologous cells, a melanoma cell line previously characterized as being HLA-A*0201 positive (Me290), a melanoma cell line known to be HLA-A*0201 negative (Me260) or cell line T2, which does not process antigen, together with the peptide of SEQ ID NO: 1. The peptide was added at 1 μM, together with varying ratios of effector (TILN) cells, and the target cells. The results presented in FIG. 1, show results obtained using LAU 132 and LAU 203, two TILN populations identified via this method. In FIG. 1, “M 10” is SEQ ID NO: 1, and the additional abbreviations are as set forth, supra. The assay was a 4-hour 51Cr release assay, carried out in the absence or presence of exogenously added peptide. In FIG. 1, open symbols stand for the absence of the peptide, and solid symbols for its presence. In this assay, the target cells were labelled with 51Cr for one hour, at 37° C., and were then washed two times. Labeled cells (1000 cells in 50 μl) were added to a 50 μl sample of effector cells (varying amounts, as indicated herein), in the presence or absence of 50 μ1 of antigenic peptide (1 μg/ml). Prior to their addition, the effector cells had been incubated for a minimum of 20 minutes at 37° C., in the presence of unlabelled natural killer (NK) cell targets (50,000 cells per well), in order to eliminate any non-specific lysis due to NK-like effectors present in the effector population. The 51Cr release was measured after 4 hours of incubation at 37° C., and percent specific lysis was calculated as:




  100
  ⁡
  
    [
    
      (
      
        
          
            experimental
            ⁢
            
              
            
            ⁢
            release
          
          -
          
            spontaneous
            ⁢
            
              
            
            ⁢
            release
          
        
        
          
            total
            ⁢
            
              
            
            ⁢
            release
          
          -
          
            spontaneous
            ⁢
            
              
            
            ⁢
            release
          
        
      
      )
    
    ]
  




As FIG. 1 shows, the two TILN populations lysed the HLA-A*0201 positive cell line equally well, whether or not the peptide was added. The HLA-A*0201 negative line, Me260, was not lysed in either situation, and T2, which does not process antigen, was lysed only when the peptide was added. These results show that the two TILN populations used hereafter recognize the epitope defined by SEQ ID NO: 1, when complexed to HLA-A*0201 positive cells.
EXAMPLE 2
The experiments described, supra, were modified somewhat, to determine if the TILNs recognized other peptides better than SEQ ID NO: 1. In these experiments, the following peptides were synthesized, using known methods:









(SEQ ID NO: 2)



Ala Ala Gly Ile Gly Ile Leu Thr Val



 



(SEQ ID NO: 3)



Ala Ala Gly Ile Gly Ile Leu Thr Val Ile



 



(SEQ ID NO: 4)



Ile Leu Thr Val Ile Leu Gly Val Leu






These peptides correspond, respectively, to amino acids 27-35, 27-36, and 32-40 of Melan-A.

TILN recognition was determined by incubating T2 cells (target), with TILNs (effector), at an effector: target ratio of 30:1. Varying concentrations of the peptides SEQ ID NOS: 1, 2, 3, or 4 were used. The 51Cr release assay discussed, supra, was used. The following Table sets forth the results of these experiments, wherein the peptide concentration is that which gave 50% of maximum activity. Relative activity is that obtained via comparison to SEQ ID NO: 2, i.e.,: [nM]50%[SEQ ID NO: 2]/[nM]50% [test peptide].










TABLE I









TILN LAU 203
TILN LAU 132












Peptidea 
Relative
Peptide
Relative


Peptide Sequence
[nM] 50%
activityb
[nM] 50%
activity














AAGIGILTV27-35
40
1
15
1


(SEQ ID NO: 2)


EAAGIGILTV26-35
1.5
27
1
15


(SEQ ID NO: 1)


AAGIGILTVI27-36
600
0.06
300
0.05


(SEQ ID NO: 3)


ILTVILGV32-40
>104
<4 × 10−3
>104
<1.5 × 10−3


(SEQ ID NO: 4)









It will be seen that SEQ ID NO: 1 had significantly higher activity than the other peptides tested.
EXAMPLE 3
A series of peptides were then synthesized, in order to attempt to determine peptides with enhanced binding to HLA-A*0201 molecules. The peptides synthesized are considered to be derivatives of SEQ ID NO: 2 (i.e., Ala Ala Gly Ile Gly Ile Leu Thr Val), and are








Ala Leu Gly Ile Gly Ile Leu Thr Val
(SEQ ID NO: 5)


 


Ala Met Gly Ile Gly Ile Leu Thr Val
(SEQ ID NO: 6)


 


Leu Ala Gly Ile Gly Ile Leu Thr Val
(SEQ ID NO: 7)


and


 


Met Ala Gly Ile Gly Ile Leu Thr Val
(SEQ ID NO: 8)


 







For SEQ ID NO:1, i.e., Glu Ala Ala Gly Ile Gly Ile


Leu Thr Val the derivatives were:









(SEQ ID NO: 9)







Glu Leu Ala Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 10)







Glu Met Ala Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 11)







Glu Ala Leu Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 12)







Glu Ala Met Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 13)







Tyr Ala Ala Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 14)







Phe Ala Ala Gly Ile Gly Ile Leu Thr Val


 









(SEQ ID NO: 15)







Ala Ala Ala Gly Ile Gly Ile Leu Thr Val


and


 









(SEQ ID NO: 16)







Ala Leu Ala Gly Ile Gly Ile Leu Thr Val






Three other control peptides were used, i.e.:










(SEQ ID NO: 17)







Glu Ile Leu Gly Phe Val Phe Thr Leu


 









(SEQ ID NO: 18)







Glu Val Asp Pro Ile Gly His Leu Tyr


and


 









(SEQ ID NO: 19)







Phe Leu Trp Gly Pro Arg Ala Leu Val.






SEQ ID NOS: 17 and 18 correspond to amino acids 58-66 of Influenza A matrix protein (“FLUMA”), and amino acids 168-176 of MAGE-3 TRAP.

In these experiments a peptide known to bind to HLA-A*0201 was used, i.e., amino acids 271-279 of the MAGE-3 TRAP (SEQ ID NO: 19), in an inhibition assay, together with cytolytic T cell line 198NS (Valmori, et al., Canc. Res. 57:735 (1997) which recognizes complexes of SEQ ID NO: 19 and HLA-A*0201. In these assays, varying concentrations of test peptides (1 μM to 100 μM) were incubated with 51Cr labelled T2 cells (1000 cells/well), for 15 minutes, at room temperature. A suboptimal dose of SEQ ID NO: 19 was then added (1nM), together with CTL 198NS, in an amount sufficient to create a 5/1 effector/target ratio. A 51Cr release assay was then carried out, in accordance with the method set forth, supra. The amount of test peptide needed to inhibit recognition of complexes by the CTL was calculated, and then binding affinity of each peptide, relative to SEQ ID NO: 2, was calculated, using the formula:




  R
  =
  
    
      I
      ⁢
      
        
      
      ⁢
      
        
          D
          50
        
        ⁡
        
          (
          
            SEQ
            ⁢
            
              
            
            ⁢
            ID
            ⁢
            
              
            
            ⁢
            NO
            ⁢
            
              :
            
            ⁢
            2
          
          )
        
      
    
    
      I
      ⁢
      
        
      
      ⁢
      
        
          D
          50
        
        ⁡
        
          (
          
            test
            ⁢
            
              
            
            ⁢
            peptide
          
          )
        
      
    
  




If R is greater than one, then the tested peptide bound to HLA-A*0201 with greater affinity than SEQ ID NO: 2. A value less than one indicates lower affinity. The results are set forth below:












TABLE II








Relative





Competitor2
competitor
SEQ


Peptide
Sequence
[μM] 50%
activity
ID NO:



















Melan-A27-35
AAGIGILTV
60
1
2



ALGIGILTV
1.5
40
5



AMGIGILTV
2
30
6



LAGIGILTV
65
1
7



MAGIGILTV
55
1
8


Melan-A26-35
EAAGIGILTV
15
4
1



ELAGIGILTV
6.5
9
9



EMAGIGILTV
20
3
10



EALGIGILTV
100
0.6
11



EAMGIGILTV
100
0.6
12



YAAGIGILTV
4
15
13



FAAGIGILTV
2
30
14


Influenza A
GILGFVFTL
1
60
17


matrix58-66


MAGE-3168-176
EVDPIGHLY
>100
<0.6
21





SEQ ID NOS: 1, 5, 6, 9, 10, 13, and 14 all showed higher affinity than SEQ ID NO: 2.






EXAMPLE 4
One concern in developing MHC binding peptides is that the resulting complexes of MHC molecule and peptide be stable, preferably more stable than the peptide originally found complexed to the MHC molecule.
To test stability of the newly synthesized peptides, T2 cells were incubated, overnight, at room temperature in serum free medium with saturating amounts of peptide (10 μM), and 3 μg/ml β-microglobulin, to facilitate the assembly of the requisite MHC molecules. Peptides were then removed, and 10−4M ementine (which inhibits protein synthesis) was added. The cells were then incubated at 37° C. for varying periods of time. Aliquots of cells were stained, at various points of the incubation, with a labelled HLA-A2 specific mAb to measureHLA-A2 expression.
Stability was determined by comparison with complexes involving SEQ ID NO: 17 which were stable over a 6-hour period. The results are presented in FIGS. 2A-D. FIG. 2A shows mean fluorescence intensity for each peptide. “NC” refers to HLA-A*020 1, presented by T2 cells, in the absence of exogenous peptide, while “FLUMA” is SEQ ID NO: 17, and is an acronym for “Flu matrix antigen.” In FIG. 2A, the peptides are SEQ ID NOS: 2, 1, and 9. In FIG. 2B, they are SEQ ID NOS: 2, 7, 8, 5, 6, and 17 (“FLUMA”). In FIG. 2C, they are SEQ ID NOS: 1, 12, 11, 9, 10, and 17. In FIG. 2D, they are SEQ ID NOS: 1 13, 14, and 17. The breakup is solely to facilitate the review. FIGS. 2B-2D show relative complex stability where fluorescent intensities with test peptides were normalized, relative to the stability observed when using SEQ ID NO: 17. SEQ ID NOS: 1 and 2 both form unstable complexes, which decay within one hour. This was also found with SEQ ID NOS: 7 and 8.
On the other hand, SEQ ID NOS: 9, 10, 13, and 14 formed stable complexes over 6-hour period, while SEQ ID NOS: 5, 6, 11, and 12 formed complexes of intermediate stability.
EXAMPLE 5
The antigenic activity of each of the peptides presented, supra, when the peptide was associated with HLA-A*0201, was tested in a 51Cr assay of the type discussed, supra, using TILNs, and CTLs. Dose response analyses were performed on each peptide, and antigenic activity, relative to SEQ ID NO: 2, was calculated. These values are set forth in the following Tables III and IV and FIG. 3 which present data from TILNs, (Table III and FIG. 3) and CTLs (Table IV), respectively.
Substituting the N-terminal amino acid of SEQ ID NO: 2 with Leu or Met enhanced activity between 7.5 and 20 fold, while substitutions at the second position nearly abolished it, even though binding to HLA-A*-0201 was increased (Table III and FIG. 3).
SEQ ID NO: 1 was better recognized than SEQ ID NO: 2, and substitution of Ala in the second position of SEQ ID NO: 1 increased recognition 30- and 600 fold, respectively. Such substitutions at position 3 reduced activity, which was expected. Substitution of position 1 resulted in an increase in recognition.











TABLE III









TILN LAU 203
TILN LAU 132













Peptide

Relative

Relative



Sequence
[nM]
activity
[nM]
activity
SEQ ID NO:















AAGIGILTV
60
1
30
1
2


ALGIGILTV
>1000
<0.6
>1000
<0.03
5


AMGIGILTV
>1000
<0.6
>1000
<0.03
6


LAGIGILTV
6
10
1.5
20
7


MAGIGILTV
8
7.5
2.5
12
8


EAAGIGILTV
12
5
3
10
1


ELAGIGILTV
2
30
0.05
600
9


EMAGIGILTV
2
30
0.05
600
10


EALGIGILTV
>1000
<0.06
>1000
<0.03
11


EAMGIGILTV
>1000
<0.06
>1000
<0.03
12


YAAGIGILTV
5
20
1
30
13


FAAGIGILTV
1
60
0.05
600
14









The results obtained with CTLs are presented herein. Specifically, five independent HLA-A*0201 restricted Melan-A specific CTL clones were used, each of which is known to lyse melanoma target cells.
The CTLs recognized SEQ ID NO: 2 with varying efficiency. When Leu was used to substitute Ala at position 1, four of the five clones showed enhanced recognition, while similar substitutions at position 2 resulted in a loss of activity. Three of the five clones recognized SEQ ID NO: 1 more efficiently than SEQ ID NO: 2 but all recognized SEQ ID NO: 9 very efficiently, while recognition of SEQ ID NO: 10 resulted in decreased efficiency of recognition to differing degrees, and SEQ ID NO: 11 resulted in reduced recognition for four of five. When SEQ ID NO: 12 was tested, it was surprising that recognition improved, because TIL recognition decreased. With respect to SEQ ID NOS: 13 and 14, there was reduced recognition by the CTLs.
It can be gathered from this that SEQ ID NOS: 7 and 9 were better recognized, consistently, than the other peptides tested, while other peptides were recognized to different degrees.







TABLE IV







Recognition of peptide analogs by Melan-A specific CTL clones










Recognition 














M77.86
7.10
by clone
M77.80
1.13


















SEQ
Peptide
Peptide
Relative
Peptide
Relative
Peptide
Relative
Peptide
Relative
Peptide
Relative


ID NO:
sequence
[nm] 50%
activity
[nm] 50%
activity
[nm] 50%
activity
[nm] 50%
activity
[nm] 50%
activity





















2
AAGIGILTV
15
1
50
1
300
1
300
1
4000
1


5
ALGIGILTV
90
0.16
>1000
<0.015
>1000
<0.3
>1000
<0.3
>10000
<0.4


6
AMGIGILTV
>1000
<0.015
>1000
<0.015
>1000
<0.3
>1000
<0.3
>10000
<0.4


7
LAGIGILTV
0.08
187
1.5
33
150
2
0.03
10000
30
130


8
MAGIGILTV
0.6
.25
15
3
200
1.5
0.5
600
60
50


1
EAAGIGILTV
0.15
100
4
12
0.06
5000
600
0.5
2000
2


9
EALGIGILTV
300
0.05
>1000
<0.015
40
7.5
>1000
<0.3
>10000
<0.4


10
EAMGIGILTV
0.5
30
1
50
0.02
15000
5
60
50
80


11
ELAGIGILTV
0.015
1000
0.5
100
0.015
20000
0.5
600
20
200


12
EMAGIGILTV
550
36
>1000
<0.015
40
7.5
>1000
<0.3
>10000
<0.4


13
YAAGIGILTV
0.015
1000
35
1.4
>1000
<0.3
1000
0.3
>10000
<0.4


14
FAAGIGILTV
0.005
3000
7
7
>1000
<0.3
>1000
<0.3
200
20





Relative antigenic activity of Melan-A derived peptides was measured as described in the legend to FIG. 4 and table III.






Additional experiments are depicted in FIG. 3 which show recognition of various Melan-A peptide analogues presented by T2 cells, by TILN LAU203 and TILN LAU132. A 4-hour51Cr assay was conducted at a lymphocyte to target ration of 30:1.
The first panels of FIG. 3 (top and bottom) compare SEQ ID NOS: 2, 7, 8, 5, and 6.
The second set of panels (top and bottom) compare SEQ lID NOS: 1, 9, 10, 11, and 12.
The third set (top and bottom) compares SEQ ID NOS: 1, 13, 14, and 4.
The most important result obtained herein, however, was the fact that CTLS, induced with SEQ ID NO: 9 did recognize and lyse cells presenting the endogenous peptide when SEQ ID NO: 9 was used.
EXAMPLE 6
Based upon the preceding data, the peptide of SEQ ID NO: 9 was used for CTL induction studies.
In accordance with Vahnori, et al, supra, peripheral blood lymphocytes from HLA-A*0201 positive melanoma patients were purified by centrifugation, and were enriched for CD3+ cells. The enriched subpopulation was then selected for CD8+ cells. The resulting subpopulations routinely contained more than 90% CD8+ cells, and these were used in further experiments.
The purified, CD8+ T cells were plated, at 1−2×106 cells/well, together with 2×106 stimulator cells, the preparation of which is discussed, infra. The effector and stimulator cells were combined in a total of 2 ml of Iscove's medium which had been supplemented with 10% human serum, L-arginine (0.55 mM), L-asparagine (0.24 mM), and L-glutamine (1.5 mM), together with recombinant human IL-7 (10 ng/ml) and recombinant human IL-2 (10U/ml).
To prepare the stimulator cells, 2×106 autologous PBLs were incubated for 2 hours, at 37° C., in serum free medium, with 20 μg/ml of each peptide and 3 μg/ml β2-microglobulin. The PBLs were then washed, irradiated, (3000 rads), and then adjusted to an appropriate volume, before being added to the CD8+ cell populations. On day 7, cells were restimulated with peptide pulsed, autologous PBLs in complete medium, supplemented with 10 ng/ml of recombinant human IL-7, and 10U/ml of recombinant human IL-2. There were weekly restimulations, using PBLs which were peptide pulsed and irradiated. CTL activity was tested for the first time after the second cycle (MC-2).
The results are shown in the following table and in FIG. 4. In FIG. 4, the source of CD8+ cells used was LAU203. CTL activity was assayed seven days after the second (MC-2) restimulation. Results were obtained using SEQ ID NOS: 1 and 2. These were used to permit comparison to SEQ ID NO: 9.
Note that there was barely any activity with the parental peptides in sample LAU203, while SEQ ID NO: 9 elicited a strong CTL response. This activity was also cross reactive with SEQ ID NO: 1.
The results in the following table describe experiments using the same peptides and using PBL from eight different HLA-A2 positive melanoma patents, LAU203, LAU132, LAU145, LAU86, LAU50, LAU148, LAU161, and LAU119.










TABLE V









Percentage specific lysis




from cultures stimulated




with peptidea)












SEQ ID NO: 2
SEQ ID NO: 4
SEQ ID NO: 5











tested on:

Melan-A 27-35
Melan-A 26-35
Melan-A 26-35 A27L




















patient


T2 +



T2 +



T2 +




code
E/Tb)
T2
M10
Me260
Me290
T2
M10
Me290
Me260
T2
M10
Me290
Me260























LAU203
100
38c)
29
7
17
37
41
15
6
32
83
18
81



30
29
11
10
0
17
23
7
1
26
96
4
75



10
 3
6
2
0
9
17
0
0
17
73
1
62


LAU132
100
 9
12
1
0
19
19
6
5
34
50
6
31



30
 3
7
2
0
5
10
1
2
16
32
3
18



10
 0
0
5
1
0
0
1
0
5
23
2
6


LAU145
100
15
24
4
1
39
40
5
9
29
50
6
30



30
 9
12
3
1
15
25
2
1
10
19
5
19



10
 3
6
0
0
4
6
0
0
10
16
3
7


LAU86
100
36
29
22
5
44
38
14
10
35
45
24
15



30
17
15
9
5
20
26
6
0
24
23
10
4



10
16
5
2
0
10
10
1
0
14
9
1
0


LAU50
100
21
26
7
5
18
20
5
5
19
26
6
20



30
 7
16
4
5
8
13
1
0
10
18
3
8



10
 7
7
0
4
0
4
1
0
3
12
0
0


LAU148
100
51
39
13
4
46
45
9
0
34
39
9
4



30
19
8
5
4
20
26
1
2
19
27
9
3



10
 3
6
1
0
14
14
6
0
13
13
1
0


LAU161
100
24
22
6
1
33
31
3
1
25
38
4
23



30
 3
8
6
1
16
12
3
0
18
23
2
13



10
 2
0
5
0
9
7
2
0
5
11
3
4


LAU119
100
31
27
5
12
33
31
1
4
18
46
5
45



30
 7
13
1
1
17
23
3
4
13
39
4
25



10
 4
0
0
0
9
12
1
0
7
17
2
16


Clone 6
10
 7
73
2
73



3
 3
74
0
61



1
 0
65
0
51





a)Lytic activity was assayed 7 days after the third restimulation.


b)Lymphocyte to target cell ratio titration was performed for every assay.


c)Numbers represent the percent specific lysis obtained for each target. Me290 is a Melan-A and HLA-A*0201 positive melanoma cell line obtained from patient LAU203. Me260 is a HLA-A*0201 negative melanoma cell line obtained from patient LAU149 Each number represents the geometric mean of duplicate cultures. Bold face type indicate significant specific CTL. When the differences in specific lysis obtained on T2 cells inpresence or in absence of Melan-A 26-35 (1 μM) or Me290 and Me260 is equal or higher than 10%. A patient is considered as responder when a significant specific lysis is detected in at least one of the cultures.


d)Clone 6 is a Melan-A specific CTL clone derived from the TILN 289.






EXAMPLE 7
As was pointed out, supra, the decapeptide of SEQ ID NO: 1 had a higher efficiency of recognition than the nonamer of SEQ ID NO: 2. Experiments were carried out to determine if this was the result of better binding of the peptide of SEQ ID NO: 1 to HLA-A*0201 molecules. These involved a functional peptide competition assay. This type of assay is described by Gaugler et al., J. Exp. Med. 174: 921 (1994), incorporated by reference, but is described herein. In this assay, HLA-A*0201 expressing target cells (T2 cells) were labelled with 51Cr and than incubated, for 15 minutes, with varying concentrations of peptides. A suboptimum concentration of mutant Ras 5-14 peptide was added. This peptide has amino acid sequence:

    
    
        Lys Leu Val Val Val Gly Ala Val Gly Val (SEQ ID NO: 20).

After 15 minutes a sample of CTL clone 7 RAS was added. This CTL clone had been obtained from the draining lymph node of an HLA-A*0201 human/β-microglobulin double transgenic mouse that had been injected with the peptide of SEQ ID NO: 20. The CTLs were added at a ratio of 5 lymphocytes (10,000 cells/well): 1 target cell. The cells were incubated at 37° C. for four hours, and then the assay was terminated. In addition to the peptide of SEQ ID NO: 1, those of SEQ ID NO: 2, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 3, SEQ ID NO: 4, and

        Glu Ala Asp Pro Thr Gly His Ser Tyr (SEQ ID NO: 21),

were tested. SEQ ID NO: 21 is a known peptide, derived from MAGE-1, which is known to bind to HLA-A1 molecules and stimulate lysis. See U.S. Pat. No. 5,405,940, SEQ ID NO: 12, incorporated by reference.

    
    


When SEQ ID NO: 20 was used alone, the lysis percentage was 80%. Control lysis, with no peptide, was 4%.
The results indicated that SEQ ID NO: 1 showed five fold more efficient binding than SEQ ID NO: 2. Both SEQ ID NOS: 3 and 4 bound with activities comparable to SEQ ID NO: 2, while the control (SEQ ID NO: 21), showed no binding. Both of SEQ ID NOS: 13 and 14 showed significantly improved binding as compared to SEQ ID NO: 2. Similar results were obtained when a human CTL clone, specific for a complex of HLA-A*0201 and a different peptide, was used. The table which follows presents relative competitor activity as concentration of SEQ ID NO: 2 required to inhibit control lysis by 50%, divided by concentration of peptide being tested to secure the same result:









TABLE VI









Relative Competitor Activity












Peptide
Exp1
Exp2
Exp3







SEQ ID NO: 2
1
 1
1



SEQ ID NO: 1
4
 4
5



SEQ ID NO: 14
12 
17
20 



SEQ ID NO: 13
8
10
10 



SEQ ID NO: 3
Not Done
Not Done
2



SEQ ID NO: 4
Not Done
Not Done
2










EXAMPLE 8
Relative HLA-A*0201 peptide binding activity was then determined in another assay, based upon a flow cytometric assay. In these experiments, 2×105 T2 cells were incubated with varying concentrations of the peptides of SEQ ID NO: 1, 2, 13, 14 or 4, for 16 hours, at 23° C., in the presence of 2 μg/ml of human β2 microglobulin. Cells were washed, at 4° C., and then stained with monoclonal antibody BB7.2, labelled with FITC. This mAb is specific for a conformation dependent epitope on HLA-A2 molecules. Fluorescence index was then calculated, by using the formula (mean fluorescence of sample—mean fluorescence of background)/(mean fluorescence of background). See Nijman et al., Eur. J. Immunol. 23: 1215 (1993). Again, SEQ ID NO: 1 showed highest efficiency of binding (about 10 fold) than SEQ ID NO: 2. SEQ ID NO: 4 showed relative binding activity about the same as SEQ ID NO: 2, while SEQ ID NOS: 13 and 14 had binding activities comparable to SEQ ID NO: 1.
EXAMPLE 9
In these experiments, efficiency of peptide recognition was assessed with a panel of 13 CTL clones, all of which were specific for complexes of HLA-A*0201 and SEQ ID NO: 2.
The same type of 51Cr release assay as is described in, e.g., example 3, supra was carried out. Specifically, T2 cells were labelled with 51Cr (the sodium salt was used), in Tris-Dulbecco buffer, supplemented with 2 mg/ml bovine serum albumin, and a 1:40 dilution of W6/32 ascites as described by Gaugler et al, supra. This stabilizes the AMC molecule. The labelled cells were added to varying concentrations of peptides, and in varying amounts so as to create differing effector:target ratios. Ten of the thirteen CTL clones tested recognized the decapeptide of SEQ ID NO: 1 more efficiently than the nonapeptide of SEQ ID NO: 2, requiring concentrations of anywhere from 20 to more than 1000 fold lower than the nonapeptide to achieve half-maximal lysis. The three remaining CTLs yielded titration curves which were similar. None of the CTLs recognized complexes of SEQ ID NO: 3 and HLA-A2. In additional experiments, one of the CTL clones was tested in IL-2 release assays, with SEQ ID NO: 1 again proving to be 10 fold more efficient than SEQ ID NO: 2.
EXAMPLE 10
SEQ ID NOS: 1, 13, and 14 were then used to “dissect” the panel of the CTLs described supra. A recognition assay of the type described in example 7, supra, was carried out using these peptides. Four of the CTLs recognized SEQ ID NOS: 1, 13 and 14 equally well. A fifth CTL recognized SEQ ID NOS: 1 and 13, but not SEQ ID NO: 14. Two other CTLs recognized SEQ ID NOS: 1 and 14, but not 13. One CTL only recognized SEQ ID NO: 1.
EXAMPLE 11
A set of experiments were then carried out to study the receptors of the T cells described herein (“TCRs” hereafter), because it is known that different elements combine in the TCR repertoire, forming different TCRs as a result.
To do this, total RNA of 10 6 cells of each CTL clone tested was extracted, following Chomczynski et al., Anal. Biochem. 162: 156 (1987). Then, reverse transcription using a poly(dT) primer was carried out, following the instructions in a commercially available product. Following this, aliquots of samples were PCR amplified, using a panel of Vα and Vβ probes, and Cα/Cβ specific oligonucleotides, in accordance with Genevee, et al., Eur. J. Immunol. 22: 1261 (1992), incorporated by reference. Six different Vα segments were found, i.e., Vα2, 4, 6, 7, 14, and 21. One clone actually presented two in-frame Vα transcripts. Seven different Vβ segments were found (two clones expressed Vβ13, two expressed Vβ14, and two expressed Vβ16. Vβ2, Vβ3, Vβ37.2 and Vβ38.2 were each expressed by one clone).
EXAMPLE 12
The determination of the contribution of single amino acid side chains to the interaction between SEQ ID NO: 1 and HILA-A*0201 molecule, was studied, by testing single Ala substituted derivatives. That is to say, derivatives were prepared which were identical to SEQ ID NO: 1 but for a change at position 1, 4, 5, 6, 7, 8, 9, or 10 to Ala.
The peptides were prepared, following standard synthetic methods. Then, they were tested in a functional competition assay based upon their ability to inhibit binding of a known HLA-A*0201 binding peptide, i.e.

    
    
        Tyr Met Asp Gly Thr Met Ser Gln Val (SEQ ID NO: 22),

derived from tyrosinase, and an HLA-A*0201 restricted CTL clone, LAU 132/2. In brief, T2 cells were labelled with 51Cr in the presence of monoclonal antibody W6/32. Both the cells and monoclonal antibody are described supra. Varying concentrations of competitor peptide (50 ul volumes) were incubated with 50 ul of the 51Cr labelled T2 cells (This quantity gives 1000 cells/well) for 15 minutes, at room temperature. Then, 1 nM of the peptide of SEQ ID NO: 22 was added, which is a suboptimal dose, together with 5000 CTLs, per well (a volume of 50 ul). 51Cr release was measured after incubating for four hours at 37° C. The concentration of each competitor peptide required to inhibit 51Cr release by 50% was determined. Comparison was facilitated by calculating relative competitor activity as the concentration of SEQ ID NO: 1 needed for 50% inhibition, divided by the 50% inhibition value for the test peptide.

    
    


It was found that substituting Ala for Glu at position 1 (SEQ ID NO: 15) resulted in a 5 fold increase in competitor activity. Substitution of Glu at position 4 or 6 by Ala resulted in decreased activity, of 20 and 10 fold, as did substitution of positions 7 and 10 (about 25 fold, each time). Changes at positions 8 or 9, i.e.









(SEQ ID NO: 23)







Glu Ala Ala Gly Ile Gly Ile Ala Thr Val


and


 









(SEQ ID NO: 24)







Glu Ala Ala Gly Ile Gly Ile Leu Ala Val






did not result in significant changes in activity.

EXAMPLE 13
The stability of complexes formed by the single Ala substitutions of SEQ ID NO: 1, discussed supra, and HLA-A*0201 was then studied. Briefly, T2 cells were loaded with saturating concentrations (10 uM) of the analogs, and incubated overnight at room temperature with the peptide and β2 microglobulin (3 ug/ml), in serum free medium. Excess peptide was removed, and emetine (10−4M) was added to block protein synthesis. Cells were then incubated, for varying time periods, and aliquots were stained with fluorescent labelled anti HLA-A2 monoclonal antibody (BB7.2), to determine the amount of the molecules on the surface. Since the peptide of SEQ ID NO: 17, supra, is known to form stable complexes with HLA-A*0201 (van der Burg, J. Immunol. 156: 3308 (1996)), this peptide was used as an internal standard. Complex stability was determined by calculating mean fluorescence with analog, subtracting background fluorescence and dividing by the same values obtained using SEQ ID NO: 17. Background fluorescence was the value obtained using T2 cells treated similarly, but without peptide.
It was found that, over a period of 1-6 hours, complexes of SEQ ID NO: 1/HLA-A*0201 were unstable, and dissociated in less than an hour. SEQ ID NO: 15 formed stable complexes over the same 6-hour period. All other derivatives tested formed complexes with low stability.
EXAMPLE 14
The derivatives described supra were then tested for their relative antigenic activity. In these experiments, two TILN populations, i.e., TILN LAU 132 and TILN LAU 203, preparation of which is described, supra, and a panel of ten different cytolytic T cell lines were tested. Of the ten CTLs, five were derived from infiltrating lymphocytes or tumor infiltrating lymph nodes, and five were from normal donor peripheral blood lymphocytes. All were known to be specific for complexes of HLA-A*0201 and SEQ ID NO: 2; however, given the results discussed supra, showing superiority of SEQ ID NO: 1, this decapeptide was used for comparison.
Antigen recognition was assessed in a 51Cr release assay. Target, T2 cells were labelled with 51Cr for one hour at 37° C., then washed, twice. The labelled target cells (1000 cell samples in 50 ul) were then incubated with varying concentrations of peptides (in 50 ul volume), for 15 minutes at room temperature, before adding effector cells (50 ul). When TILNs were the effector cells, these had been preincubated for at least 20 minutes at 37° C., with unlabelled K562 cells (50,000 cells/well), to eliminate non-specific lysis due to NK-like effectors. The 51Cr was measured in supernatant, harvested after four hours of incubation at 37° C. Percent lysis was determined by subtracting spontaneously released 51Cr from 51Cr released with the tested, divided by a figure obtained by subtracting spontaneous release from total 51Cr, and multiplying the resulting figure by 100. Titration was carried out over concentrations ranging from 10−5 to 10−3M. For quantitative comparison, concentrations required for 50% maximal activity, normalized against reference values for SEQ ID NO: 2 were determined.
SEQ ID NO: 15 was found to be recognized 20-60 fold better than the parental decapeptide of SEQ ID NO: 1, by the two TILN populations, in contrast to the other variants tested. With respect to the CTLs, 8 of 10 of those tested recognized the peptide better than they recognized SEQ ID NO: 1 or 2.
Additional differences were observed with respect to the CTL specificity. Five of the ten CTLs tested recognized SEQ ID NO: I better than SEQ ID NO: 2. One of these five CTLs recognized SEQ ID NO: 1 efficiently, and SEQ ID NO: 2 poorly. Three of the remaining five clones recognized SEQ ID NOS: 1 and 2 equally efficiently, and two recognized SEQ ID NO: 2 better than SEQ ID NO: 1.
What this shows is a strong degree of diversity in fine specificity of tumor reactive CTLs.
EXAMPLE 15
A further set of experiments were then carried out to determine if diversity of antigenic specificity, as displayed by the CTL clones, supra, was a general characteristic of the T cell repertoire for the antigen SEQ ID NO: 1 or was attributable to different methodologies used to derive the CTLs. To test this, the 'source of the specific T cells had to be one which had not been subjected to antigen driven selection from in vitro stimulation with peptides. The TILN population LAU 203, described supra, was used. As was shown in the prior examples, the population exhibits relatively high CTL activity against Melan-A HLA-A*0201 positive melanoma cells. CTL clones were derived from this population, by limiting dilution cultures, in the presence of irradiated, allogenic PBMCs, Epstein Barr Virus transformed B lymphocytes, phytohemagglutinin, and recombinant IL-2. Using standard probability models, clones were derived from cultures having probable clonality of higher than 90%. These were then expanded, by plating 5×103 cells, every 3-4 weeks, into microtiter plates, together with irradiated feeder cells (5×104 allogenic PBMCs, and 2.104 EBV transformed B cells), with PHA and recombinant IL-2.
Two independent experiments were carried out, resulting in 130 growing clones. When these were tested in a 51Cr release assay, of the type described supra, 11 of these were found to recognize at least one of SEQ ID NO: 1 and 2.
In order to determine fine specificity, the type of antigen recognition assay described supra was carried out, using SEQ ID NOS: 1, 2 and 15. It was found that four clones recognized SEQ ID NO: 1 better than SEQ ID NO: 2 (i.e., relative antigenic activity was at least 10 fold greater), six clones recognized the two peptides equally well, and one recognized SEQ ID NO: 2 better than SEQ ID NO: 1. Nine CTLs recognized SEQ ID NO: 15 better than SEQ ID NO: 1 and 2, with one of the clones actually recognizing SEQ ID NO: 15 at nanomolar concentrations, in contrast to micromolar concentrations for the peptides SEQ ID NO: 1 and SEQ ID NO: 2.
EXAMPLE 16
The in vitro immunogenicity of the peptides of the invention was determined. To do this, PBMCs from LAU 203 (1.0×107 cells per test), were stimulated by adding 1 μM of peptide into the culture medium containing the cells. The peptides tested were those defined by SEQ ID NOS: 1, 2, 9, 15 and 16. The peptide defined by SEQ ID NO: 17 was used as a negative control.
Following the addition of the peptides, the cultures were stimulated weekly with autologous PBMCs which had been pulsed for 1 hour with one of the peptides listed supra, at 37° C. In other words, a culture treated with SEQ ID NO: 1 was restimulated by having PBMCs pulsed with SEQ ID NO: 1. The restimulating cells were washed, thoroughly, and irradiated prior to their use.
Seven days after stimulation, the cultures were monitored to determine presence of CD8+ cells, which were reactive with tetramers of HLA-A2 and SEQ ID NO: 9. This step was repeated a total of three times, over a 3-week period. To make the tetramers, it was first necessary to prepare constructs which would encode modified HLA-A*0201 molecules. To do this, total RNA was extracted from HLA-A*0201 positive cells, and HLA-A*0201 was then cloned, using specific primers for the molecule, and reverse transcription polymerase chain reaction (RT-PCR). Altman et al., Science 274:94-96 (Oct. 4, 1996) incorporated by reference, was followed. Simultaneously, with the RT-PCR, the amino terminal nucleotide sequence was altered to optimize protein expression in the vector used. See Garboczi et al., Proc. Natl. Acad. Sci. USA 89:3429 (1992) incorporated by reference. Once this was done, the extracellular coding portion of the molecule was amplified, again using specific primers. The resulting construct was recloned into a vector which would produce a BirA biotinylation recognition site in frame at the 3′-end of the HLA-A*0201 heavy chain. The modified HLA-A*0201 and β2 microglobulin were overexpressed in separate E. coli cultures. The resulting inclusion bodies were purified and the HLA and β2 microglobulin recombinant proteins were solubilized into urea, and then refolded in a refolding solution, at 4° C. to form complexes. (The refolding solution contained 100 mM Tris, at pH 8.0, L-arginine, 400 mM, EDTA, 2 mM, reduced glutathione, 5 mM, oxidized glutathione, 0.5 mM, PMSF, 0.1 mM, HLA heavy chain and β2 microglobulin, 1 μM, and 10 μM of the peptide of interest). The refolding solution was concentrated to 7.5 ml, using standard techniques. Then, refolding buffer was exchanged with BirA reaction buffer (Tris 100 mM, pH 7.5, NaCl 200 MM, MgCl2 5 mM, PMSF 100 μM, leupeptin 1 μM, and pepstatin 1 μM), the last three being added immediately before use.
The complexes were then biotinylated with biotin holoenzyme synthase (the BirA enzyme) by combining the refold mix containing the HLA-A2 complex with 50 μM enzyme, 100 mM biotin in 200 mM Tris, and 100 mM adenosine triphosphate. The mixture was incubated overnight at room temperature. The biotinylated complexes were then purified, and combined with phycoerythrin-labeled streptavidin, to produce tetrameric structures. These were isolated, and reconstituted in small volumes, at a concentration of 1 mg/ml.
Peptides of SEQ ID NO: 9 were added to bind to the tetramers. The total number of T cells positive for the tetramers relative to the total number of CD8+ cells in each sample was determined. These results are shown in FIG. 5. The analogues were all found to have induced CD8+ cells specific for SEQ ID NO: 9.
EXAMPLE 17
Seven days after the third stimulation cycle, the cultures were tested in a 51Cr release assay to determine if they could lyse T2 cells in the presence or absence of SEQ ID NO: 1. These assays were carried out essentially as described in example 14, supra. The results are presented in FIG. 6. It was found that stimulation with the analogues actually resulted in more vigorous expansion of CD8+ cells reactive with the tetramers described supra, than did stimulation with SEQ ID NO: 1 or SEQ ID NO: 2. Further, the Melan-A specific lysis correlated directly with the percentage of the CD8+ cells which were also tetramer specific, suggesting comparable lytic capacity.
EXAMPLE 18
A further set of experiments were carried out to study the antigen specificity of CD8+, tetramer positive cells. To do this, the CD8+ tetramer positive cells were purified from each culture using standard flow cytometry sorting methods. The cells were then expanded in vitro, using standard mitogen stimulation techniques. They were then tested for their lytic activity on T2 cells, following the method of the previous example, in the presence or absence of the peptides used in the in vitro stimulation outlined supra, or SEQ ID NO: 1.
The results, presented in FIG. 7 show that each culture exhibited a high level of specific lysis against both target cells pulsed with the testing peptide and with SEQ ID NO: 1.
FIG. 7 also documents tumoricidal capacity of different cultures, by assessing this capacity against autologous Melan-A+ melanoma line Me 290. See example 1, supra. High tumoricidal activity was observed, with 50% maximal tumoricidal activity being observed at an effector/target ratio of 3:1 for SEQ ID NO: 2, 7:1 for SEQ ID NO: 1, 4:1 for SEQ ID NO: 15, 5:1 for SEQ ID NO: 9, and 15:1 for SEQ ID NO: 16.
EXAMPLE 19
Affinity of antigen recognition and relative antigenic activity of the different cell populations was then quantitated, using a standard CTL assay, along the lines of the assay of example 3, supra. Various ranges of peptide concentrations were used to develop titration curves, one of which is shown in FIG. 8. These data are summarized in Table VII, which follows:







TABLE VIII







Relative Potency of Melan-A Monospecific CTL Lines After


Tetramer-Guided Fluorescent Cytometry Sorting.









Culture stimulated with SEQ ID NO:













2
1
15
9
16











(A)


Pepticle [nM] 50%












 2
25
20
25
35
50


 1
1
2.5
3
3
15


15
0.04
0.04
0.15
0.08
0.15


 9
0.001
0.15
0.03
0.03
0.3


16
0.001
0.015
0.01
0.003
0.03







(B)


Relative antigenic activity:












 2
1
1
1
1
1


 1
25
8
8
12
3


15
625
500
166
437
333


 9
25 × 103
133
833
1666
166


16
25 × 103
1333
2500
16 × 103
1666









Values are the peptide concentration required for 50% maximal activity).
The affinity of the different lines for parental peptides was very similar, except for the line obtained after in vitro stimulation with SEQ ID NO: 16. This line was found to recognize complexes of HLA-A2/SEQ ID NO: 1 about 2 fold less efficiently, and complexes of HLA-A2/SEQ ID NO: 15 to 15 fold less efficiently than othe cell lines.
With respect to the second part of Table VIII it must be noted that regardless of the peptide used to stimulate expansion, all of the cell lines recognized complexes containing SEQ ID NO: 1 better than complexes containing SEQ ID NO: 2. Peptide analogues were recognized more efficiently than parental sequences by all lines, notwithstanding differences in relative antigenicity for different lines. A preference of a cell line for an analogue did not always correlate with the analogue used to generate the cell line.
The foregoing examples, as will be seen, describe the various features of the invention. These include peptides which bind to HLA molecules, such as HLA-A2 molecules, exemplified by HLA-A*0201, which may also provoke proliferation of cytolytic T cells. These peptides, as will be seen from the data herein, are nonapeptides or decapeptides. As with all peptides, the first amino acid is the amino terminus, and the last one is the carboxy terminus. The peptides of the invention may be decapeptides, which have a Val moiety at the C, or carboxy terminus. They may have at the amino terminus, Tyr or Phe when the second amino acid is Ala. In another embodiment, the amino terminus is Glu followed by Ala, Leu or Met in the second and third position, and terminate with Val, wherein if position two is Ala, position three must be Met or Leu, and vice versa. The peptides having the amino acid sequences set forth in any of SEQ ID NOS: 5 and 8-14 are exemplary.
Also a part of the invention are isolated cytolytic T cell lines which are specific for complexes of these peptides and their MHC binding partner, i.e., an HLA molecule, such as an HLA-A2 molecule, HLA-A*0201 being especially preferred.
The ability of these peptides to bind to HLA molecules makes them useful as agents for determining presence of HLA-A2 positive cells, such as HLA-A*0201 positive cells, by determining whether or not the peptides bind to cells in a sample. This “ligand/receptor” type of reaction is well known in the art, and various methodologies are available for determining it.
A further aspect of the invention are so-called “mini genes” which carry information necessary to direct synthesis of modified decapeptides via cells into which the mini genes are transfected. Mini genes can be designed which encode one or more antigenic peptides, and are then transferred to host cell genomes via transfection with plasmids, or via cloning into vaccinia or adenoviruses. See, e.g., Zajac, et al., Int. J. Cancer 71: 496 (1997), incorporated by reference.
The peptides may be combined with peptides from other tumor rejection antigens to form ‘polytopes’. Exemplary peptides include those listed in U.S. patent application Ser. No. 08/672,351, 08/718,964, now abandoned, Ser No. 08/487,135, now U.S. Patent Nos. 5,821,122, 08/530,569 and 08/880,963 all of which are incorporated by reference.
Additional peptides which can be used are those described in the following references, all of which are incorporated by reference: U.S. Pat. Nos. 5,405,940; 5,487,974; 5,519,117; 5,530,096; 5,554,506; 5,554,724; 5,558,995; 5,585,461; 5,589,334; 5,648,226; and 5,683,886; PCT International Publication Nos. 92/20356; 94/14459; 96/10577; 96/21673; 97/10837; 97/26535; and 97/31017 as well as pending U.S. application Ser. No. 08/713,354.
Polytopes are groups of two or more potentially immunogenic or immune stimulating peptides, which can be joined together in various ways, to determine if this type of molecule will stimulate and/or provoke an immune response.
These peptides can be joined together directly, or via the use of flanking sequences. See Thompson et al. Proc. Natl. Acad. Sci. USA 92(13): 5845-5849 (1995), teaching the direct linkage of relevant epitopic sequences. The use of polytopes as vaccines is well known. See, e.g., Gilbert et al., Nat. Biotechnol. 15(12): 1280-1284 (1997); Thomson et al., supra; Thomson et al., J. Immunol. 157(2): 822-826 (1996); Tam et al., J. Exp. Med. 171(1): 299-306 (1990), all of which are incorporated by reference. The Tam reference in particular shows that polytopes, when used in a mouse model, are useful in generating both antibody and protective immunity. Further, the reference shows that the polytopes, when digested, yield peptides which can be and are presented by MHCs. Tam shows this by showing recognition of individual epitopes processed from polytope ‘strings’ via CTLs. This approach can be used, e.g., in determining how many epitopes can be joined in a polytope and still provoke recognition and also to determine the efficacy of different combinations of epitopes. Different combinations may be ‘tailor-made’ for the patients expressing particular subsets of tumor rejection antigens. These polytopes can be introduced as polypeptide structures, or via the use of nucleic acid delivery systems. To elaborate, the art has many different ways available to introduce DNA encoding an individual epitope, or a polytope such as is discussed supra. See, e.g., Allsopp et al., Eur. J. Immunol. 26(8); 1951-1959 (1996), incorporated by reference. Adenovirus, pox-virus, Ty-virus like particles, plasmids, bacteria, etc., can be used. One can test these systems in mouse models to determine which system seems most appropriate for a given, parallel situation in humans.
They can also be tested in human clinical trials.
Also, a feature of the invention is the use of these peptides to determine the presence of cytolytic T cells in a sample. It was shown, supra, that CTLs in a sample will react with peptide/MHC complexes. Hence, if one knows that CTLs are in a sample, HLA-A2 positive cells can be “lysed” by adding the peptides of the invention to HLA-A2 positive cells, such as HLA-A*0201 positive cells, and then determining, e.g., radioactive chromium release, TNF production, etc. or any other of the methods by which T cell activity is determined. Similarly, one can determine whether or not specific tumor infiltrating lymphocytes (“TILs”) are present in a sample, by adding one of the claimed peptides with HLA-A2 positive cells to a sample, and determining lysis of the HLA-A2 positive cells via, e.g., 51Cr release, TNF presence and so forth. In addition, CTL may be detected by ELISPOT analysis. See for example Schmittel et al. (1997). J. Immunol. Methods 210: 167-174 and Lalvani et al (1997). J. Exp. Med. 126: 859 or by FACS analysis of fluorogenic tetramer complexes of MHC Class I/peptide (Dunbar et al (1998), Current Biology 8: 413-416. All are incorporated by reference.
Of course, the peptides may also be used to provoke production of CTLs. As was shown, supra, CTL precursors develop into CTLs when confronted with appropriate complexes. By causing such a “confrontation” as it were, one may generate CTLs. This is useful in an in vivo context, as well as ex vivo, for generating such CTLs.
Other features of the invention will be clear to the skilled artisan, and need not be repeated here.
The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, it being recognized that various modifications are possible within the scope of the invention.

## Claims

1. An isolated nucleic acid molecule which consists of a nucleotide sequence that encodes a peptide consisting of ten amino acids, said peptide having Val at its carboxy terminus, Glu at its amino terminus, and the second and third amino acids from the N-terminus are Ala, Leu or Met, with the proviso that when the second amino acid is Ala, the third amino acid must be Leu or Met, and when the third amino acid is Ala, the second amino acid must be Leu or Met, wherein said peptide binds to an HLA-A2 molecule.

2. The isolated nucleic acid molecule of claim 1, wherein said peptide consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12.

3. An expression vector which encodes a peptide, comprising the isolated nucleic acid molecule of claim 1.

4. An isolated nucleic acid molecule consisting of a nucleotide sequence which encodes a peptide selected from the group consisting of SEQ ID NO: 23 and SEQ ID NO: 24.

5. An isolated nucleic acid molecule consisting of a nucleotide sequence which encodes a peptide selected from the group consisting of SEQ ID NO: 7 and SEQ ID NO: 8.

6. An expression vector comprising the isolated nucleic acid of claim 4.

7. An expression vector comprising the isolated nucleic acid of claim 5.