Patent application title: HPV Vaccine Comprising Peptides From Host Cell Proteins
Stephen Tze Kwung Man (Heath Park, GB)
IPC8 Class: AA61K3912FI
Class name: Drug, bio-affecting and body treating compositions antigen, epitope, or other immunospecific immunoeffector (e.g., immunospecific vaccine, immunospecific stimulator of cell-mediated immunity, immunospecific tolerogen, immunospecific immunosuppressor, etc.) virus or component thereof
Publication date: 2009-09-17
Patent application number: 20090232842
The present invention relates to a human papillomavirus (HPV) vaccine that
comprises peptides from host cell proteins and more particularly, a
vaccine that is directed against cancers that are associated with HPV
infections, such as cervical cancer, head and neck cancer and skin
cancers. The peptides comprise fragments of host cell proteins that have
been targeted for degradation by HPV proteins, such as E6 and E7 and are
presented on the surface of HPV infected cells in relatively large
amounts. These peptides can be recognised by CTL and elicit an immune
response, and are therefore ideal tumour-specific markers. The invention
also relates to novel peptide: peptide complexes such as peptide/HLA
complexes and their use in a tumour-specific vaccine.
1. A vaccine for treating HPV-associated diseases, comprising: at least
one isolated, purified, synthesised or recombinant peptide, wherein the
peptide is a fragment of a host cell protein that has been degraded by a
human papillomavirus (HPV) oncoprotein, and can elicit a cytotoxic
T-lymphocyte (CTL) response when administered to a mammal.
2. A vaccine according to claim 1, wherein the mammal is human.
3. A vaccine according to claim 1, wherein the oncoprotein is E6 or E7.
4. A vaccine according to claim 1, wherein the host cell protein comprises one or more of the proteins shown in Table 3.
5. A vaccine according to claim 1, wherein the peptide is HPV-specific or tumour-specific, meaning that it is presented in high amounts on the cell surface of HPV transformed or tumour cells, relative to normal cells.
6. A vaccine according to claim 5, wherein the peptide is 9-30 amino acids in length.
7. A vaccine according to claim 6, wherein the peptide is 9-11 amino acids in length.
8. A vaccine according to claim 7, wherein said vaccine comprises one or more of the peptides selected from the peptides shown in Table 4 (SEQ ID NO. 1-161).
9. A vaccine according to claim 1, wherein the CTL response is HPV-specific or tumour-specific, meaning that the CTL can recognise HPV-transformed cells or tumour cells expressing the peptide of said vaccine.
10. A vaccine according to claims 1, 3, 4, 5, 8, or 9, which further comprises a major histocompatibility complex molecule.
11. A vaccine according to claim 10, wherein the major histocompatibility complex molecule is a class I molecule.
12. A vaccine according to claim 10, wherein the major histo-compatibility complex molecule is a human leucocyte antigen (HLA).
13. A vaccine according to claim 10, wherein the major histocompatibility complex molecule comprises one or more of those shown in Table 1.
14. A vaccine for treating HPV-associated diseases, comprising. at least one isolated, purified, synthesised or recombinant nucleic acid molecule encoding at least one peptide selected from the peptides shown in Table 4 (SEQ ID NO. 1-161), and optionally a major histocompatibility complex molecule comprising at least one of the major histocompatibility complex molecules shown in Table 1.
15. A vaccine according to claim 14, wherein the nucleic acid molecule is in a vector and comprises a recombinant construct.
16. A vaccine according to claim 15, wherein the construct is adapted for the expression of said peptide or peptide/HLA complex in a selected host system.
17. A vaccine according to claim 14, wherein the disease is any one of a cervical cancer, a head and neck squamous cell cancer, a non-melanoma skin cancer, a liver cancer, a mesothioloma, or a prostate cancer.
18. A vector comprising a nucleic acid molecule encoding a peptide selected from the peptides shown in Table 4 (SEQ ID NO. 1-161), and optionally, at least one major histocompatibility complex molecule selected from those listed in Table 1.
19. A host cell transformed or transfected by a vector according to claim 18.
20. A vector according to claim 18, wherein said vector is a cell, plasmid, virus, live organism or other vehicle having incorporated expressibly therein a nucleic acid molecule encoding a peptide selected from the peptides shown in Table 4 (SEQ ID NO. 1-161) and optionally, a major histocompatibility complex molecule selected from those listed in Table 1.
21. A method of manufacturing a vaccine, which method comprises: culturing a host cell transformed or transfected with a vector according to claim 18, and isolating/purifying the resulting construct product.
22. A method of identifying HPV-specific or tumour-specific CTL, or the CTL receptors thereof, comprising:(a) culturing a sample containing CTL with at least one peptide that represents a fragment of a host cell protein that is degraded by HPV proteins when said host cell is transformed or transfected by HPV, whereby said peptide is ultimately presented on a surface of a virally-infected cell; and(b) selecting CTL that recognise said peptide by binding thereto and, where the CTL receptor is to be identified, determining the nature of the receptor that binds said peptide.
23. A method according to claim 22, wherein the peptide is selected from the peptides shown in Table 4 (SEQ ID NO. 1-161).
24. A method according to claim 22 or claim 23, wherein the CTL are CD8.sup.+ cells.
25. A peptide, or nucleic acid molecule encoding same, selected from the peptides shown in Table 4 (SEQ ID NO 1-161).
26. A method of treatment, comprising administering a vaccine according to claim 1 to a mammal to be treated.
27. The method according to claim 26, wherein the mammal is human.
This application is a continuation utility patent application from
U.S. Utility patent application Ser. No. 11/671,095, which in turn is a
continuation of international application number PCT/GB2005/002962
(publication no. WO 2006/013336) filed on Jul. 27, 2005 entitled HPV
VACCINE COMPRISING PEPTIDES FROM HOST CELL PROTEINS, and claims the
benefit of priority in the above-mentioned United States and
international applications, and also the benefit of priority in the
corresponding British national patent application no. GB 0417430.6 filed
on Aug. 5, 2004 and entitled A NOVEL HPV VACCINE COMPRISING PEPTIDES FROM
HOST CELL PROTEINS, the disclosures of each of which are incorporated
herein in their entirety by reference.
FIELD OF THE INVENTION
The present invention relates to a human papillomavirus (HPV) vaccine that comprises peptides from host cell proteins and more particularly, but not exclusively, to a vaccine that is directed against cancers that are associated with HPV infections, such as cervical cancer, head and neck cancer and skin cancers. The peptides comprise fragments of host cell proteins that have been targeted for degradation by HPV proteins, such as E6 and E7. Further, the invention relates to the identification of novel peptides and uses thereof. Additionally, the invention relates to novel peptide: peptide complexes and uses thereof.
BACKGROUND TO THE INVENTION
Human papillomavirus (HPV) is a very common virus that causes abnormal growth of tissue on the feet, hands, vocal cords, mouth and genital organs. Over 60 types of HPV have been identified and each type infects certain parts of the body. HPV is mainly spread through physical contact with an infected individual. In the majority of cases, HPV disappears within 1-2 years and indeed, during the course of the infection, may be subclinical; the individual may be unaware of their infection. However, in a small number of cases, HPV can progress and develop into cancer.
There are two kinds of abnormal tissue caused by HPV: condyloma (warts) and dysplasia (pre-cancer). Wart-like growths can be found in any infected areas and may cause itching, burning or slight bleeding. In these instances, antiviral creams may be prescribed or, in some cases, the growth may be removed or destroyed by cold cautery (freezing that destroys tissue) or hot cautery (burning warts off with an electric instrument or laser treatment).
Where HPV infection progresses to cancer, cancer patients are treated by a combination of surgery, radiotherapy and chemotherapy. However, radiotherapy and chemotherapy have the disadvantage of destroying healthy as well as malignant cells, and can thus cause severe side effects, while surgery is invasive and leaves the patient open to secondary infections. These side effects and risks are undesirable, and coupled to this is the fact that these treatments are not always successful, resulting in the majority of patients entering relapse and so representing with the disease.
It is therefore clear that more effective treatments are required, and it has been suggested that the specificity of the immune system might be harnessed against virally infected cells. This concept has been termed "immunotherapy".
In particular, it has been shown that cancer patients have T cells that are capable of recognising their tumour cells, but these cells do not divide and differentiate into cytotoxic T lymphocytes (CTL) which are capable of killing these cells.
Cytotoxic T lymphocytes kill "target" cells, such as virally-infected cells, and have also been implicated in the "immune surveillance" of cancer cells. The majority of CTL belong to the CD8+-subset of T cells and have T-cell receptors (TCR). These TCR are able to recognise peptides when they are expressed on the surface of cells in association with class 1 major histocompatibility complex (MHC) molecules. In man, each class of MHC is represented by more than one locus; these are called human leucocyte antigen (HLA). The class 1 HLA loci are HLA-A, -B, -C, -E, -F and -G. Additionally each HLA has different alleles and Table 1 lists those alleles that have been identified to date.
When a CTL encounters an antigen/MHC complex for which its TCR is specific, it enters the cell cycle and goes through several rounds of mitosis, followed by differentiation into an effector/killer cell. Differentiation includes forming a large number of modified lysosomes that contain the cell-killing proteins perforin and granzyme. Once the CTL have killed the target cells most of them will die, although a small proportion become memory cells that can respond to the antigen quickly if it reappears.
Tumour-reactive cytotoxic T lymphocytes have been shown to mediate tumour regression in animal models (1) and in man (2), and there has thus been an interest in using tumour-specific CTL's as an immunotherapy for human cancers.
In this regard monoclonal antibodies have been shown to be effective against some cancers, especially cancers of white blood cells, and are targeted at a molecule or receptor that is associated with cancer cells. Table 2 lists some of these antibodies and their mechanism of action.
Alternatively, dendritic-cell vaccines have been used to elicit a tumour-specific CTL response. Dendritic cells are the most potent antigen-presenting cells and they act by engulfing antigen, processing it into peptides and presenting it to T cells. To make a dendritic-cell vaccine, dendritic cells are harvested, exposed in vitro to antigen associated with the type of tumour in the patient, and then re-injected into the patient. To date these vaccines have shown some promise against melanoma, prostrate cancer and lymphoma.
Ideally these vaccines target molecules that are expressed on cancer cells, but not on healthy cells. However such tumour-specific antigens have been hard to find, and as a result many of the immune agents now in use also target healthy cells in the hope that these cells, eventually, will be replaced. As with radiotherapy and chemotherapy, this treatment can cause severe side effects and also leads to the potential for autoimmunity (3). Indeed, in the case of a telomerase vaccine, this protein is also present in the stem cells of bone marrow, reproductive organs and perhaps other tissues. Further, the antigen to which some dendritic cells are exposed include tyrosinase, which is to be found in melanocytes, or prostatic acid phosphatase (PAP), which is to be found in prostate cells.
It is therefore clear that additional viral therapies are needed, particularly for those patients with an advanced stage disease that has failed to respond to conventional viral or cancer treatments.
Recently, a number of studies have shown that high-level expression of certain proteins in tumour cells is sufficient to allow CTL to discriminate between tumours and normal cells (4,5).
One way of avoiding autoimmunity in tumour immunotherapy is to target the 15% of human malignancies that are associated with viruses. Of these the strongest association is between cervical cancer and human papillomarivus, with 99.7% of cervical cancers containing HPV DNA (6). There are over 25 HPVs that infect the genital mucosa and give rise to malignancies such as cervical cancer, head and neck cancers and skin cancers. These "high risk" HPVs are characterised by at least two oncogene products: E6 and E7, which act to immortalise and transform, in the cervix, epithelial cells. The expression of these proteins is thought to be essential to retain the transformed phenotype of the cancer cell and so these non-self viral proteins are therefore attractive targets for CTL mediated immunotherapy.
CTL active against HPV E6/E7 can be induced by vaccination (7) and such CTL have been detected with variable frequency in patients with premalignant cervical disease (8) or cancer (9). However it has been difficult to generate these CTL in vitro, probably because they occur at low frequency (10). A major limitation of using these proteins as tumour-specific targets is that they are expressed at low levels in cancer cells (11). Furthermore, the E6 and E7 proteins themselves are small and contain few epitopes suitable for recognition by CTL (12).
The present invention aims to overcome these problems by identifying and then targeting peptides that are recognised by CTL, which peptides are specific to HPV transformed cells and are very unlikely to give rise to autoimmunity. These peptides are either uniquely presented or over-presented in HPV transformed cells, and the proteins from which these peptides are derived are, typically, either absent or appear to be expressed at very low levels in HPV transformed cells. In contrast, these proteins occur at normal or high levels in normal cells.
The invention is based on the mechanism that HPV E6 and E7 oncoproteins use to mediate targeted degradation of host cell proteins such as retinoblastoma proteins (Rb), C-MYC and HMCM7, among others (see Table 3), which takes place during transformation of the infected cell.
It is well known that HPV oncoproteins bind to and facilitate the degradation of host cell proteins, such as Rb. Thus, analysis of HPV transformed cervical carcinomas reveals no apparent expression of full-length Rb protein, whereas normal cells have high cellular levels of the Rb protein, as this is not normally proteolytically degraded (13).
It has been shown that Rb proteins are degraded by the ubiquitin-dependant proteolysis system (13), and more recently, it has come to light that intracellular organelles called proteasomes play a role in mediating degradation (18,19) of host cell proteins after interaction with E6 or E7 oncoproteins.
We have recognised the fact that the degradation of, for example ubiquinated protein substrates by proteasomes, is possibly the major mechanism by which peptides recognised by CTL's are generated (20, 21). For example, in a virally infected cell, newly synthesised viral proteins in the cytoplasm are degraded by proteasomes into peptide fragments. These peptides are transported into the endoplasmic reticulum (ER) by transporter associated with antigen processing (TAP) proteins. Once inside the ER, the peptides will bind to free MHC class I molecules and beta 2 microglobulin to form a mature MHC/peptide complex. This is transported to the cell surface where it may be recognised by CTL. FIG. 1 shows a diagrammatic representation of this process.
Accordingly, the present invention is based on the theory that in HPV transformed cells, Rb proteins (and other proteins, see Table 3) will be targeted for degradation, processed and peptides thereof will be presented on the surface of the cell as peptides that can be recognised by CTL. In non-HPV transformed, or normal, cells these proteins will not be degraded significantly, so these peptides, effectively, will not be available for CTL recognition. Thus, HPV transformed cells should have high levels of, for example, Rb derived peptides typically co-presented on the cell surface in a peptide HLA complex, but low intracellular levels of the full-length proteins, contrary to normal cells (FIG. 2).
The use of host cell proteins as targets for immunotherapy is not novel. However, in all previous instances this approach has relied on the over-expression of proteins in tumours, compared to normal cells. For example, host cell proteins such as p53 (5), Wilms transcription factor (WT1), Her 21Neu (16) and hTert (17) have been proposed as "tumour-specific" antigens, as all of these are over-expressed in tumour cells. To our knowledge, this is the first time that a HPV or cancer vaccine has been directed at "tumour-specific" proteins, and more particularly peptides thereof, that are expressed at normal, low, or undetectable levels in HPV transformed cells, compared to normal cells.
Previously, high levels of antigen expression were thought advantageous in order to allow CTL to discriminate between tumour cells and normal cells.
Additionally, up until now HPV vaccines have comprised proteins that are produced by HPV, not host proteins that are targeted for degradation by this virus.
In summary, the current invention relies on a relatively high level of presentation of peptides at the cell surface but not necessarily on relatively high levels of expression, or apparent expression, of the corresponding proteins in the virally-infected cell. In fact, low level or no expression of the tumour-specific protein would typically indicate that the protein was being targeted for degradation by viral proteins and so was present at low intracellular levels, but following degradation, presented at the cell membrane and so was available as a peptide for CTL recognition.
Accordingly, in one aspect of the invention, there is therefore provided a vaccine comprising: at least one isolated, purified, synthesised or recombinant peptide, wherein the peptide is a fragment of a host cell protein that has been degraded by human papillomavirus oncoproteins, and can elicit a CTL response when administered to a mammal.
Reference herein to a cell protein that has been degraded by human papillomavirus oncoproteins includes reference to a protein that has been selectively targeted for degradation by HPV oncoproteins and so includes a protein that, in a HPV transformed cell, would be selectively targeted for degradation or a protein that is acted upon by human HPV oncoproteins in such a way that it is, directly or indirectly, degraded, most typically but not exclusively, by the ubiquitin pathway.
In a preferred embodiment of the invention the mammal is human.
Preferably, the oncoprotein is E6 or E7.
The host cell protein may be any protein that is degraded by viral proteins, such as E6 or E7, and Table 3 lists those proteins that are currently known to be targeted for degradation by E6 or E7.
Preferably, the peptide is HPV-specific or tumour-specific, meaning that it is presented in high amounts on the cell surface of HPV transformed or tumour cells, relative to normal cells.
Even more preferably, the peptide is 9 to 30 amino acids in length.
Alternatively, the peptide may be 9 to 11 amino acids in length.
The CTL response is preferably a HPV-specific or tumour-specific CTL response, meaning that the CTL can recognise HPV transformed cells or tumour cells expressing the peptides of the vaccine.
More preferably, the vaccine comprises one or more of the peptides shown in Table 4 (SEQ ID NOS: 1-163).
More preferably still, the vaccine comprises any of the aforementioned peptides plus a further protein or peptide comprising a major histocompatability complex molecule, ideally, a class I molecule and more specifically a human leucocyte antigen (HLA), and more ideally still a HLA selected from Table 1.
In another aspect of the invention, there is provided a vaccine comprising: at least one isolated, purified, synthesised or recombinant peptide, wherein the peptide is chosen from those listed in Table 4.
In yet another aspect of the invention, there is provided a vaccine comprising: at least one isolated, purified, synthesised or recombinant peptide selected from Table 4 and, further at least one isolated, purified, synthesised or recombinant HLA selected from those listed in Table 1.
In a further aspect of the invention, there is provided a vaccine comprising: at least one isolated, purified, synthesised or recombinant nucleic acid molecule encoding any peptide or peptide/HLA complex as described above.
In this embodiment, the nucleic acid molecule may be in the form of a vector that comprises a recombinant construct. Ideally the construct is adapted for the expression of said vaccine in a selected host system. The host system is a cell, plasmid, virus, live organism or other similar vehicle.
According to a further aspect of the invention there is provided a host cell transformed or transfected with the vector of the invention.
Additionally, the present invention provides a method of manufacturing a vaccine, which method comprises; culturing a host cell transformed or transfected with a vector comprising a recombinant construct as described above; and isolating/purifying the resulting construct product.
The peptides of the present invention may also be used to generate and isolate HPV-specific or tumour-specific cytotoxic T lymphocytes or their T cell receptors or the genes encoding said receptors, in vitro, for use in adoptive immunotherapy. This could for example be carried out by culturing T lymphocytes with at least one of the peptides described above.
According to yet a further aspect of the invention there is provided a method of identifying HPV-specific or tumour-specific cytotoxic T lymphocytes comprising:
(a) culturing a sample containing cytotoxic T lymphocytes with at least one peptide that represents a fragment of a host cell protein which is degraded by HPV proteins when said host cell is transformed or transfected by HPV whereby said peptide is ultimately presented on a surface of a virally infected cell; and(b) selecting CTL that recognise said peptide by binding thereto.
In a preferred method of the invention said peptide is one selected from the list shown in Table 4. In yet a further preferred method of the invention the CTL are CD8+ cells.
It will be apparent to those skilled in the art that CTL receptors may further be identified using the aforementioned method.
The present invention can be used to treat HPV associated diseases and particularly cancer, preferably cervical cancer, head and neck squamous cell cancer, non-melanoma skin cancers, liver cancer, mesothioloma or prostrate cancer.
Furthermore, the present invention also provides a method of treatment, which method comprises administering a vaccine as described above, to a mammal to be treated. Ideally, the mammal is human.
According to a further aspect of the invention there is provided a peptide, or a nucleic acid molecule encoding same, selected from the list shown in Table 4.
In a further embodiment of the invention, said peptide is for use as a vaccine and in particular for use as a HPV vaccine to treat HPV associated disorders.
According to a further aspect of the invention there is provided a complex comprising at least one of the peptides listed in Table 4 in association with a HLA co-presenting peptide.
More preferably the HLA peptide is one of the peptides listed in Table 1 and more specifically HLA-A binding protein and more specifically still HLA-A 0201.
According to a further aspect of the invention there is provided the use of a HPV-specific peptide for the production of a HPV vaccine wherein said peptide is a fragment of a mammalian cell protein that has been degraded by human papillomavirus oncoproteins and which is presented, in combination with HLA, at the surface of the transformed or transfected HPV cell whereby the recognition of this peptide HLA complex by a cytotoxic T lymphocyte results in the elicitation of an immune response.
The invention will now be described by way of the following examples and with reference to the following Figures wherein:
FIG. 1 shows a mechanism for T cell recognition of host cell proteins in cells transformed by human papillomavirus;
FIG. 2 shows a difference in presentation of host cell peptides in normal and HPV transformed cells;
FIG. 3 shows HLA-A2 binding of host protein derived peptides. Specifically, HLA-A*0201 expression of T2 cells was monitored by flow cytometry after overnight incubation with 100 μg test peptides. Each peptide was tested in quadruplicate. A % increase in HLA-A*0201 expression of above 50% was considered significant;
FIG. 4 shows generation of T cell responses in vivo against a peptide derived from human Rb protein. Specifically, HLA-A2/Kb transgenic mice were immunised with 100 μg of test peptide emulsified in incomplete freunds adjuvant. Two to four mice were tested for each peptide. Ten to eleven days later, mice were sacrificed and splenocytes tested in ELISPOT assays. These measured the numbers of IFNproducing T cells (spots) specific for the immunising peptide. Positive results were confirmed in at least two further repeat experiments. Representative data from 1 experiment testing M158-66, Rb1, Rb7 and BAK18 peptides, are shown;
FIG. 5 shows CD8+ T cells recognising Rb7 can be detected in healthy HLA-A2+ donors. Specifically, CD8+ T cells were cultured with Rb7 (panels C&D) or Melan-A/Mart126-35 (panels A&B) peptides for 14 days On day 0 and day 14 days, the numbers of peptide specific CD8+ T cells were measured using appropriate fluoresceinated peptide:HLA-A2 pentamers. These were analysed on a flow cytometer and expressed as % of gated cells, excluding dead and CD14+ cells. Results for donor 5 (from table 4) are shown; and
FIG. 6 shows functional CD8+ T cells recognising Rb7 can be detected in healthy donors. Specifically, peripheral blood lymphocytes from HLA-A2+ healthy donors were enriched for CD8+ T cells, then cultured for 14 days with Rb7 peptide and antigen presenting cells (APC). The cultured cells were harvested and tested in enzyme linked immunospot (ELISPOT) assays to measure the numbers of T cells able to secrete IFN--in response to Rb7 peptide. Three (A, B, C) out of seven donors were capable of making significant responses (number of spots for T cells+Rb7+PBMC >2 standard deviations above T cells+PBMC).
Candidate 9 or 10 amino acid peptides from 15 proteins were selected for analysis, see Table 4 for the full list of peptides. One hundred and two peptides predicted to bind to HLA-A*0201 were selected according to published algorithms (33,34). (Table 4). The algorithm we used has been used previously to successfully predict other tumour-specific CTL epitopes (17). We chose HLA-A*0201 as the co-presenting peptide as this is the most common HLA allele (˜40%) among Caucasians, and there are well-defined in vivo and in vitro model systems to facilitate proof of concept experiments. From the initial list of 102 peptides, 62 were synthesized for testing.
Peptides were Tested for Binding to HLA-A*0201.
CTL recognise peptides bound to HLA class I molecules on the cell surface. Therefore peptides must demonstrate binding to HLA to be useful. This can be measured by using a cell based assay measuring an increase in HLA-A*0201 expression resulting from binding.
A cell-based peptide binding assay ((35)) was used to show that the majority (43162) of candidate peptides could bind to HLA-A*0201 (Table 3 FIG. 3).
HLA-A2 Binding of Host Protein Derived Peptides.
HLA-A*0201 expression of T2 cells was monitored by flow cytometry after overnight incubation with 100 μg test peptides. Each peptide was tested in quadruplicate. A percentage increase in HLA-A*0201 expression of above 50% was considered significant.
The level of binding observed could be classified as either strong or moderate, and was comparable to two well-known HLA-A*0201 restricted CTL epitopes (influenza M1 and EBV BMFL1)(FIG. 3).
43 of the peptides that showed a greater than 50% increase in HLA-A*0201 expression were chosen as candidates for testing in immunogenicity experiments.
Testing In Vivo Immunogenicity in Mice.
We have used HLA-A*0201 transgenic mice to test potential human vaccines (36). These mice can be immunised with peptides together with adjuvant to monitor development of in vivo responses. These responses were detected using ELISPOT assays to measure the numbers of IFN-γ securing peptide specific T cells in the spleen.
This was done with 20 peptides from the Rb(6), Muppl (7), BAK (3), DLG (2), AP (2) proteins. All peptides were chosen on the strength of peptide binding (FIG. 3). The M158-66 peptide from influenza, a known HLA-A*0201 binder was used as a positive control. Significant T cell responses were seen against the positive control M158-66 peptide (7/12 mice) and a peptide from Rb485-493 (Rb7) protein (7/10 mice). The results are shown in FIG. 4.
Testing In Vitro Immunogenicity using Human T Lymphocytes.
The candidate peptides must be capable of activating human T lymphocytes that can recognise and kill cancer cells. We detected peptide specific T cells in the peripheral blood of patients with cervical cancer. This proved the concept that such peptides can be immunogenic despite being derived from "self" proteins.
Detection of Peptide Specific T Cells
T cells reactive against peptides of the invention should be preferentially found in HLA-A2+ patients with cervical cancer. Blood samples from 4 patients (3 with cervical cancer, 1 with premalignant disease, CIN3) were tested for the presence of CD8+ T cells recognising Rb7 peptide. Fluoresceinated multimeric HLA-A2/peptide complexes were used to measure numbers of peptide specific T cells by flow cytometry (10). This assay demonstrated that T cells specific for Rb7 peptide could be detected at low frequency in the blood of 2 patients with cervical cancer. These frequencies were similar to those previously obtained for HPV16 E7 peptide specific T cells (10). This suggests that it should be possible to isolate and propagate Rb specific T cells for further experiments.
Using the technique described above, T lymphocytes recognising certain "self" tumour antigens such as melan-A can also be readily detected in healthy donors (50). However it is usually the case that T lymphocytes recognising "self" antigens are difficult to detect in healthy donors. Blood samples from 8 healthy donors (all HLA-A2+) were tested for the presence of CD8+ T cells recognising Rb7 peptide and melan-A peptide, using appropriate fluoresceinated multimers (pentamers). T lymphocytes recognising Rb7 peptide could be detected at variable but generally low frequencies in all 8 healthy donors (Table 6). By contrast T lymphocyte responses against melan-A were extremely high frequency, confirming previous reports (50). The highest frequency of T lymphocytes specific for Rb7 was found in donor 5 (FIG. 5).
The assays described above demonstrate that human T cells recognising Rb7 can be detected in both patients and healthy donors. ELISPOT assays were used to determine whether Rb7 peptide specific CD8+ T lymphocytes cultured from healthy donors, were capable of secreting IFN-γ. Seven healthy donors were tested, with 3 donors demonstrating detectable numbers of IFN-γ secreting T lymphocytes (FIG. 5).
Overall these results suggest that host cell protein fragments produced by HPV processing, such as the Rb7 peptide, is immunogenic for human CD8+ T lymphocytes, and can elicit functional (IFN-γ secretion) responses. This suggests that it should be possible to isolate and propagate large numbers of Rb specific T cells for either experimental or clinical therapeutic use.
TABLE-US-00001 Full List of HLA Class I alleles assigned as of July 2005 HLA-A HLA-B HLA-C HLA-E HLA-F HLA-G A*01010101 B*070201 Cw*010201 E*01010101 F*010101 G*010101 A*01010102N B*070202 Cw*010202 E*01010102 F*010102 G*010102 A*010102 B*070203 Cw*010203 E*01030101 G*010103 A*010103 B*070204 Cw*0103 E*01030102 G*010104 A*0102 B*0703 Cw*0104 E*010302 G*010105 A*0103 B*0704 Cw*0105 E*010303 G*010106 A*0104N B*0705 Cw*0106 E*010304 G*010107 A*0106 B*0706 Cw*0107 E*0104 G*010108 A*0107 B*0707 Cw*0108 G*0102 A*0108 B*0708 Cw*0109 G*0103 A*0109 B*0709 Cw*0110 G*010401 A*0110 B*0710 Cw*0111 G*010402 A*0111N B*0711 Cw*020201 G*010403 A*0112 B*0712 Cw*020202 G*0105N A*0113 B*0713 Cw*020203 G*0106 A*0114 B*0714 Cw*020204 A*0115N B*0715 Cw*020205 A*02010101 B*0716 Cw*0203 A*02010102L B*0717 Cw*0204 A*020102 B*0718 Cw*0205 A*020103 B*0719 Cw*0206 A*020104 B*0720 Cw*0207 A*020105 B*0721 Cw*0208 A*020106 B*0722 Cw*0209 A*020107 B*0723 Cw*0210 A*020108 B*0724 Cw*0211 A*020109 B*0725 Cw*0212 A*020110 B*0726 Cw*030201 A*020111 B*0727 Cw*030202 A*0202 B*0728 Cw*030301 A*020301 B*0729 Cw*030302 A*020302 B*0730 Cw*030303 A*0204 B*0731 Cw*030304 A*0205 B*0732 Cw*030401 A*020601 B*0733 Cw*030402 A*020602 B*0734 Cw*030403 A*020603 B*0735 Cw*0305 A*0207 B*0736 Cw*0306 A*0208 B*0737 Cw*0307 A*0209 B*0738 Cw*0308 A*0210 B*0739 Cw*0309 A*0211 B*0740 Cw*0310 A*0212 B*0741 Cw*0311 A*0213 B*0742 Cw*0312 A*0214 B*0743 Cw*0313 A*0215N B*080101 Cw*0314 A*0216 B*080102 Cw*0315 A*021701 B*0802 Cw*0316 A*021702 B*0803 Cw*0317 A*0218 B*0804 Cw*0318 A*0219 B*0805 Cw*0319 A*022001 B*0806 Cw*04010101 A*022002 B*0807 Cw*04010102 A*0221 B*0808N Cw*040102 A*0222 B*0809 Cw*040103 A*0224 B*0810 Cw*0403 A*0225 B*0811 Cw*040401 A*0226 B*0812 Cw*040402 A*0227 B*0813 Cw*0405 A*0228 B*0814 Cw*0406 A*0229 B*0815 Cw*0407 A*0230 B*0816 Cw*0408 A*0231 B*0817 Cw*0409N A*0232N B*0818 Cw*0410 A*0233 B*0819N Cw*0411 A*0234 B*0820 Cw*0412 A*023501 B*0821 Cw*0413 A*023502 B*0822 Cw*0414 A*0236 B*0823 Cw*0415 A*0237 B*0824 Cw*0416 A*0238 B*0825 Cw*0417 A*0239 B*1301 Cw*050101 A*0240 B*130201 Cw*050102 A*0241 B*130202 Cw*0502 A*0242 B*1303 Cw*0503 A*0243N B*1304 Cw*0504 A*0244 B*1306 Cw*0505 A*0245 B*1307N Cw*0506 A*0246 B*1308 Cw*0507N A*0247 B*1309 Cw*0508 A*0248 B*1310 Cw*0509 A*0249 B*1311 Cw*0510 A*0250 B*1312 Cw*0511 A*0251 B*1313 Cw*0602 A*0252 B*1401 Cw*0603 A*0253N B*140201 Cw*0604 A*0254 B*140202 Cw*0605 A*0255 B*1403 Cw*0606 A*0256 B*1404 Cw*0607 A*0257 B*1405 Cw*0608 A*0258 B*140601 Cw*0609 A*0259 B*140602 Cw*0610 A*0260 B*1407N Cw*0611 A*0261 B*15010101 Cw*0612 A*0262 B*15010102N Cw*0613 A*0263 B*150102 Cw*070101 A*0264 B*150103 Cw*070102 A*0265 B*150104 Cw*070103 A*0266 B*150105 Cw*07020101 A*0267 B*1502 Cw*07020102 A*0268 B*1503 Cw*07020103 A*0269 B*1504 Cw*0703 A*0270 B*1505 Cw*070401 A*0271 B*1506 Cw*070402 A*0272 B*1507 Cw*0705 A*0273 B*1508 Cw*0706 A*027401 B*1509 Cw*0707 A*027402 B*1510 Cw*0708 A*0275 B*151101 Cw*0709 A*0276 B*151102 Cw*0710 A*0277 B*1512 Cw*0711 A*0278 B*1513 Cw*0712 A*0279 B*1514 Cw*0713 A*0280 B*1515 Cw*0714 A*0281 B*1516 Cw*0715 A*0282N B*15170101 Cw*0716 A*0283N B*15170102 Cw*0717 A*0284 B*151702 Cw*0718 A*0285 B*1518 Cw*0719 A*0286 B*1519 Cw*0720 A*03010101 B*1520 Cw*0721 A*03010102N B*1521 Cw*0722 A*03010103 B*1523 Cw*0723 A*030102 B*1524 Cw*0724 A*030103 B*1525 Cw*0725 A*030104 B*1526N Cw*0726 A*0302 B*1527 Cw*0727 A*0303N B*1528 Cw*0728 A*0304 B*1529 Cw*0729 A*0305 B*1530 Cw*0730 A*0306 B*1531 Cw*080101 A*0307 B*1532 Cw*080102 A*0308 B*1533 Cw*0802 A*0309 B*1534 Cw*0803 A*0310 B*1535 Cw*0804 A*0311N B*1536 Cw*0805 A*0312 B*1537 Cw*0806 A*0313 B*1538 Cw*0807 A*0314 B*1539 Cw*0808 A*0315 B*1540 Cw*0809 A*0316 B*1542 Cw*0810 A*0317 B*1543 Cw*0811 A*110101 B*1544 Cw*0812 A*110102 B*1545 Cw*120201 A*110103 B*1546 Cw*120202 A*110104 B*1547 Cw*120203 A*110105 B*1548 Cw*120301 A*1102 B*1549 Cw*120302 A*1103 B*1550 Cw*120303 A*1104 B*1551 Cw*120401 A*1105 B*1552 Cw*120402 A*1106 B*1553 Cw*1205 A*1107 B*1554 Cw*1206 A*1108 B*1555 Cw*1207 A*1109 B*1556 Cw*1208 A*1110 B*1557 Cw*1209 A*1111 B*1558 Cw*1210 A*1112 B*1560 Cw*1211 A*1113 B*1561 Cw*1212 A*1114 B*1562 Cw*1213 A*1115 B*1563 Cw*1214 A*1116 B*1564 Cw*1215 A*1117 B*1565 Cw*140201 A*1118 B*1566 Cw*140202 A*1119 B*1567 Cw*140203 A*1120 B*1568 Cw*140204 A*1121N B*1569 Cw*1403 A*1122 B*1570 Cw*1404 A*1123 B*1571 Cw*1405 A*2301 B*1572 Cw*1406 A*2302 B*1573 Cw*1407N A*2303 B*1574 Cw*150201 A*2304 B*1575 Cw*150202 A*2305 B*1576 Cw*1503 A*2306 B*1577 Cw*1504 A*2307N B*1578 Cw*150501 A*2308N B*1579N Cw*150502 A*2309 B*1580 Cw*150503 A*2310 B*1581 Cw*150504 A*2311N B*1582 Cw*1506 A*2312 B*1583 Cw*1507 A*24020101 B*1584 Cw*1508 A*24020102L B*1585 Cw*1509 A*240202 B*1586 Cw*1510 A*240203 B*1587 Cw*1511 A*240204 B*1588 Cw*1512 A*240205 B*1589 Cw*1513 A*240206 B*1590 Cw*1514 A*240301 B*1591 Cw*160101 A*240302 B*1592 Cw*160102 A*2404 B*1593 Cw*1602 A*2405 B*1594N Cw*160401 A*2406 B*1595 Cw*1606 A*2407 B*1596 Cw*1607 A*2408 B*1597 Cw*1701 A*2409N B*1598 Cw*1702 A*2410 B*1599 Cw*1703 A*2411N B*180101 Cw*1801 A*2413 B*180102 Cw*1802 A*2414 B*1802 A*2415 B*1803 A*2417 B*1804 A*2418 B*1805 A*2419 B*1806 A*2420 B*1807 A*2421 B*1808 A*2422 B*1809 A*2423 B*1810 A*2424 B*1811 A*2425 B*1812 A*2426 B*1813 A*2427 B*1814 A*2428 B*1815 A*2429 B*1817N A*2430 B*1818 A*2431 B*1819 A*2432 B*1820 A*2433 B*2701 A*2434 B*2702 A*2435 B*2703 A*2436N B*270401 A*2437 B*270402 A*2438 B*270502 A*2439 B*270503 A*2440N B*270504 A*2441 B*270505 A*2442 B*270506 A*2443 B*270507 A*2444 B*270508 A*2445N B*270509 A*2446 B*2706 A*2447 B*2707 A*2448N B*2708 A*2449 B*2709 A*2450 B*2710 A*2451 B*2711 A*2452 B*2712 A*2453 B*2713 A*250101 B*2714 A*250102 B*2715 A*2502 B*2716 A*2503 B*2717 A*2504 B*2718 A*260101 B*2719 A*260102 B*2720 A*260103 B*2721
A*260104 B*2723 A*2602 B*2724 A*2603 B*2725 A*2604 B*2726 A*2605 B*2727 A*2606 B*2728 A*260701 B*2729 A*260702 B*2730 A*2608 B*350101 A*2609 B*350102 A*2610 B*350103 A*2611N B*350104 A*2612 B*350201 A*2613 B*350202 A*2614 B*3503 A*2615 B*350401 A*2616 B*350402 A*2617 B*3505 A*2618 B*3506 A*2619 B*3507 A*2620 B*3508 A*2621 B*350901 A*2622 B*350902 A*2623 B*3510 A*2624 B*3511 A*2625N B*3512 A*2626 B*3513 A*29010101 B*351401 A*29010102N B*351402 A*290201 B*3515 A*290202 B*3516 A*290203 B*3517 A*2903 B*3518 A*2904 B*3519 A*2905 B*3520 A*2906 B*3521 A*2907 B*3522 A*2908N B*3523 A*2909 B*3524 A*2910 B*3525 A*2911 B*3526 A*2912 B*3527 A*2913 B*3528 A*2914 B*3529 A*300101 B*3530 A*300102 B*3531 A*300201 B*3532 A*300202 B*3533 A*300203 B*3534 A*3003 B*3535 A*3004 B*3536 A*3006 B*3537 A*3007 B*3538 A*3008 B*3539 A*3009 B*3540N A*3010 B*3541 A*3011 B*3542 A*3012 B*3543 A*3013 B*3544 A*3014L B*3545 A*3015 B*3546 A*310102 B*3547 A*3102 B*3548 A*3103 B*3549 A*3104 B*3550 A*3105 B*3551 A*3106 B*3552 A*3107 B*3553N A*3108 B*3554 A*3109 B*3555 A*3110 B*3556 A*3111 B*3557 A*3112 B*3558 A*3201 B*3559 A*3202 B*3560 A*3203 B*3561 A*3204 B*3701 A*3205 B*3702 A*3206 B*3703N A*3207 B*3704 A*3208 B*3705 A*3209 B*3706 A*3210 B*3707 A*3301 B*3708 A*330301 B*3709 A*330302 B*3801 A*3304 B*380201 A*3305 B*380202 A*3306 B*3803 A*3307 B*3804 A*3308 B*3805 A*3401 B*3806 A*3402 B*3807 A*3403 B*3808 A*3404 B*3809 A*3405 B*3810 A*3406 B*3811 A*3601 B*39010101 A*3602 B*39010102L A*3603 B*390103 A*3604 B*390104 A*4301 B*390201 A*6601 B*390202 A*6602 B*3903 A*6603 B*3904 A*6604 B*3905 A*680101 B*390601 A*680102 B*390602 A*680103 B*3907 A*6802 B*3908 A*680301 B*3909 A*680302 B*3910 A*6804 B*3911 A*6805 B*3912 A*6806 B*391301 A*6807 B*391302 A*6808 B*3914 A*6809 B*3915 A*6810 B*3916 A*6811N B*3917 A*6812 B*3918 A*6813 B*3919 A*6814 B*3920 A*6815 B*3922 A*6816 B*3923 A*6817 B*3924 A*6818N B*3925N A*6819 B*3926 A*6820 B*3927 A*6821 B*3928 A*6822 B*3929 A*6823 B*3930 A*6824 B*3931 A*6825 B*3932 A*6826 B*3933 A*6827 B*3934 A*6828 B*400101 A*6901 B*400102 A*7401 B*400103 A*7402 B*400104 A*7403 B*400105 A*7404 B*400201 A*7405 B*400202 A*7406 B*400203 A*7407 B*4003 A*7408 B*4004 A*7409 B*4005 A*7410 B*40060101 A*7411 B*40060102 A*8001 B*400602 B*4007 B*4008 B*4009 B*4010 B*4011 B*4012 B*4013 B*401401 B*401402 B*401403 B*4015 B*4016 B*4018 B*4019 B*4020 B*4021 B*4022N B*4023 B*4024 B*4025 B*4026 B*4027 B*4028 B*4029 B*4030 B*4031 B*4032 B*4033 B*4034 B*4035 B*4036 B*4037 B*4038 B*4039 B*4040 B*4042 B*4043 B*4044 B*4045 B*4046 B*4047 B*4048 B*4049 B*4050 B*4051 B*4052 B*4053 B*4054 B*4055 B*4056 B*4057 B*4058 B*4059 B*4060 B*4061 B*4101 B*4102 B*4103 B*4104 B*4105 B*4106 B*4107 B*4201 B*4202 B*4204 B*420501 B*420502 B*4206 B*44020101 B*44020102S B*440202 B*440203 B*440301 B*440302 B*4404 B*4405 B*4406 B*4407 B*4408 B*4409 B*4410 B*4411 B*4412 B*4413 B*4414 B*4415 B*4416 B*4417 B*4418 B*4419N B*4420 B*4421 B*4422 B*4423N B*4424 B*4425 B*4426 B*4427 B*4428 B*4429 B*4430
B*4431 B*4432 B*4433 B*4434 B*4435 B*4436 B*4437 B*4438 B*4439 B*4440 B*4441 B*4442 B*4501 B*4502 B*4503 B*4504 B*4505 B*4506 B*4507 B*4601 B*4602 B*4603 B*4604 B*4605 B*47010101 B*47010102 B*4702 B*4703 B*4704 B*4705 B*4801 B*4802 B*4803 B*4804 B*4805 B*4806 B*4807 B*4808 B*4809 B*4810 B*4811 B*4812 B*4813 B*4901 B*4902 B*4903 B*4904 B*5001 B*5002 B*5004 B*510101 B*510102 B*510103 B*510104 B*510105 B*510106 B*510107 B*510201 B*510202 B*5103 B*5104 B*5105 B*5106 B*5107 B*5108 B*5109 B*5110 B*5111N B*5112 B*511301 B*511302 B*5114 B*5115 B*5116 B*5117 B*5118 B*5119 B*5120 B*5121 B*5122 B*5123 B*5124 B*5126 B*5127N B*5128 B*5129 B*5130 B*5131 B*5132 B*5133 B*5134 B*5135 B*5136 B*5137 B*5138 B*520101 B*520102 B*520103 B*520104 B*5202 B*5203 B*5204 B*5205 B*5206 B*5207 B*5208 B*530101 B*530102 B*530103 B*5302 B*5303 B*5304 B*5305 B*5306 B*5307 B*5308 B*5309 B*5310 B*5401 B*5402 B*5403 B*5404 B*5405N B*5406 B*5407 B*550101 B*550102 B*5502 B*5503 B*5504 B*5505 B*5507 B*5508 B*5509 B*5510 B*5511 B*5512 B*5513 B*5514 B*5515 B*5516 B*5517 B*5518 B*5519 B*5601 B*5602 B*5603 B*5604 B*560501 B*560502 B*5606 B*5607 B*5608 B*5609 B*5610 B*5611 B*5612 B*5613 B*5614 B*5615 B*5616 B*570101 B*570102 B*570103 B*5702 B*570301 B*570302 B*5704 B*5705 B*5706 B*5707 B*5708 B*5709 B*5801 B*5802 B*5804 B*5805 B*5806 B*5807 B*5808 B*5809 B*5810N B*5811 B*5901 B*670101 B*670102 B*6702 B*7301 B*7801 B*780201 B*780202 B*7803 B*7804 B*7805 B*8101 B*8102 B*8201 B*8202 B*8301 B*9501 B*9502 B*9503 B*9504
TABLE-US-00002 TABLE 2 Monoclonal antibodies used to treat cancer, their target and mechanism of action. Name of monoclonal antibody Target/Mechanism of action Rituximab (Rituxan ®) Used to treat B-cell lymphomas, acts by binding to the CD20 molecule present on all B cells. Herceptin ® Binds to HER2, a growth factor receptor found on some tumour cells, such as breast cancers and lymphomas. Alemtuzumab (MabCampath ®) Used to treat chronic lymphocytic leukaemia. Binds to the CD52 molecule found on all white blood cells. Lym-1 (Oncolym ®) Used to treat lymphoma. Binds to the histocompatibility antigen found on lymphoma cells. Bevacizumab (Avastin ®) Used to treat tumours. Binds to vascular endothelial growth factor, which is found in healthy as well as malignant cells. Cetuximab (Erbitux ®) Used to treat colorectal cancers. Binds to epidermal growth factor receptor, which is also found on normal epithelial cells. Telomerase antibody Used to treat cancers in general. Binds to telomerase, which is the protein responsible for cancer cells over-riding the usual apoptosis mechanisms. This protein is also present on normal cells.
TABLE-US-00003 TABLE 3 Host cell proteins known to be targeted for degradation following binding to HPV E6 or E7 proteins. Host cell HPV Gene Accession target* protein Other names name number Function Location Reference Retinoblastoma 1 E7 Retinoblastoma RB1 M15400 cell cycle Nuclear (19) susceptibility regulation, protein tumour suppressor E6AP E6 Human UBE3A AF002224 proteolysis; Cytosolic (24) papillomavirus E6 binds to associated HPV16&18 protein E6 to target (E6AP), Ubiquitin p53 for protein ligase degradation, E3A (UBE3A) can also target itself for ubiquination and degradation C-MYC E6 v-myc MYC AY214166 cell cycle, Nuclear (25) myelocytomatosis gene viral oncogene transcription homolog (avian), myc proto- oncogene product HSCRIB E6 scribbled SCRIB AY062238 cell cycle membrane (26) homologue, vartul HMCM7 E6 minichromosome MCM7 AB004270 DNA nuclear (27) maintenance replication deficient 7, CDC47 MAGI1 E6 membrane MAGI1 AB010894 Signalling, membrane (28) associated tight guanylate kinase, junctions, WW and PDZ cell domain adhesion containing 1, BAIAP1, BAP1, MAGI-1, AIP3 SIPA1L1 E6 signal-induced SIPA1L1 AB007900 GTPase membrane (29) proliferation- activating associated 1 like protein 1, E6 targetted protein 1 (E6TP1) DLG1 E6 discs, large DLG1 U13897 cell growth, membrane (30) homolog 1 adhesion, (DLG1, HDLG), signalling synapse associated protein 97 (SAP97), hdlg BAK E6 BCL2- BAK1 U23765 pro- membrane (31) antagonist/killer 1 apoptotic, in presence of appropriate stimuli binds to BCL-2 to accelerate cell death MPDZ E6 multiple PDZ MPDZ AF093419 tight membrane (32) domain protein junction (MUPP1) formation MGMT E6 O-6- MGMT M29971 DNA repair nuclear (33) methylguanine- DNA methyltransferase MAGI-2 E6 membrane MAGI2 AB014605 same as membrane (34) associated magi-1 guanylate kinase, WW and PDZ domain containing 2, activin receptor interacting protein 1 (ARIP1) MAGI-3 E6 membrane MAGI3 AF213259 same as membrane (34) associated magi-1 guanylate kinase, WW and PDZ domain containing 3 Tuberin E6 tuberous TSC2 AB014460 tumour membrane (35) sclerosis 2 suppressor, (TSC2) GTPase signalling N-MYC E6 v-myc MYCN M13228 tumour membrane (25) myelocytomatosis suppressor viral related oncogene, neuro- blastoma derived (avian), N-MYC proto-oncogene protein *Proteins are listed by their agreed standard names, rather than the published names.
TABLE-US-00004 TABLE 4 Host cell proteins and HLA-A*0201 binding peptides Starting SEQ ID Protein Pos Sequence T0.5 NO. Retinoblastoma 563 WLSDsPLFDL 5375 1 Retinoblastoma 475 KLLNdNIFHM 858 2 Retinoblastoma 75 WLTWeKVSSV 736 3 Retinoblastoma 646 SLSLFYKKV 396 4 Retinoblastoma 447 KLGVrLYYRV 365 5 Retinoblastoma 218 LMLCvLDYFI 261 6 Retinoblastoma 485 SLLACALEV 257 7 Retinoblastoma 157 VLFALFSKL 255 8 Retinoblastoma 648 SLFYkKVYRL 182 9 Retinoblastoma 824 KMTPrSRILV 176 10 Retinoblastoma 679 IIWTIFQHTL 157 11 Retinoblastoma 188 ALVLKVSWI 132 12 Retinoblastoma 76 LTWEKVSSV 129 13 Retinoblastoma 703 IMMCSMYGI 109 14 Retinoblastoma 900 KLAEmTSTRT 107 15 Retinoblastoma 219 MLCVLDYFI 98 16 BAK 150 FLGQvTRFVV 761 17 BAK 129 ALLGFGYRL 300 18 BAK 188 ILNVIVVLGV 272 19 BAK 182 NLGNgPILNV 160 20 BAK 195 VVLLGQFVV 91 21 BAK 191 VLVVIGVVLL 84 22 BAK 145 GLTGFLGQV 79 23 DLG 355 ALYDRLADV 2099 24 DLG 275 NLHGvFVAEV 608 25 DLG 345 GLPGDSFYI 333 26 DLG 148 QLLEfNGINL 324 27 DLG 666 VLWIPACPL 301 28 DLG 497 VLILgPLLDV 272 29 DLG 301 LILEyGSLDV 247 30 DLG 480 SLAYqRVQKV 160 31 DLG 498 LILGPLLDV 138 32 DLG 178 ILAQYNPHV 118 33 E6AP 127 YLTEeKVYEI 453 34 E6AP 449 FINEPLNEV 415 35 E6AP 748 YLFRpEEIEL 364 36 E6AP 657 VLYQSLKDL 267 37 E6AP 785 VLIREFWEI 253 38 E6AP 226 KLGPDDVSV 243 39 E6AP 283 YLNLFIIGM 200 40 E6AP 785 VLIReFWEIV 153 41 E6AP 477 FMTCpFILNA 144 42 E6AP 262 YLSPnVECDL 98 43 C-MYC 133 CMWSgFSAAA 113 44 C-MYC 68 GLCSpCYVAV 104 45 C-MYC 177 YLQDLSAAA 94 46 C-MYC 133 CMWSGFSAA 57 47 MUPP1 745 LLPGdRLMFV 1496 48 MUPP1 692 AMWEaGIQHI 590 49 MUPP1 607 LLGENHQDV 485 50 MUPP1 981 YLLEQSSLA 347 51 MUPP1 1650 LLGAiIIHEV 272 52 MUPP1 814 GLADkPLFRA 272 53 MUPP1 606 TLLGeNHQDV 257 54 MUPP1 1547 SLLKtAKMTV 257 55 MUPP1 1772 ILMVNGEDV 214 56 MUPP1 1524 KVGDQILAV 201 57 MUPP1 1766 LMQGdQILMV 196 58 MUPP1 592 KLFSGDELL 136 59 MUPP1 87 TLQNESFLL 124 60 MUPP1 312 GMSSeQVAQV 116 61 MUPP1 751 LMFVNDVNL 97 62 E6TP1 855 SMGAIVWAV 867 63 E6TP1 886 VLIEgETKSV 485 64 E6TP1 960 GLGQLCFHV 403 65 E6TP1 877 LLGIsNEFIV 281 66 E6TP1 1009 QMIDILRTSV 206 67 E6TP1 1592 VLFSsTYPSL 202 68 E6TP1 783 FLLAKVINA 194 69 E6TP1 45 SLGSsVMAPV 160 70 E6TP1 641 FLQLLGERV 157 71 E6TP1 339 ILFDLNEAI 132 72 E6TP1 1522 KLIDLESPT 107 73 MAGI-1 69 LLLEvQCVRV 1794 74 MAGI-1 262 TLQEtALPPV 656 75 MAGI-1 1054 KVGDRILAV 201 76 MAGI-1 161 FLTVkEFLDL 187 77 MAGI-1 80 GLPRyDVLGV 160 78 MAGI-1 717 LLVQrGCLPV 118 79 MAGI-1 527 VLGHTHAQV 118 80 MCM7 356 RLAQHITYV 880 81 MCM7 335 LLSRfDLLWL 459 82 MCM7 60 KMQEHSDQV 353 83 MCM7 259 VLADgGVCCI 167 84 MCM7 439 ALARIRMVDV 160 85 MCM7 381 KLMRrYIAMC 148 86 MCM7 178 LLLLLVGGV 131 87 MCM7 481 ALDEyEELNV 114 88 MCM7 273 KMAEaDRTAI 108 89 Vartul 713 KLLEvNGVAL 1134 90 Vartul 99 SLPAsLSFLV 403 91 Vartul 348 YLLPQQPPL 364 92 Vartul 229 ILTEnLLMAL 342 93 Vartul 244 KLTKITNLNV 243 94 Vartul 15 FMQLVELDV 231 95 Vartul 1199 KLDYrALAAV 224 96 Vartul 68 ALNDvSLQAL 201 97 Vartul 63 SLAHIALNDV 160 98 Vartul 992 ILAVNGQDV 118 99 Vartul 849 VLSINGVDV 118 100 Vartul 129 ALPNIRELWL 117 101 MGMT 98 VLWKLLKVV 925 102 MGMT 161 GLAVKEWLL 160 103 MGMT 167 WLLAhEGHRL 364 104 MGMT 89 FQQEsFTRQV 101 105 N-Myc 421 VILKkATEYV 162 106 440 LLLEkEKLQA 128 107 446 KLQArQQQLL 75 108 MAGI-2 65 LLLEvNETPV 1794 109 993 KLIKdAGLSV 243 110 970 KVGDRILAV 201 111 43 YLGEvKPGKV 171 112 76 GLTIrDVLAV 160 113 528 AIMERPPPV 145 114 751 AIYESRQQV 125 115 481 VLGHTHADV 118 116 639 GLCEGDLIV 117 117 65 LLLEvNETPV 1794 118 993 KLIKdAGLSV 243 119 970 KVGDRILAV 201 120 43 YLGEvKPGKV 171 121 76 GLTIrDVLAV 160 122
528 AIMERPPPV 145 123 751 AIYESRQQV 125 124 481 VLGHTHADV 118 125 639 GLCEGDLIV 117 126 MAGI-3 70 VLLEvNGTPV 1794 127 502 FQLVpVNQYV 660 128 503 QLVPVNQYV 383 129 11 WLSKvQECAV 320 130 923 KVGDHISAV 201 131 726 KLDPSEVYL 164 132 654 NLTHIQVVEV 160 133 200 FQPDPVDQV 150 134 1067 NMGLFILRL 135 135 1121 LLLLrPGTGL 134 136 1122 LLLRPGTGL 134 137 499 VQMFQLVPV 102 138 70 VLLEvNGTPV 98 139 502 FQLVpVNQYV 91 140 503 QLVPVNQYV 85 141 11 WLSKvQECAV 79 142 Tuberin 464 KVLDVLSFV 4088 143 176 FLLVLVNLV 2723 144 1060 WLVGnKLVTV 736 145 291 LLRGAVFFV 659 146 1702 IVSDrNLPFV 537 147 80 ALWKAVADL 408 148 1208 WLMSLENPL 364 149 688 LLFRvLLQCL 309 150 117 GVLRaLFFKV 248 151 1065 KLVTVTTSV 243 152 464 KVLDvLSFVL 236 153 155 YLEEeLADFV 226 154 258 KLMRNLLGT 222 155 1033 YVFSNFTAV 197 156 235 SLPLFIVTL 187 157 612 LQAFdFLFLL 187 158 617 FLFLIRADSL 178 159 506 KLATgLLVDL 172 160 360 ILLNIIERL 151 161
TABLE-US-00005 TABLE 5 Summary of peptide binding No. peptides Source protein binding BAK 6/7 DLG 7/10 CMYC 2/4 E6AP 9/10 MUPP1 13/15 Retinoblastoma 6/16 Total 43/62
TABLE-US-00006 TABLE 6 Frequency of CD8+ T cells recognising Rb peptide in healthy volunteers. Peripheral blood lymphocytes from HLA-A2+ healthy donors were enriched for CD8+ T cells, then cultured for 14 days with Rb7 peptide and antigen presenting cells (APC) or Melan-A (Mart126-35) peptide. Cells were harvested and tested with HLA-A2/Rb7 pentamer or HLA-A2/Melan-A pentamer. The numbers of CD8+ pentamer+ T lymphocytes were measured by flow cytometry, excluding dead and CD14+ cells. Frequency of CD8+ pentamer+ cells Donor Rb Melan A 1 1/2500 1/24 2 1/1000 1/4 3 1/1000 1/3 4 1/909 1/3 5 1/120 1/4 6 1/3333 1/208 7 1/2000 1/3 8 1/2500 1/3
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161110PRTHuman 1Trp Leu Ser Asp Ser Pro Leu Phe Asp Leu1 5 10210PRTHuman 2Lys Leu Leu Asn Asp Asn Ile Phe His Met1 5 10310PRTHuman 3Trp Leu Thr Trp Glu Lys Val Ser Ser Val1 5 1049PRTHuman 4Ser Leu Ser Leu Phe Tyr Lys Lys Val1 5510PRTHuman 5Lys Leu Gly Val Arg Leu Tyr Tyr Arg Val1 5 10610PRTHuman 6Leu Met Leu Cys Val Leu Asp Tyr Phe Ile1 5 1079PRTHuman 7Ser Leu Leu Ala Cys Ala Leu Glu Val1 589PRTHuman 8Val Leu Phe Ala Leu Phe Ser Lys Leu1 5910PRTHuman 9Ser Leu Phe Tyr Lys Lys Val Tyr Arg Leu1 5 101010PRTHuman 10Lys Met Thr Pro Arg Ser Arg Ile Leu Val1 5 101110PRTHuman 11Ile Ile Trp Thr Leu Phe Gln His Thr Leu1 5 10129PRTHuman 12Ala Leu Val Leu Lys Val Ser Trp Ile1 5139PRTHuman 13Leu Thr Trp Glu Lys Val Ser Ser Val1 5149PRTHuman 14Ile Met Met Cys Ser Met Tyr Gly Ile1 51510PRTHuman 15Lys Leu Ala Glu Met Thr Ser Thr Arg Thr1 5 10169PRTHuman 16Met Leu Cys Val Leu Asp Tyr Phe Ile1 51710PRTHuman 17Phe Leu Gly Gln Val Thr Arg Phe Val Val1 5 10189PRTHuman 18Ala Leu Leu Gly Phe Gly Tyr Arg Leu1 51910PRTHuman 19Ile Leu Asn Val Leu Val Val Leu Gly Val1 5 102010PRTHuman 20Asn Leu Gly Asn Gly Pro Ile Leu Asn Val1 5 10219PRTHuman 21Val Val Leu Leu Gly Gln Phe Val Val1 52210PRTHuman 22Val Leu Val Val Leu Gly Val Val Leu Leu1 5 10239PRTHuman 23Gly Leu Thr Gly Phe Leu Gly Gln Val1 5249PRTHuman 24Ala Leu Tyr Asp Arg Leu Ala Asp Val1 52510PRTHuman 25Asn Leu His Gly Val Phe Val Ala Glu Val1 5 10269PRTHuman 26Gly Leu Pro Gly Asp Ser Phe Tyr Ile1 52710PRTHuman 27Gln Leu Leu Glu Phe Asn Gly Ile Asn Leu1 5 10289PRTHuman 28Val Leu Trp Ile Pro Ala Cys Pro Leu1 52910PRTHuman 29Val Leu Ile Leu Gly Pro Leu Leu Asp Val1 5 103010PRTHuman 30Leu Ile Leu Glu Tyr Gly Ser Leu Asp Val1 5 103110PRTHuman 31Ser Leu Ala Tyr Gln Arg Val Gln Lys Val1 5 10329PRTHuman 32Leu Ile Leu Gly Pro Leu Leu Asp Val1 5339PRTHuman 33Ile Leu Ala Gln Tyr Asn Pro His Val1 53410PRTHuman 34Tyr Leu Thr Glu Glu Lys Val Tyr Glu Ile1 5 10359PRTHuman 35Phe Ile Asn Glu Pro Leu Asn Glu Val1 53610PRTHuman 36Tyr Leu Phe Arg Pro Glu Glu Ile Glu Leu1 5 10379PRTHuman 37Val Leu Tyr Gln Ser Leu Lys Asp Leu1 5389PRTHuman 38Val Leu Ile Arg Glu Phe Trp Glu Ile1 5399PRTHuman 39Lys Leu Gly Pro Asp Asp Val Ser Val1 5409PRTHuman 40Tyr Leu Asn Leu Phe Ile Ile Gly Met1 54110PRTHuman 41Val Leu Ile Arg Glu Phe Trp Glu Ile Val1 5 104210PRTHuman 42Phe Met Thr Cys Pro Phe Ile Leu Asn Ala1 5 104310PRTHuman 43Tyr Leu Ser Pro Asn Val Glu Cys Asp Leu1 5 104410PRTHuman 44Cys Met Trp Ser Gly Phe Ser Ala Ala Ala1 5 104510PRTHuman 45Gly Leu Cys Ser Pro Ser Tyr Val Ala Val1 5 10469PRTHuman 46Tyr Leu Gln Asp Leu Ser Ala Ala Ala1 5479PRTHuman 47Cys Met Trp Ser Gly Phe Ser Ala Ala1 54810PRTHuman 48Leu Leu Pro Gly Asp Arg Leu Met Phe Val1 5 104910PRTHuman 49Ala Met Trp Glu Ala Gly Ile Gln His Ile1 5 10509PRTHuman 50Leu Leu Gly Glu Asn His Gln Asp Val1 5519PRTHuman 51Tyr Leu Leu Glu Gln Ser Ser Leu Ala1 55210PRTHuman 52Leu Leu Gly Ala Ile Ile Ile His Glu Val1 5 105310PRTHuman 53Gly Leu Ala Asp Lys Pro Leu Phe Arg Ala1 5 105410PRTHuman 54Thr Leu Leu Gly Glu Asn His Gln Asp Val1 5 105510PRTHuman 55Ser Leu Leu Lys Thr Ala Lys Met Thr Val1 5 10569PRTHuman 56Ile Leu Met Val Asn Gly Glu Asp Val1 5579PRTHuman 57Lys Val Gly Asp Gln Ile Leu Ala Val1 55810PRTHuman 58Leu Met Gln Gly Asp Gln Ile Leu Met Val1 5 10599PRTHuman 59Lys Leu Phe Ser Gly Asp Glu Leu Leu1 5609PRTHuman 60Thr Leu Gln Asn Glu Ser Phe Leu Leu1 56110PRTHuman 61Gly Met Ser Ser Glu Gln Val Ala Gln Val1 5 10629PRTHuman 62Leu Met Phe Val Asn Asp Val Asn Leu1 5639PRTHuman 63Ser Met Gly Ala Ile Val Trp Ala Val1 56410PRTHuman 64Val Leu Ile Glu Gln Glu Thr Lys Ser Val1 5 10659PRTHuman 65Gly Leu Gly Gln Leu Gly Phe His Val1 56610PRTHuman 66Leu Leu Gly Ile Ser Asn Glu Phe Ile Val1 5 106710PRTHuman 67Gln Met Ile Asp Leu Leu Arg Thr Ser Val1 5 106810PRTHuman 68Val Leu Phe Ser Ser Thr Tyr Pro Ser Leu1 5 10699PRTHuman 69Phe Leu Leu Ala Lys Val Ile Asn Ala1 57010PRTHuman 70Ser Leu Gly Ser Ser Val Met Ala Pro Val1 5 10719PRTHuman 71Phe Leu Gln Leu Leu Gly Glu Arg Val1 5729PRTHuman 72Ile Leu Phe Asp Leu Asn Glu Ala Ile1 5739PRTHuman 73Lys Leu Ile Asp Leu Glu Ser Pro Thr1 57410PRTHuman 74Leu Leu Leu Glu Val Gln Gly Val Arg Val1 5 107510PRTHuman 75Thr Leu Gln Glu Thr Ala Leu Pro Pro Val1 5 10769PRTHuman 76Lys Val Gly Asp Arg Ile Leu Ala Val1 57710PRTHuman 77Phe Leu Thr Val Lys Glu Phe Leu Asp Leu1 5 107810PRTHuman 78Gly Leu Pro Arg Tyr Asp Val Leu Gly Val1 5 107910PRTHuman 79Leu Leu Val Gln Arg Gly Gly Leu Pro Val1 5 10809PRTHuman 80Val Leu Gly His Thr His Ala Gln Val1 5819PRTHuman 81Arg Leu Ala Gln His Ile Thr Tyr Val1 58210PRTHuman 82Leu Leu Ser Arg Phe Asp Leu Leu Trp Leu1 5 10839PRTHuman 83Lys Met Gln Glu His Ser Asp Gln Val1 58410PRTHuman 84Val Leu Ala Asp Gln Gly Val Cys Cys Ile1 5 108510PRTHuman 85Ala Leu Ala Arg Leu Arg Met Val Asp Val1 5 108610PRTHuman 86Lys Leu Met Arg Arg Tyr Ile Ala Met Cys1 5 10879PRTHuman 87Leu Leu Leu Leu Leu Val Gly Gly Val1 58810PRTHuman 88Ala Leu Asp Glu Tyr Glu Glu Leu Asn Val1 5 108910PRTHuman 89Lys Met Ala Glu Ala Asp Arg Thr Ala Ile1 5 109010PRTHuman 90Lys Leu Leu Glu Val Asn Gly Val Ala Leu1 5 109110PRTHuman 91Ser Leu Pro Ala Ser Leu Ser Phe Leu Val1 5 10929PRTHuman 92Tyr Leu Leu Pro Gln Gln Pro Pro Leu1 59310PRTHuman 93Ile Leu Thr Glu Asn Leu Leu Met Ala Leu1 5 109410PRTHuman 94Lys Leu Thr Lys Leu Thr Asn Leu Asn Val1 5 10959PRTHuman 95Phe Met Gln Leu Val Glu Leu Asp Val1 59610PRTHuman 96Lys Leu Asp Tyr Arg Ala Leu Ala Ala Val1 5 109710PRTHuman 97Ala Leu Asn Asp Val Ser Leu Gln Ala Leu1 5 109810PRTHuman 98Ser Leu Ala His Leu Ala Leu Asn Asp Val1 5 10999PRTHuman 99Ile Leu Ala Val Asn Gly Gln Asp Val1 51009PRTHuman 100Val Leu Ser Ile Asn Gly Val Asp Val1 510110PRTHuman 101Ala Leu Pro Asn Leu Arg Glu Leu Trp Leu1 5 101029PRTHuman 102Val Leu Trp Lys Leu Leu Lys Val Val1 51039PRTHuman 103Gly Leu Ala Val Lys Glu Trp Leu Leu1 510410PRTHuman 104Trp Leu Leu Ala His Glu Gly His Arg Leu1 5 1010510PRTHuman 105Phe Gln Gln Glu Ser Phe Thr Arg Gln Val1 5 1010610PRTHuman 106Val Ile Leu Lys Lys Ala Thr Glu Tyr Val1 5 1010710PRTHuman 107Leu Leu Leu Glu Lys Glu Lys Leu Gln Ala1 5 1010810PRTHuman 108Lys Leu Gln Ala Arg Gln Gln Gln Leu Leu1 5 1010910PRTHuman 109Leu Leu Leu Glu Val Asn Glu Thr Pro Val1 5 1011010PRTHuman 110Lys Leu Ile Lys Asp Ala Gly Leu Ser Val1 5 101119PRTHuman 111Lys Val Gly Asp Arg Ile Leu Ala Val1 511210PRTHuman 112Tyr Leu Gly Glu Val Lys Pro Gly Lys Val1 5 1011310PRTHuman 113Gly Leu Thr Ile Arg Asp Val Leu Ala Val1 5 101149PRTHuman 114Ala Ile Met Glu Arg Pro Pro Pro Val1 51159PRTHuman 115Ala Ile Tyr Glu Ser Arg Gln Gln Val1 51169PRTHuman 116Val Leu Gly His Thr His Ala Asp Val1 51179PRTHuman 117Gly Leu Cys Glu Gly Asp Leu Ile Val1 511810PRTHuman 118Leu Leu Leu Glu Val Asn Glu Thr Pro Val1 5 1011910PRTHuman 119Lys Leu Ile Lys Asp Ala Gly Leu Ser Val1 5 101209PRTHuman 120Lys Val Gly Asp Arg Ile Leu Ala Val1 512110PRTHuman 121Tyr Leu Gly Glu Val Lys Pro Gly Lys Val1 5 1012210PRTHuman 122Gly Leu Thr Ile Arg Asp Val Leu Ala Val1 5 101239PRTHuman 123Ala Ile Met Glu Arg Pro Pro Pro Val1 51249PRTHuman 124Ala Ile Tyr Glu Ser Arg Gln Gln Val1 51259PRTHuman 125Val Leu Gly His Thr His Ala Asp Val1 51269PRTHuman 126Gly Leu Cys Glu Gly Asp Leu Ile Val1 512710PRTHuman 127Val Leu Leu Glu Val Asn Gly Thr Pro Val1 5 1012810PRTHuman 128Phe Gln Leu Val Pro Val Asn Gln Tyr Val1 5 101299PRTHuman 129Gln Leu Val Pro Val Asn Gln Tyr Val1 513010PRTHuman 130Trp Leu Ser Lys Val Gln Glu Cys Ala Val1 5 101319PRTHuman 131Lys Val Gly Asp His Ile Ser Ala Val1 51329PRTHuman 132Lys Leu Asp Pro Ser Glu Val Tyr Leu1 513310PRTHuman 133Asn Leu Thr His Leu Gln Val Val Glu Val1 5 101349PRTHuman 134Phe Gln Pro Asp Pro Val Asp Gln Val1 51359PRTHuman 135Asn Met Gly Leu Phe Ile Leu Arg Leu1 513610PRTHuman 136Leu Leu Leu Leu Arg Pro Gly Thr Gly Leu1 5 101379PRTHuman 137Leu Leu Leu Arg Pro Gly Thr Gly Leu1 51389PRTHuman 138Val Gln Met Phe Gln Leu Val Pro Val1 513910PRTHuman 139Val Leu Leu Glu Val Asn Gly Thr Pro Val1 5 1014010PRTHuman 140Phe Gln Leu Val Pro Val Asn Gln Tyr Val1 5 101419PRTHuman 141Gln Leu Val Pro Val Asn Gln Tyr Val1 514210PRTHuman 142Trp Leu Ser Lys Val Gln Glu Cys Ala Val1 5 101439PRTHuman 143Lys Val Leu Asp Val Leu Ser Phe Val1 51449PRTHuman 144Phe Leu Leu Val Leu Val Asn Leu Val1 514510PRTHuman 145Trp Leu Val Gly Asn Lys Leu Val Thr Val1 5 101469PRTHuman 146Leu Leu Arg Gly Ala Val Phe Phe Val1 514710PRTHuman 147Ile Val Ser Asp Arg Asn Leu Pro Phe Val1 5 101489PRTHuman 148Ala Leu Trp Lys Ala Val Ala Asp Leu1 51499PRTHuman 149Trp Leu Met Ser Leu Glu Asn Pro Leu1 515010PRTHuman 150Leu Leu Phe Arg Val Leu Leu Gln Cys Leu1 5 1015110PRTHuman 151Gly Val Leu Arg Ala Leu Phe Phe Lys Val1 5 101529PRTHuman 152Lys Leu Val Thr Val Thr Thr Ser Val1 515310PRTHuman 153Lys Val Leu Asp Val Leu Ser Phe Val Leu1 5 1015410PRTHuman 154Tyr Leu Glu Glu Glu Leu Ala Asp Phe Val1 5 101559PRTHuman 155Lys Leu Met Arg Asn Leu Leu Gly Thr1 51569PRTHuman 156Tyr Val Phe Ser Asn Phe Thr Ala Val1 51579PRTHuman 157Ser Leu Pro Leu Phe Ile Val Thr Leu1 515810PRTHuman 158Leu Gln Ala Phe Asp Phe Leu Phe Leu Leu1 5 1015910PRTHuman 159Phe Leu Phe Leu Leu Arg Ala Asp Ser Leu1 5 1016010PRTHuman 160Lys Leu Ala Thr Gln Leu Leu Val Asp Leu1 5 101619PRTHuman 161Ile Leu Leu Asn Ile Ile Glu Arg Leu1 5
Patent applications by Stephen Tze Kwung Man, Heath Park GB
Patent applications in class Virus or component thereof
Patent applications in all subclasses Virus or component thereof