Cancer vaccine based on MHC-ii epitope selection

Abstract

The present disclosure provides a vaccine against cancers that express MHC-II. That includes hormone positive breast cancers and some prostate cancers and melanoma. It is possible, based on a genomic test of the individual, to either (1) design a personal vaccine consisting of a polytope based on epitopes from the TAA that in most cases display on MHC-II and not on MHC-I, or (2) select previously manufactured sequences based on epitopes from the TAA as constituents of the vaccine, such that the cancer after vaccination will reveal itself to the immune system and get eradicated while there are little side effects in that the vaccine will not make the immune system harm the healthy tissue.

Description

BACKGROUND / SUMMARY Background of the Invention

[0001] The present invention relates to the use of the immune system of a human to recognize and kill or prevent a disease like cancer - in the following “the cancer”. In the following, key functions related to the functioning of the immune system are presented, in order to explain the background of invention, and not in order to explain the immune system to a person not acquainted with it. The present invention relates to a cancer vaccine as well as a method for producing a cancer vaccine. The invention further relates to specific epitopes and concatenated epitopes and the use thereof for treatment of cancer. The present invention further relates to a library of concatenated epitopes.

[0002] Cancers are the cause of death of many humans, and most cancers are not completely eradicated once they develop, in that current treatments rarely use the immune system to eradicate them. They may in some cases use the immune system to make the cancer treatments more effective e.g. by making T cells more effective through checkpoint inhibition treatments, which dominate current immunology treatments for cancer. But the previous uses of the immune system rarely makes it remove the cancer completely once it is discovered, or prevent it from developing, as it can do with other diseases. One of the causes is that a cancer develops in cells that express the same on the surface to the immune system, as healthy cells do, and the immune system through its functionality - e.g. through its selection of T cells - is barred from attacking healthy cells (in order to prevent autoimmune diseases from happening).

[0003] In order to elicit an immune response the cancer must be recognized on either the major histocompatibility complex I or II (MHC-I or MHC-II). It is done by the presentation of epitopes, which are a part of an antigen, wrapped into an MHC molecule. This complex of an epitope wrapped into MHC serves as a Ligand for the T Cell Receptor (TCR), such that if the said Ligand matches a TCR of a T cell, then said T cell is attracted and its activation is initiated.

[0004] The functioning and appearance of the MHC-I and MHC-II molecules are determined by the following genes: • MHC-I: HLA-A, HLA-B, HLA-C; and of without significance for interaction with T cells: HLA-E, HLA-F, HLA-G, and HLA-H. • MHC-II: HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5.

[0005] The selection of T cells in the thymus ensures that the matching to a TCR will not be likely, if the protein is naturally occurring in the tissue above a certain threshold (except in the event of an autoimmune disorder). This process is often referred to as “negative selection”, where the T cells that would have attacked healthy tissue are killed (negatively selected) by exposing them to something that looks the same as healthy tissue, before letting them out of the thymus into the body (and killing them if they are “auto-reactive” and therefore choose to attack the healthy tissue). However this negative selection is not perfect, and it is more harsh on T cells associated with MHC-I (CD8+, where it is estimated that approx. 1% auto-reactive T cells are allowed through), whereas it is more lax on T cells associated with MHC-II (CD4+, where it is estimated that more than 15% auto-reactive T cells are allowed through). The percentages (1% for CD8+ and 15% for CD4+, respectively, are unsure, and they vary according to how well the matter that the T cells represent through their T Cell Receptor (TCR) is expressed on the healthy tissue, suggesting that if the matter is strongly expressed on healthy tissue, then the percentages are lower, and conversely if the matter is only vaguely expressed on the healthy tissue, then the percentages are higher. In most cases, the amount of T cells that escape this “negative selection” despite being auto-reactive is high enough to fulfil the role that we describe below of killing the Antigen Presenting Cell (APC), even though it is not high enough to elicit an effective immune response.

[0006] It is known that auto-reactive T cells that would have attacked matter on healthy tissue like “Invariant Chain” (li) of the CD8+ type are negatively selected or cleared almost completely (with a percentage significantly lower than 1%).

[0007] T cells of the type CD8+ - Cytotoxic T Lymphocytes (CTL) - are potentially bound to MHC-I, i.e. to Ligands consisting of an epitope wrapped into an MHC-I molecule. The CD8+ CTLs may then kill the cell that presents the said Ligand.

[0008] T cells of the type CD4+ - Helper T cells (Th), and potentially other CD4+ T cells and CD4+ cells that are themselves cytotoxic (CD4+ CTLs) - are potentially bound to MHC-II, i.e. to Ligands consisting of an epitope wrapped into an MHC-II molecule. The fact that CD4+ cells can be cytotoxic themselves is a rather new discovery, not reflected in most overviews of the CD4+ phenotypes, and currently a CTL is often assumed to be a CD8+ T cell.

[0009] The immune system has several response mechanisms, e.g. the following: • A (professional) Antigen Presenting Cell (APC) scouts the body and digests “everything” it meets on its way and presents it - partially - in the form of Epitopes on MHC-I and on MHC-II. Each APC has several (millions) of MHC-I as well as millions of MHC-II molecules with epitopes in them on their surface, and it presents it before and after entering the Lymph Node (LN). • The T cells of type CD8+ kill the APCs even before they arrive at the LN, if what they present is covered already by an immune reaction, in which case there are already many CD8+ T cells out there, in order to prevent an overreaction in the immune response. • When the APC arrives in the LN, where naive (ready-for-action) T cells reside, it attracts both types of T cells (CD8+ and CD4+), provided they have escaped the negative selection (which they have in most cases, to some extent) - based on a match between the TCR and the epitopes wrapped in MHC-I or MHC-II, respectively. For all naturally occurring matters, there are both MHC-I and MHC-II content, and thus when digested by APCs, the said APCs always have both MHC-I and MHC-II on their surface, and they always attract both types of T cells. • The APC then sends “signal 2” or the “co-stimulatory signal” to the T cells, and they embark on the activation journey. • The CD8+ T cells are faster in all they do than the CD4+ T cells, but otherwise the two types of T cells are rather similar - they specialize into CD8+ or CD4+ rather late in their development in the thymus. They both require and respond the same way to the same set of costimulatory signals. • The CD8+ T cells get to the end of the activation journey first (before the CD4+ T cells), at which point or stage they become cytotoxic - and they therefore kill the APC. At this time the CD4+ T cells attached to the APC have not come to the stage yet, where they become cytotoxic (which, in cases other than cancer, would be useless anyway, because no tissue that should be killed expresses MHC-II). Therefore the CD4+ T cells stop at this “intermediary” stage where they have developed into “helper cells”, where one of their roles is to “shout” (by means of producing cytokines) to the B cells that they should kill the invader (the normal non-cancer source of epitopes on the surface of the APCs). Thus the CD8+ T cells in normal non-cancer situations are ready to kill infected body cells (that express the MHC-I part of the invader), a role of killing internals that they are specialized to do, and CD4+ T cells mobilize B cells to kill the invader, before it infects the body - a role of killing externals that B cells are specialized to do. Together these two killing roles do away with infections effectively in normal noncancer situations.

[00010] Problems with the immune response when it relates to cancer • Many cancers have “learned” (through Darwinistic selection) to tune down MHC-I presentation (they have “turned down channel 1”), and they therefore become invisible to CD8+ T cells. • Most cancers have conversely not turned down “channel 2” (they have not inactivated the MHC-II presentation machinery) - because nothing happens there anyway (they have not been threatened to be killed based on the expression on MHC-II). So the CD4+ T cells can easily see the cancer, being tuned in on channel 2, but they only shout (to B cells), they are not cytotoxic, and thus they do not harm the cancer cells. • However the B cells are not so good at killing cancer cells (which are internals) as they are at killing externals (invaders). • Therefore we hypothesize that if we make the CD4+ T cells cytotoxic, then they will kill the cancer (to the cancer’s surprise). And this killing will happen much faster than the time it takes the cancer cells to “learn” to turn down “channel 2”. • Since the CD4+ T cells react on antigens that are present in all of the cancer cells (as is the case with Tumor Associated Antigens (TAAs) as opposed to the mutated Tumor Specific Antigens (TSAs) that are not present in all of the cancer cells), they have the potential to kill all of the cancer cells.

[00011] The CD4+ cells may therefore do one of several things: (a) They may attract CD8+ cytotoxic T cells, which in turn kill the cell that presents the said Ligand consisting of an epitope wrapped into MHC-II, (b) (as described above) they may directly kill the cell (being a CD4+ cytotoxic T cell), (c) they may through the secretion of cytokines attract B cells that directly or through antibodies that they produce kill the cell with the Antigen, or (d) some other immune reaction. It is likely that some significant immune reaction happens, i.e. one or several of (a), (b), (c), and (d), since it seems that some MHC-II gene alleles have a strong influence on the occurrence of and are in some cases even protective for breast cancer according to a number of studies. Whether the immune reaction consists of one or a combination of the above mechanisms - including whether there exist further mechanisms elicited by MHC-II and CD4+ T cells - does not affect the present invention.

[00012] There is a growing interest in using MHC-II, either as a supplement to MHC-I (“activating both arms of the immune system”) or alone.

[00013] All cells with a nucleus (that is all cells of the human body with a few exceptions like red blood cells) have the ability to express MHC-I on their surface.

[00014] Only cells of the type “professional Antigen Presenting Cells”, sometimes just called “Antigen Presenting Cells”, (APC) and some cancer cells, and a few more infrequent types and situations including epithelial cells after inflammation, have the ability to express MHC-II on their surface. The APCs include Dendritic Cells (DCs), Macrophages, and B-cells. The fact that some cancers can present MHC-II is a rather new discovery, not reflected in most overviews, and it is generally assumed that MHC-II is only present on the surface of APCs. The cancers that can express MHC-II include • breast cancer (BC), • prostate cancer (PCa), • melanoma, • colorectal cancer, • ovarian cancer, • classic Hodgkin lymphoma, • glioma, and • non-small cell lung cancer (NSCLC). We are currently not sure that all of MHC-II is expressed on these cancers, and we are not sure that all variants of the above cancers express MHC-II.

[00015] Accordingly, there is a need in the art for new vaccine technologies focusing on epitopes presented by the MHC-II molecule.

[00016] Proteins are cut into epitopes before being attempted to be wrapped into an MHC molecule. The said epitope usually has the length 9, spanning from 8 to 14 (amino acids), in MHC I and the length 15, spanning from 13 to 25 (amino acids), in MHC-II. Then these epitopes can be presented, wrapped into MHC, on the surface of the cell, if they pass a number of further steps in the Antigen Presentation Pathway (APP), of which the wrapping with the MHC molecule is one step.

[00017] The APP for MHC-II is called the MHC-II Presentation Pathway, depicted in FIG 10. It can be seen from the figure that the protein, which is cut into epitopes (similar to peptides, as depicted in the figure) must find its way into the MHC-II Loading Compartment (“MIIC”), where the peptides of the protein must replace the “CLIP” sequences originating from the Invariant Chain in order to enter the MHC-II molecule and subsequently be presented on the surface of the cell.

[00018] The proteins that have the possibility to be cut into epitopes that after being wrapped into an MHC molecule may be presented to and match a TCR of a T cell, and thus trigger an immune response, are called Antigens. Antigens are thus either (1) purely external (e.g. pathogens that represent a disease), (2) mutated proteins that haven’t been present prior to the mutation, or (3) proteins that are expressed in an amount that is significantly above normal.

[00019] Tumor Specific Antigens (TSAs) are - mostly - mutated proteins (i.e. generated by a gene that is mutated). They are thus very immunogenic candidates of Antigens in that they are not associated with a normal “healthy” level (of expression), and TSAs are thus the focus of much of the cancer vaccine effort. But TSAs come with two main problems: (1) To capture them, a sample of the tumor is needed and must be extracted e.g. as a biopsy, and (2) since they come into existence due to a mutation, it is likely that the cancer can mutate again, away from the protein, and thus the cancer can live on in cells that do not express the TSA. In any case the vaccine requires the cancer to be there, so it can only be therapeutic, not preventative.

[00020] Tumor Associated Antigens (TAAs) are examples of proteins that have a lower level of expression in normal tissue and a higher level in cancer tissue. The fact that cells with normal levels of these Antigens still express them, means that there is either a threshold mechanism, or an accepted low level of killing of healthy cells, or they will be ineffective at any level as Antigens, because the selection of T cells in the thymus will make it hard to find a T cell whose TCR matches the Antigen. This mechanism is not causally determined, only empirically. In any event the effectiveness of a TAA as a vaccine candidate depends on whether there is a wide distance between how much it is expressed in the cancer on the one side and how much it is expressed in normal tissue - so that an appropriate amount of vaccine can be determined in order to “teach” the immune system to kill the cancer cells and not the healthy tissue. “Teach” in this case means adjusting (enhancing) the number of T cells so that they will leave the healthy tissue alone or not substantially kill it.

[00021] All cells (with a nucleus) use the presentation of epitopes from their proteins on MHC-L This includes the APCs and all the cancer cells as well as all other cells (with a nucleus). See FIG 1.

[00022] The APCs can swallow and digest exterior Antigens (a process called phagocytosis), so that they are presented on the MHC-II (and the MHC-I) of the said APCs, together with the internal proteins of the said APCs (cut into epitopes and wrapped into MHC-II). The presentation of said Antigen cut into epitopes (also called peptides) wrapped into MHC is referred to as the “peptide-MHC complex” (pMHC).

[00023] The APCs can also swallow and digest interior cells including sick or dying cancer cells and thus present epitopes from the Antigens present in the cancer cells wrapped in MHC-I and MHC-II as pMHC on the surface of said APCs.

[00024] Some cancer cells can present their internal proteins and thus Antigens, cut into epitopes, on MHC-II (the cancer cell types mentioned above).

[00025] The APCs travel to organs like the Lymph Node (LN) and are exposed to and attract T cells there, if there is a match between the T Cell Receptor (TCR) and the pMHC on the surface of the APC, this match being referred to as “signal 1” in the “2 (or sometimes 3) signal theory”: The “signal 1” must be followed by one or several signals in “signal 2” in order to activate the T Cell and make it develop from “naive” to the stage that it should, expand, proliferate, so that it can do its job. Examples of said Signals are given in the following Table 1 , and a more extensive list of Signals are given in the reference on the URL “https: / / www.ncbi.nlm.nih.gov / pmc / articles / PMC3786574 / ”. If there is no “signal 2” after “signal 1” the T cell may become anergic. Table 1 Signal Signal Type Signal Name APC | Inhibitor Signal 1 Primary pMHC to TCR pMHC (unspecified 1 or II) TCR (unspecified 1 ior II) Signal 2 Coactivating CD40 CD40 TD40L Early pMHC to CD3 pMHC (unspecified 1 or II) TD3 CD80 toCD28 CD80 (B7.1) GD28 i;                                                                    i CD86 to CD28 CD86 (B7.2) GD28 : ICOSLG to CD28 ICOSLG (B7.H2) (CD275) GD28 ICOSLG to ICOS ICOSLG (B7.H2) (CD275) NCOS LFA-1 to ICAM-1 ICAM-1 (CD54) TFA-1 i;                                                                    i 4-1BB 4-1BBL 4-1BB i;                                                                    i Coactivating Late OX40 OX40 L bX40 (TNFRSF4) i(CD134) CD70 to CD27 CD70 TD27 (TNFRSF7) Signal iiiM Signal Type Signal Name APC Inhibitor | icRTAM-Necl2 Interaction Nectin-like molecule- 2 (Necl2) CRTAM Effector TD-1 PD-L1 PD-1 X | ^CD86 to CTLA-4 CD86 (B7.2) CTLA-4 (CD152) X TD80 to CTLA-4 CD80 (B7.1) CTLA-4 (CD152) x 1 hCOSLG to CTLA-4 ICOSLG (B7.H2) (CD275) CTLA-4 (CD152) x 1 Signal 3 Cytokines ilL-12 IL-12 IL-12R Unknown Unknown CD5 autoreactivity CD72 CD5

[00026] The focus of prior art has traditionally been on MHC-I mechanisms for cancer vaccines and immunotherapy for cancer in general. This can be because there is a simpler mechanism behind this kind of immunity against cancer, with CD8+ CTLs doing the killing directly, not being aware that this is the case for MHC-II as well. Much of the focus has then been on (1) turning “cold” tumors into “hot” tumors (helping the MHC-I function of making the cancer visible to CD8+ CTLs) and on checkpoint inhibition of these CD8+ CTLs (avoidance of two mechanisms that can slow down or inactivate CD8+ CTLs: The PD-1 and CTLA-4 receptors).

[00027] The recent focus of prior art has furthermore been on TSA, not TAA. This focus on TSA has the following drawbacks: • The cancer may mutate away from the specific antigen • The antigen may not represent the full cancer • There may be errors in the extraction and detection process

[00028] Cyclin D1 (having the gene code and abbreviation CCND1) is an example of a TAA, in that it is expressed in elevated amounts in among others the following cancers: • Breast cancer (in particular the hormone positive BCs, the so-called ER+ BCs, which constitute more than half the BCs, cf. https: / / v17.proteinatlas.org / ENSG00000110092-CCND1 / pathology and https: / / www.genome.jp / pathway / hsa05224 (top right)), • prostate cancer (cf. https: / / v17.proteinatlas.org / ENSG00000110092-CCND1 / pathology and https: / / www.genome.jp / pathway / hsa05215 (bottom right)), • melanoma (cf. https: / / v17.proteinatlas.org / ENSG00000110092-CCND1 / pathology andhttps: / / www.kegg.jp / pathway / hsa05218 (top right)), • liver cancer, • renal cancer, and • urothelial cancer

[00029] Cyclin D1 and MHC-II are thus both expressed on the following cancers: • Breast cancer (ER+ BCs), • prostate cancer, and • melanoma.

[00030] It has not - in relation to prior art - been possible to create a situation with pure MHC-II and no MHC-I on the surface of an APC and thus observe the effect of this situation on the CD4+ cells and their potential development into cytotoxicity, when there is no “disturbance” from CD8+ T cells (that then do not kill the APC).

[00031] It is known e.g. in the paper on the URL “https: / / www.frontiersin.Org / articles / 10.3389 / fimmu.2017.00194 / full”, describing a situation related to influenza with infection in the lungs and especially if this infection has reduced the MHC-I presentation as a virus immune escape mechanism, that the CD4+ cells, which as is normal have “stopped their development into toxicity” in the LN (we call this “point A”), can continue their “activation journey” from the “helper cell stage” into toxicity as shown in FIG 7 (we call this “point B”), if they are continually exposed to the antigen by APCs (which APCs can then continue giving the “co-stimulatory signal” or the said Signal 2), and especially so, if the CD8+ T cells are hampered due to MHC-I being reduced. So if “point A” is achieved in the LN and “point B” is achieved in the lungs (because MHC-I is hampered in the lungs), then achieving “Point B” may also happen in the LN, if MHC-I is hampered in the LN, as shown in FIG 8.

[00032] Other TAAs than Cyclin D1 (CCND1) include: Mucin-1 (MUC1), Mucin 16, Carcinoembryonic antigen (CEA - often specifically in the form of CEACAM5, but also in the form of CEACAMx, where x is x is 1,3, 4, 6, 7, 8,16,18,19, 20, or 21), Human Epidermal Receptor 2 (HER2 or ERBB2), Telomerase Reverse Transcriptase (TERT), Wilms Tumor Gene (WT-1), Sialyl-Tn, Myc proto-oncogene protein (MYC), Prostatespecific membrane antigen (PSMA), Prostatic Acid Phosphatase (PAP), Prostate Specific Antigen (PSA), Cancer / testis antigen 1 (NY-ESO-1), Melanoma antigen preferentially expressed in tumors (PRAME), Melanoma-associated antigen 1 (MAGEA1), Melanoma-associated antigen 3 (MAGEA3), Prostate stem cell antigen (PSCA), B-lymphocyte antigen CD19 (CD-19), Cellular tumor antigen p53 (TP-53), GTPase KRas (KRAS), Keratin, type I cytoskeletal 19 (Cyfra 21-1), Cellular retinoic acid-binding protein 1 (CRABP1), Cellular retinoic acid-binding protein 2 (CRABP2), Folate receptor (F0LR1), Kallikrein-10 (KLK10), Baculoviral IAP repeat-containing protein 5 (BIRC5 or Survivin), Insulin, Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), Epidermal growth factor receptor (EGFR), Protein LYRIC (Metadherin), Tumor protein D52, Ephrin type-A receptor 2 (EphA2), Tyrosinase, and Alphafetoprotein (AFP).

[00033] These TAAs all have the ability to be cut into epitopes presented by a MHC II molecule, which are not presented by the MHC I molecule. This ability is dependent on the genotype of the human subject. Different genotypes may facilitate different epitopes being generated and presented from a particular TAA.

[00034] The above-mentioned TAAs are listed in the Table 2 below, where it can be seen which of the MHCII expressing cancers they each presumably relate to (are expressed by). It may happen that any TAA may be expressed by other cancers than shown with an “X” in the figure. Table 2 Antigen iiiii Breast Cancer Classic Hodgkin lymphoma Colorectal Cancer Glioma Melanoma NSCLC (Non Small Cell Lung Cancer) Ovarian Cancer Prostate Cancer [US incidence] 310,720 siiiifi 153,810] 25,400 100,640 199.393 19,680 299,010 CEACAM1 464 X X X CEACAM1.2 526 X X X CEACAM3 252 X X X CEACAM5 702 X X X CEACAM6 344 X X X CRABP1 137 X CRABP2 138 X Cyclin D1 295 X X X Cyfra 21-1 400 X EGFR 1,091 X X X X X X X X EphA2 976 X X X X X Antigen liiOi Breast Cancer Classic Hodgkin lymphoma Colorectal Cancer Glioma Melanoma NSCLC (Non Small Cell Lung Cancer) Ovarian Cancer Prostate Cancer F0LR1 257 X HER2 1,225 X X X X IGF2BP3 579 X X X X X X X X IGF2BP3.2 291 X X X X X X X X KLK10 276 X KRAS 189 X X X X MAGEA1 309 X X X MAGEA3 314 X X X Metadherin 582 X X X X X X Mucin 1 iso 2 264 X Mucin 1 iso 3 255 X Mucin 16 14,507 X MYC iso 1 454 X X X NY-ESO-1 180 X X X PAP 386 X PRAME 509 X X PSA 261 X PSCA 114 X PSMA (iso 1) 750 X PSMA (iso 3) 735 X Sialyl-Tn iso 1 600 X Sialyl-Tn iso 2 468 X Survivin 142 X X X X X X X X TERT 1,132 X X TP-53 393 X X X Tumor protein D52 224 X WT-1 502 X X X X

[00035] Cyclin D1 is presented more weakly on MHC-I than on MHC-II compared to other TAAs cf. FIG 4. For all the mentioned TAAs there seems to be a similar MHC-I presentation per length of the protein (measured in the number of Amino Acids) but a very dissimilar MHC-II presentation per length as can be seen in FIG 5. In this figure, the right hand part depicts those TAAs that are “loud on MHC-H”, i.e. the TAAs which are likely to be more extensively presented on MHC-II than on MHC-I. TAAs that are “loud on MHC-H” are most likely to fit well into the present invention.

[00036] What the implication will be of the presumed immunogenicity of the TAA diagrammed vertically in FIG 5is unknown: (1) High immunogenicity would mean that there are more T cells of both types available, and it hinges on the ability to avoid the interaction of the CD8+ T cells, (2) Low immunogenicity mean that there are less T cells of both types available, and the immune reaction hinges on whether it is possible to avoid the CD8+ T cells completely while having enough CD4+ T cells to make them expand. It is hard to conclude whether (1) or (2) is “better”, or whether other factors need to be taken into account.

[00037] Probably because of this fact of “loudness on MHC-H” as well as the prevalent focus on MHC-I the Antigen Cyclin D1 is rarely listed in overviews of potential TAAs. Overviews present other TAAs like MUC1, CEA, HER2, TERT etc.

[00038] Cyclin D1 is well differentiated i.e. highly expressed in cancerous tissue compared to normal tissue compared to other TAAs cf. https: / / v17.proteinatlas.org / ENSG00000110092-CCND1 / pathology and https: / / www.antibodypedia.com / gene / 3660 / CCND1 (click on “More gene data” and scroll down to “Tissue RNA expression).

[00039] Cancers often have the ability to silence the MHC-I, but leaving MHC-H untouched for those cancers, which express MHC-H.

[00040] Taking this fact together with the fact that the TAAs to the right in FIG 5 already are more poorly presented on MHC-I than on MHC-H means that whenever an expression of the said TAA’s epitope surfaces - in particular when it surfaces on MHC-II, it is most likely from a cancer cell (with the exception of a weak expression on the APCs).

[00041] This may explain why some MHC-H alleles are protective of breast cancer as reported in several publications, the same alleles producing an MHC-H molecule seemingly good at binding some of the TAAs. This fact suggests that if the ability of CD4+ T cells in the rest of the cases to “see” the TAA epitopes is elevated, then in those cases the cancers expressing MHC-II may trigger an immune response that kills them.

[00042] Accordingly, there is a need in the art for new vaccine technologies focusing on epitopes derived from tumor associated antigens being presented by the MHC II molecule, which are not presented by the MHC I molecule in order to sustain the situation of CD8+ T cells not killing the APCs and hampering the CD4+ T cells in becoming cytotoxic.

[00043] The area of cancer vaccine comprises as a key step to predict whether a protein under consideration as parts of an Antigen or a subset of it, called an epitope, will pass through an important step of the APP being whether the Antigen is able to be cut into epitopes and one or several of these epitopes will bind to MHC and then possibly be presented on the surface of the cell. This analysis depends on the allele of the MHC genes - in MHC-I the genes named HLA-A, HLA-B, HLA-C, and to some extent the other MHC-I genes - and in MHC-II the genes named HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, and to some extent the other MHC-II genes. This prediction can be carried out as a computer based program of which one is available as the services on the URL https: / / services.healthtech.dtu.dk / services / NetMHCpan-4.1 / (or as approved later) for MHC-I (referred to hereinafter as “URL MHC-I”) and on the URL https: / / services.healthtech.dtu.dk / services / NetMHCIIpan-4.3 / (or as approved later) for MHC-II (referred to hereinafter as “URL MHC-H”). It is known that if this prediction shows that an epitope can not bind to the MHC in question, then it will not show on the surface of the cell. So the binding of epitopes is a necessary condition for them to be shown.

[00044] This prediction analysis is carried out either based on knowledge of the alleles of the human being considered to have the vaccine or on a significant set of alleles that appear with a significant frequency in the human population.

[00045] This prediction analysis calculation is deemed to have converged to precision or optimality, but it is likely to become updated in the future to become even better. For an allele of either MHC-I or MHC-II each possible epitope of a protein is associated with a score that puts the said epitope in the category of being either • A “non-binder”, • a “weak binder” (WB), or • a “strong binder” (SB) with an example of parts of the TAA CEACAM5 (and only “strong binders”) shown in the following Table 3. Table 3 jo MHC Peptide if Core Core_Rel|score_EL|Per centRank_EL|BindLevel| 16(H la-(dPA10202-(dPBIIOOOI Q.RLLLTASLLTFWNP 3[LLTASLLTF 0.96(0.433418] 0.73 i< := SB ] 16]HLA-(DPA10202-(DPB10401 Q.RLLLTASLLTFWNP 3jLLTASLLTF 0.97(0.205445] 0.82|< := SB ; 19(DRB1_15O1 20(hLA- (DQ.A10103- (DQ.B10503 LLTASLLTFWNPPTTAK LTASLLTFWNPPTTAK s]lltfwnppt 4|lltfwnppt 1(0.724538] 0.7(0.3286551 0.84]< 0.68(< := SB     ] := SB     I 20(HLA-(DQA10103-(□QB10501 LTASLLTFWNPPTTAK 4]LLTFWNPPT 0.72(0.065854] 0.92]< := SB i 20]DRBl_1502 LTASLLTFWNPPTTAK 4|lltfwnppt 0.99(0.7042751 0.96(< := SB I 20[DRBl_1501 LTASLLTFWNPPTTA 4|lltfwnppt 1 IO.697404 i 0.93^< := SB ] 20(dRB1_1501 LTASLLTFWNPPTTAK 4^LLTFWNPPT 1(0.791038] 0.62]< := SB i 20(dRB1_1501 LTASLLTFWNPPTTAKL 4|LLTFWNPPT 1(0.688751( 0.97(< := SB i

[00046] “Strong binders” are deemed statistically to almost certainly bind to the corresponding MHC molecule and thus possibly move to the cell surface and display to the immune system, “weak binders” can maybe bind to the MHC molecule, and “nonbinders” are certain not to bind to the MHC molecule and will therefore not display at the cell surface to the immune system. Brief disclosure of the invention

[00047] The invention is in the area of vaccination, i.e. the injection of a chemical agent containing an active substance that invokes a reaction of the immune system in a human.

[00048] The presently disclosed subject matter relates generally to killing cells (i.e. inducing apoptosis by means of immune system cells attaching to cancer cells and other immune system responses).

[00049] The invention makes use of a computational environment in order to compute the right vaccine ingredient, which uses computational models that mimic the functioning of the immune system, including alleles of genes behind the immune system as well as the proteins that the system reacts on.

[00050] The invention further makes use of technologies to produce the vaccine based on the said computational model and the vaccine ingredient data. The invention does not comprise any of these further vaccine production technologies.

[00051] Accordingly, in a first aspect, the present invention relates to a method for producing a cancer vaccine composition for the treatment or prevention of cancer in a human subject, the method comprising the steps of a) selecting one or more epitopes or concatenated epitopes derived from a tumor associated antigen (TAA), such that the selected epitopes bind to MHC-II in the subject, thereby providing pool of epitopes and concatenated epitopes binding to MHC-II in the subject, b) removing, from the pool of epitopes and concatenated epitopes selected in step a), epitopes and concatenated epitopes comprising an epitope binding to MHC-I in the subject, thereby providing a pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject, c) optionally combining one or more of the epitope(s) and concatenated epitopes provided in step b into a polytope comprising the one or more selected epitopes and concatenated epitopes (but observing that no MHC-I binding epitopes arise in the combinations), d) optionally providing a molecule carrying information capable of facilitating the in vivo production of the one or more epitope and concatenated epitopes provided in step b or the polytope provided in step c, e) combining the one or more epitopes and concatenated epitopes selected from the pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject provided in step b, or a polytope provided in step c, or the information carrying molecules provided in step d, with suitable pharmaceutically acceptable excipients.

[00052] In this respect, it should be noted that the term “concatenated epitope” means a peptide sequence comprising more than one predicted epitope within the same sequence. The epitopes are concatenated in the same sequence and may overlap with respect to each individual peptide sequence. As an example, an epitope consisting of the sequence ABC and another epitope consisting of the sequence BCD may give rise to the concatenated epitope ABCD. As a further example, an epitope consisting of the sequence ABC and another epitope consisting of the sequence DEF may give rise to the concatenated epitope ABCDEF. As a further example, an epitope consisting of the sequence ABC and another epitope consisting of the sequence EFG may give rise to the concatenated epitope ABCDEFG. Typically, when identifying predicted epitopes according to the present invention, the most suitable predictions are identified as hot spot sequences comprising concatenated epitopes. Analyzing identified hot-spots (concatenated epitopes) for binding to MHC-II and subsequently for binding to MHC-II for the relevant subject genotype forms the basis of the present invention.

[00053] Preferably, the steps a) and b) are accomplished by selecting an appropriate TAA, preferably a TAA as provided in the present description, and analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes by use of an algorithm which predicts the behavior of the immune system for the respective TAA as well as for any sequence of epitopes that are considered to make up the respective TAA, given data on the gene alleles of the subject.

[00054] More preferably, the analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes or concatenated epitopes is accomplished by use of appropriate algorithms which are available for computing a binding probability for each epitope of the TAA for binding to MHC-II and MHC-I. appropriate algorithm is provided on the URL MHC-I, or as a subsequently improved version thereof, for MHC-I, and on the URL MHC-II, or as a subsequently improved version thereof, for MHC-II.

[00055] In a second aspect, the present invention relates to the use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen, wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC-II) in the subject, and wherein the epitopes or concatenated epitopes are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC-I) in the subject. This aspect may also be defined as a method of treatment or preventive treatment of cancer in a subject.

[00056] This aspect may also be defined as the use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in the subject, wherein the subject is characterized in having a genotype facilitation the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject. This aspect may also be defined as a method of treatment or preventive treatment of cancer in a subject.

[00057] In a third aspect, the present invention relates to a cancer vaccine comprising one or more specifically selected epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), said selected epitope(s) or concatenated epitopes activating an immune response via the Major Histocompatibility Complex II (MHC II) in a subject, said epitopes being characterized by a) consisting of more than 13 amino acids but less than 25 amino acids, preferably 15 amino acids.

[00058] Preferably, the epitopes are one or more concatenated epitopes of a tumor associated antigen (TAA). Each epitope or concatenated epitope must consist of no more than 25% of the amino acids of the TAA. Concatenated epitope consisting of more than 25% of the amino acids of the TAA have a high probability of comprising epitope sequences binding and activating the MHC-I part of the immune system and are therefore unsuitable for the purposes of the present invention. Likewise, concatenated epitopes consisting of more than 50 amino acids such as more than 45 the amino acids of the TAA have a high probability of comprising epitope sequences binding and activating the MHC-I part of the immune system and are therefore undesirable for the purposes of the present invention. Preferably, the concatenated epitopes according to the invention comprises less than 50 amino acids such as less than 45.

[00059] Polytopes according to the invention may, however, be longer than 50 amino acids. Care should be taken only not to introduce epitope sequences binding and activating the MHC-I part of the immune system by any sequence linking the respective epitopes and concatenated epitopes.

[00060] It should be noted that the epitopes and concatenated epitopes provided in the sequence listing may comprise additional amino acids in the N-terminal and / or C-terminal part of the sequence without deviating from the present invention. Any such additional amino acids must, however, be evaluated not to result in the generation of an MHC-I epitope.

[00061] It should also be noted that epitopes and concatenated epitopes identified according to the invention and appearing from the sequence listing may often be shortened in the N-terminal and / or C-terminal part of the sequence without deviating from the present invention. Any such shortening must, however, be evaluated not to result in the abolishment of the MHC-II epitope binding. Generally, shortening by 1,2, 3, 4 or 5 amino acids in the N-terminal and / or C-terminal part of the sequence does not to result in the abolishment of the MHC-II epitope binding and therefore does not result in a deviation from the present invention.

[00062] Preferably, the vaccine is for use in the treatment or preventive treatment of cancer in a subject having a genotype facilitation the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject.

[00063] In a fourth aspect, the present invention relates to a library or sequence catalog of cancer vaccine epitopes or concatenated epitopes derived from a tumor associated antigen (TAA) wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in a human subject.

[00064] In a fifth aspect, the present invention relates to a concatenated epitope comprising a peptide sequence according to the sequence listing or a derivative thereof wherein the sequence is shortened or increased in length by 1,2, 3, 4 or 5 amino acids in the N-terminal and / or by 1,2, 3, 4 or 5 amino acids in the C-terminal part of the concatenated epitope. The concatenated epitope may further comprise an adjuvant sequence. Adjuvant sequences may enhance MHC-II binding of the epitopes and concatenated epitopes according to the invention.

[00065] Preferably, the library or sequence catalog consists of epitopes or concatenated epitopes that are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC I) in a human subject. The library preferably comprises at least 4, such as at least 5, such as at least 6 such as at least 7 epitopes or concatenated epitopes for each relevant TAA. Preferably these epitopes and concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence. The library preferably comprises in total at least 20, such as at least 30, such as at least 40 such as at least 50 epitopes or concatenated epitopes. Preferably these epitopes and concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing.

[00066] Preferably, in all aspects of the present invention, the epitopes are concatenated epitopes. Even more preferably, the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing or a derivative thereof wherein the sequence is shortened by 1,2, 3, 4 or 5 amino acids in the N-terminal and / or by 1,2, 3, 4 or 5 amino acids in the C-terminal part of the concatenated epitope. The concatenated epitope comprising a peptide sequence according to the sequence listing are preferred. Even more preferably, the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321,342, 350, 354, 355, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581,582, 620, 621,622, 623, 624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561,1562, 1575, and 1607.

[00067] As a personalized vaccine, the specifically selected epitope(s) shall activate an immune response via the Major Histocompatibility Complex II (MHC II) in the subject, and shall not activate an immune response via the Major Histocompatibility Complex I (MHC I) in the same subject.

[00068] Such epitopes from TAAs may be selected based on the specific genotype of the subject with respect to alleles of Major Histocompatibility Complex I (MHC I) and MHC II. As described below, the specific genotype of the particular subject results in different processing of the TAAs and the production of different relevant epitopes binding MHC II and MHC I.

[00069] Relevant selected epitope(s) activating an immune response via the Major Histocompatibility Complex II (MHC II) in a subject appear from the sequence listing. Each individual may benefit from one or more of these epitopes as active ingredient in a cancer vaccine depending on the individual genotype. Typically, up to 4 or more epitopes or concatenated epitopes from each relevant TAA constitute a vaccine. Preferred vaccines according to the invention therefore comprise at least 4 epitopes. Typically, up to 16 or more epitopes or concatenated epitopes constitute a vaccine. Preferred vaccines according to the invention therefore comprise epitopes form more than one TAA, such as 2 or 3 TAAs. Preferably, a vaccine comprises epitopes from at least 2, such as at least 3 such as at least 4 TAAs.

[00070] The exact number depends on the specific situation, where the number 16 is derived from the case that (1) around 4 epitopes or concatenated epitopes are selected within a TAA, given the individual genotype, and (2) around 4 TAAs are selected for the cancer type in question - and 4 times 4 is 16. Polytopes

[00071] Multiple selected epitopes and concatenated epitopes can be combined into a so-called polytope by adding them as chains on a string potentially introducing linker amino acids.

[00072] The area of cancer vaccine further comprises a vaccine technology where the selected polytope is used as a vaccine agent e.g. by using its digital equivalent transformed into mRNA as input to the generation of a part of the vaccine agent. The FDA approved mRNA vaccines for COVID-19, and this method is frequently being used in clinical trials today, cf e.g. the paper on the URL “https: / / www.ncbi.nlm.nih.gov / pmc / articles / PMC10132791”. Other vaccine methods beyond mRNA comprise • SAM: Self Amplifying mRNA vaccine • LNP mRNA: Lipid nanoparticles mRNA vaccine • Virus Vector vaccine • DC (Dendritic Cell) vaccine • ISV: In situ vaccine

[00073] Thus, as an alternative, the active agent according to all the aspects of the invention is an agent facilitation the in vivo production in the subject of the one or more specifically selected epitope(s), such as an mRNA molecule coding for the in vivo production of the specifically selected epitope(s).

[00074] The epitopes of an Antigen that bind to an MHC molecule and thus potentially are presented to the immune system vary a lot for different HLA alleles. This means that the Position in the protein that represents the antigen from which a “strong binder” epitope exists varies a lot depending on the allele. Thus, each TAA may result in different epitopes being presented by MHC molecules depending on the alleles of the subject.

[00075] For the Antigen Cyclin D1, having a protein length of 295 (amino acids), the number of MHC-II “strong binders” according to the prediction service on the URL MHC-II varies depending of the selected MHC-II from none (0) to 11, with most in the bracket of 1 - 8. And less “strong binders” in MHC-I. Any human expresses up to six different MHC-I and up to 12 different MHC-II molecules, and despite the fact that a molecule has no “strong binder”, then another human will most likely have a strong binder. We have computed an estimate of the share of the world’s population based on the URL “https: / / allelefrequencies.net / hla.asp”, which seems according to the prediction service on the URL MHC-II, that have no MHC-II strong binders among the epitopes of Cyclin D1 given their allele combination, to be less than 1% (0.3%).

[00076] It is therefore in most cases (for all TAAs) possible to identify one or several epitopes from that TAA that bind strongly to MHC-II and not at all to MHC-I. It may be that a “strong binder” to MHC-I is fully embedded in a “strong binder” to MHC-II, and it is therefore discarded (omitted in the final polytope).

[00077] The allele frequencies of the World population can be deduced from the URL “https: / / allelefrequencies.net / hla.asp”. It includes, at the top (for information): MHC-I: HLA-A - ordered with descending likelihood, top 5 shown: HLA-A02:01 25% HLA-A01:01 12% HLA-A03:01 12% HLA-A24:02 10% HLA-B - ordered with descending likelihood, top 5 shown: HLA-B07:02 10% HLA-B08:01 8% HLA-B15:01 7% HLA-B44:02 5% HLA-B35:01 5% HLA-C - ordered with descending likelihood, top 5 shown: HLA-C07:01 3% HLA-C07:02 3% HLA-C04:01 3% HLA-C06:02 3% HLA-C 12:03 2% Leading to the likelihood of having the MHC-I combinations (assuming that there is no cross-coupling or covariance, normally attributed to haplotypes) - ordered with descending likelihood, top 5 shown: HLA-A02:01 HLA-B07:02 HLA-C07:01 0.079% HLA-A02:01 HLA-B07:02 HLA-C07:02 0.078% HLA-A02:01 HLA-B07:02 HLA-C04:01 0.070% HLA-A02:01 HLA-B08:01 HLA-C07:01 0.062% HLA-A02:01 HLA-B08:01 HLA-C07:02 0.062% There are at least 9,000 such allele combinations on MHC-I based on a very limited sample of allowable alleles (HLA-B representing 89% of the world’s population, HLA-C representing only 23% of the world’s population). MHC-II: HLA-DPx (where “x” is either “A1” or “B1”) - haplotypes ordered with descending likelihood, top 5 shown: HLA-DPA102:02-DPB105:01 21% HLA-DPA101:03-DPB104:01 15% HLA-DPA101:03-DPB102:01 14% HLA-DPA101:03-DPB104:02 10% HLA-DPA101:03-DPB103:01 3% HLA-DQx (where “x” is either “A1” or “B1”) - haplotypes ordered with descending likelihood, top 5 shown: HLA-DQA105:01-DQB103:01 9% HLA-DQA103:01-DQB103:02 9% HLA-DQA101:02-DQB106:02 8% HLA-DQA101:01-DQB105:01 8% HLA-DQA105:01-DQB102:01 7% HLA-DRx (where “x” is either “B1”, “B3”, “B4”, or “B5”) - ordered with descending likelihood, top 5 shown: DRB1 07:01 10% DRB1_15:01 8% DRB1_03:01 7% DRB1_11:01 6% DRB1 01:01 5% Leading to the likelihood of having the MHC-II combinations (assuming that there is no further cross-coupling) - ordered with descending likelihood, top 5 shown: HLA-DPA10202-DPB10501 HLA-DQA10501-DQB10301 DRB1_0701 0.18% HLA-DPA10202-DPB10501 HLA-DQA10301-DQB10302 DRB1_0701 0.17% HLA-DPA10202-DPB10501 HLA-DQA10102-DQB10602 DRB1_0701 0.17% HLA-DPA10202-DPB10501 HLA-DQA10101-DQB10501 DRB1_0701 0.16% HLA-DPA10202-DPB10501 HLA-DQA10501-DQB10301 DRB1 1501 0.14% There are at least 1,195,000 such allele combinations on MHC-II. The likelihoods of MHC-I and MHC-II can then be multiplied together. Brief Summary of the Invention

[00078] This invention is a cancer vaccine, i.e. it triggers an immune response to fight or prevent cancer after injecting the vaccine in the human body. It thereby supplements existing cancer treatments or makes some of them obsolete and / or makes the treatment more effective.

[00079] This invention utilizes that some cancers express MHC-II, and the antigens that these cancers over-express have been visible so far (prior to the cancer) only on MHC-I, where the T cell response has been reduced.

[00080] This invention utilizes the antigen's MHC-II, while it silences and thus avoids MHC-I, based on the personal allele composition. For the antigen Cyclin D1 the binding positions (i.e. the epitopes) are widely spread for different alleles, and this allows for a very short selection of epitopes into a polytope - that varies greatly with the personal allele composition. It is doable, however, to identify and select epitopes that bind to MHC-II while no part of them binds to MCH-I for most alleles when targeting Cyclin D1, because it expresses low on MHC-I (has few “strong binders” there). However the concept is generic for all antigens in all cancers that express MHC-II.

[00081] This invention educates the immune system part MHC-II while it avoids harming healthy tissue and preventing as much as possible auto-immune disorders as well as making the MHC-II arm cytotoxic by not matching the immune system part MHC-I. The fact that the MHC-II arm becomes cytotoxic, when not matching the immune system part MHC-I is the mechanism described in FIG 8 and FIG 9.

[00082] Cancers further often silence MHC-I, leaving side effects to healthy tissue unaffected in that the healthy tissue still expresses MHC-I.

[00083] The T cells of the immune system part MHC-II have generally not seen these epitopes before the cancer, because healthy tissue (except APCs) express only MHC-I.

[00084] The cancers that express MHC-II include: • Breast cancer (BC), • prostate cancer (PCa), • melanoma, • colorectal cancer, • ovarian cancer, • classic Hodgkin lymphoma, • glioma, and • non-small cell lung cancer It may be that not all of MHC-II is expressed, in which case this must be taken into account.

[00085] This invention utilizes that CD4+ cells responding to MHC-II can be cytotoxic (CD4+ CTL), e.g. by the mechanism depicted in FIG 8, where this cytotoxic behavior is assumed to be reserved to MHC-I, to CD8+ CTLs. Or it utilizes a similar strong immune response, as suggested by references that point to the existence of protective MHC-II alleles.

[00086] Some TAAs have a low expression on healthy tissue, and they are therefore likely to not be associated with inhibitory CD4+ Tregs (since at least outside the thymus they must come from the APCs).

[00087] The overview of cancers that express both MHC-II and the TAAs include those listed in Table 2.

[00088] The prediction of the binding to MHC-I and to MHC-II is calculated based on either (1) a list of epitopes coupled with their respective MHC alleles or (2) a computer algorithm taking the allele composition determined from a genomic test as input, from which the epitopes or concatenated epitopes (e.g. the one or more epitopes or concatenated epitopes or polytopes according to the invention that binds to MHC-II but not to MHC-I is derived). It may be that a “cut” or transition over two substrings in a polytope cannot avoid the creation of epitopes with a binding property on either MHC-I or on MHC-II no matter what amino acids are put in between the epitopes, then one of the substrings may either be discarded from the polytope, or the two separate polytopes may be devised as separate proteins in the vaccine.

[00089] The vaccine is then produced to include the epitopes or concatenated epitopes (e.g. the one or more epitopes or concatenated epitopes or polytopes according to the invention as an active ingredient (or several polytopes cf. above)). This is referred to as the Personal Vaccine.

[00090] The vaccine may as an alternative be selected from a set of pre-tested and approved set of epitopes or concatenated epitopes with the desired behavior. This is referred to as the Sequence Catalog. A set of selected, pre-tested and approved set of epitopes or concatenated epitopes is provided in the sequence listing appended to the present application.

[00091] The said Personal Vaccine is manufactured to one patient only based on the MHC-I and MHC-II allele of the patient. Based on the allele of the subject, suitable TAA epitopes or concatenated epitopes binding to MHC-II and not comprising sequences binding MHC-I may be selected using e.g. the databases provided herein as the URL MHC-I, or as a subsequently improved version thereof, for MHC-I, and as the URL MHC-II, or as a subsequently improved version thereof, for MHC-II . Preferably, the selection of suitable TAA epitopes or concatenated epitopes binding to MHC-II and not comprising sequences binding MHC-I may be done by selecting one or more of the sequences from the Sequence Catalog provided with the sequence listing presented herein. The personal vaccine manufactured according to the invention have the following characteristics: • No sequencing and uncertainty of deriving a (set of) TSAs is required: so it is faster, cheaper, and more certain; • both approaches require an inexpensive and fast (1) genomic test of 11 genes that each comes in two alleles (the “HLA typing”) • and optionally (2) an expression analysis. • The manufacturing of a “personal vaccine” will always be expensive and more time consuming than the selection of sequences.

[00092] The selection of sequences from the said Sequence Catalog is based on the following elements • Any sequence must contain epitopes that are triggered by one or several of the MHC-II alleles of the human subject. • Any sequence must not contain any epitopes that are triggered by any of the MHCI alleles of the human subject.

[00093] The Sequence Catalog for each TAA consists both manually identified as well as auto-generated sequences.

[00094] The Sequence Catalog comprises sequences that are already validated, i.e. sequences of concatenated epitopes validated for binding and presentation by MHC-II and not comprising sequences of epitopes binding to MHC-I in subjects of specific alleles, and sequences predicted to have these characteristic but not yet validated. The sequences 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321,342, 350, 354, 355, 356, 358, 359, 360, 361,362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439 and 440 derived from CEACAM5; the sequences 51,469, 495, 498, 499, 500 derived from Cyclin D1; the sequences 101,580, 581,582, 620, 621,622, 623, 624, 625, 626, 627 derived from MAGEA3; the sequences 105, 106, 108, 629, 631 derived from NY-ESO-1; the sequences 173, 174, 176, 177, 178, 179, 180, 803, 805, 806, 807, 895, 896, 897, 904, 905, 906 derived from TERT; the sequences 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575 and 1607 derived from HER2 are all presently validated.

[00095] The vaccine may be a preventative vaccine (before the cancer is detected) or a treatment vaccine (after the cancer is detected). The vaccine may contain the active agent (i.e. the one or more epitopes or concatenated epitopes or polytopes according to the invention) alone or together with other active ingredients or devised together with other vaccines. If the vaccine is given as several injections, it may be regulated, i.e. the dose of subsequent injections may be determined based on measures of effectiveness etc.

[00096] The vaccine may be one of the following vaccine technologies, or another: • mRNA vaccine, • SAM: Self Amplifying mRNA vaccine, • LNP mRNA: Lipid nanoparticles mRNA vaccine, • Virus Vector vaccine • DC vaccine, or • ISV: In situ vaccine.

[00097] The invention accounts for physiological limits and ordering of sequences; potentially repeating “good ones” (those that are validated)

[00098] The invention performs the dose calculation, taking into account epitopes that are not presented as well as epitopes that are validated.

[00099] The invention supports the recalculation of master data and running on several versions - so that it can be used in multiple countries or regions based on their approval of different master data - and based on different speeds of approval of a new set of master data etc. [000100] The one or more epitopes or concatenated epitopes or polytopes according to the invention may be improved by adjuvants to facilitate the functionality. These adjuvants may be specific peptide sequences that are added either as “in string adjuvants”, where the adjuvant is attached to the active agent with an optional spacer, or they may be added as separate active ingredients that are administered along with the vaccine. Brief Description of the Drawings FIG 1: Cell types and MHC-I and II. The figure shows that some cancer cells (e.g. breast cancer, prostate cancer, melanoma, non-small cell lung cancer (NSCLC)) express (communicate on) MHC-II - something otherwise reserved far APCs, when there is no cancer. AH cells with a nucleus communicate on MHC-I. FIG 2: The CD4 r cells having the role of (a) attracting CD8+ Cytotoxic T cells, (b) being cytotoxic themselves, and (c) helping B cells. FIG 3: The first step of the Antigen Presentation Pathway: Protein to MHC (I or II) binding. Part A: The protein e.g. “Cyclin D1” with its composition of amino acids, one per box. Part B: Modified protein to encompass only the strong binders. Part C: The same as part B, just emphasizing that there are a new set of amino acids that are now consecutive and will become epitopes, these epitopes should not become "strong binders” or “weak binders” and make unforeseen consequences of being presented -of. part E. Part D: The modified protein of part C cut into epitopes by the phagocytosis of the cell (the length of 3 amino acids is shown as an example, in reality the epitopes are longer, often 15 for MHC-II). Part E: The epitopes that hold the new transitions of amino acids in the modified protein to be checked for binding to the MHC. Part F: The binding of an epitope to the MHC molecule - so that the epitope together with the MHC molecule can migrate to the surface of the cell and be displayed to the immune system (act as ligands to a T cell’s receptor, TCR). FIG 4: Ranking of alleles both in MHC-I and MHC-II according to how well they are predicted to present the proteins shown in the header (Cyclin DI, Mucin 1, CEA, and TERT respectively) - these proteins being candidates as Antigens for Breast Cancer. It is seen that for Cyclin DI in particular the alleles behind MHC-II ail rank higher that the alleles behind MHC-I, whereas for the other proteins some of the alleles behind MHC-I (A*, BR and CD are ranked higher than some of the alleles behind MHC-II. FIG 5: The classification of TAAs according to (1) how well they express MHC-II (as the number of strong binders divided by the length of the TSS) - also called their "loudness on MHC-II, and (2) how immunogenic we assume they are, based on the inversion of how strongly they are expressed by healthy tissue. FIG 6: Activation of T cells (CD8 for MHC-I, CD4 for MHC-II) in the lymph node when encountering an ARC (e.g. a Dendritic Cell) by means of the activation signals. Since the CD8 kills the APC at the end of its activation, but before the CD4 is activated, the CD4 T cell stops its activation at the stage "CD4 Helper T cell" FIG 7: Continuation of activation process of a CD4 Helper T cell e.g. in the lung, and with absence of a CDS T ceil until the CD4 T cell becomes fully activated as a “Cytotoxic T ceir. FIG 8: The full activation all the way from a “naive' T cell into becoming cytotoxic in the absence of CD8 T cells, when the ARC contains no MHC-I on its surface, in the lymph node. FIG 9: Overview of the vaccination and action process, with main steps 1 through 4. FIG 10: Overview of the MHC-II presentation pathway with focus on the MHC-II loading compartment (“MHO”). FIG 11: Example of sequences and their total likelihood or share of alleles that trigger epitopes that are part of said sequences. FIG 12: Example of sequences and the alleles that trigger epitopes in them - detailing the bottom of FIG 11. FIG 13: Sequence 1 or SEQ1 is an example of a joined-up sequence that consists of (1) “CEACAM 1A val”. (2) “CEACAM 5A”, (3) “CEACAM 11 val”. and (4) “CEACAM 20 val" with a set of spacers between them - such that humans with certain MHC-I alleles must avoid “SEQ1” to get no MHC-I response. SEQ2 is created by prolonging each element of "SEQ1” so as to include more MHC-I alleles FIG 14: Comparison of personal vaccine with manually and automatically generated sequences. Detailed Description of the Invention [000101] The invention relates to triggering a response from the immune system by injecting once or several times an agent containing an antigen (a protein) or parts of the antigen, a so-called polytope, or several polytopes. The purpose of the immune response is to partly or fully eradicate the cells that represent the illness, which may be cancer, in the following “the cancer”. [000102] If a test is carried out on the human, and if it shows that the cancer expresses MHC-II or part of it as well as the said Antigen, the said Polytope can possibly be designed such that it binds to and therefore possibly displays on MHC-II and not on MHC-I. It therefore elicits an immune response that may lead to fully or partly eradicating the cancer without implying the cells that represent the healthy tissue and express MHCI. Except for those humans that have a cancer expressing MHC-II, but where the antigen doesn’t bind to MHC-II and therefore does not display. For Cyclin D1 it is estimated that 0.3% of humans have no strong binder for MHC-II. [000103] One Antigen protein that we consider appropriate for this is Cyclin D1 (having the gene code CCND1). It has a low expression on MHC-I, and it is expressed with a low level in healthy tissue cells. It is likely that the immune system has not prior to the vaccination produced any T cells for MHC-II with T cell receptors (TCR) that match a polytope based on Cyclin D1, because prior to the cancer only the low level of Cyclin D1 in APCs has displayed on MHC-II. Other TAAs appear from the present disclosure. Preferred TAAs are CEACAM5, Cyclin D, MAGEA3, NY-ESO-1, TERT, and HER2. CEACAM5 is a particularly preferred TAA. [000104] The invention is based on the selection of a subset of the epitopes or concatenated epitopes of the TAA for vaccination that are completely or almost completely silent on MHC-I but presented by on MHC-II. Then there will be no added CD8+ CTLs, and the added CD4+ cytotoxic T cells and other immune response on MHC-II will only kill cancer cells (and maybe a few additional APCs). [000105] If the invention is used in the treatment setting, the invention may further involve making a test on a sample from the cancer (e.g. a biopsy) or other expert knowledge to establish whether (1) the cancer expresses MHC-II or a part of it and (2) the cancer over-expresses the Antigen (e.g. the antigen Cyclin D1), i.e. significantly more than it is expressed in healthy tissue. It is expected that a subset of Breast Cancer, Prostate Cancer, and Melanoma all express both MHC-II and over-express Cyclin D1. [000106] A genomic test is preferably carried out in order to derive the allele composition of the HLA genes of the human (e.g. a swab of the mouth). This test includes a subset of or the complete set of the alleles of the HLA genes: • MHC-I: HLA-A, HLA-B, HLA-C. • MHC-II: HLA-DPA1, HLA- DPB1, HLA-DQA1, HLA-DQA2, HLA- DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB3, HLA- DRB4, and HLA- DRB5. Personal vaccine: [000107] A computer program as currently defined in the URL MHC-I, or as a subsequently improved version thereof, for MHC-I, and in the URL MHC-II, or as a subsequently improved version thereof, for MHC-II, may be used to predict the binding data for the antigen (e.g. Cyclin D1 and subsequently for polytopes derived from it cf. the description below) given particular alleles or haplotypes (combinations of alleles). The computer program provides as part of its output a property for each epitope and each allele being one of: a “non-binder”, a “weak binder” (WB), and a “strong binder” (SB), representing the likelihood of the epitope binding to that MHC molecule (given the allele): A “strong binder” (SB) is likely to bind to the MHC in question cf. F on FIG 3 and can thus show together with the MHC molecule on the cell surface to the immune system, a “weak binder” (WB) may or may not bind to the MHC and show together with the MHC molecule on the cell surface to the immune system, with a likelihood of more than 1% but less than 100%, and a “non-binder” will not bind to the MHC and therefore with almost certainty not show together with the MHC molecule on the cell surface to the immune system. Epitopes or concatenated epitopes fulfilling the criteria “strong binder” (or in particular cases “weak binders”) to HMC-II and non-binder to MHC-I for the particular allele of the subject are thereafter selected. [000108] Using an antigen polytope as a vaccination agent to trigger an immune reaction on MHC-II of the adaptive immune system, either as prevention of, or as treatment of, a cancer of the types that express MHC-II. The antigen polytope vaccine may be together with other agents in the vaccine that trigger other immune responses on MHC-I or MHC-II or both. [000109] The epitopes or concatenated epitopes or Polytope according to the invention is determined by the following steps 1 to 6: Step 1: We construct, using the output from the service of URL MHC-II or the stand alone service or a similar or optimized service for MHC-II, a database with or list of the binding properties of the combination of • all epitopes of the antigen on MHC-II (epitopes of the length 13-25 amino acids, or a subset of these epitopes having lengths e.g. just one length 15, out of the full length of the antigen cf. A on FIG 3) and • all alleles (or haplotypes) constituting the different MHC-II molecules. • This implies identifying an epitope as one of (1) a non-binder, (2) a “weak binder” (WB), or (3) a “strong binder” (SB) - with any particular allele or combination of alleles. Step 2: Selection of those epitopes (by e.g. position in the sequence of the full length antigen) that constitute “strong binders” (SBs) with the specific combination of alleles for the subject. Cf. B on FIG 3. The “strong binders” may constitute sequences that are concatenated epitopes such as consecutive epitopes that are longer than the length of the individual epitopes - in FIG 3 the epitope length of 3 is used as a simplistic example cf. D on FIG 3. If there are no “strong binders” for the specific allele combination, then include the WBs. Step 3: Optional construction of an “a priori polytype” by appending the epitopes above -marking the “cuts” i.e. the joining points of epitopes in the polytope. The said Cuts are all inside the polytope. Cf. C on FIG 3. The said A Priori Polytope is then modified as follows: Step 4: Check on both MHC-I and MHC-II, using the services of URL MHC-I and URL MHC-II or the stand alone services or similar or optimized services, whether the said A Priori Polytope, focusing on the epitopes that are now created around the said Cuts, will trigger a “strong binder” (SB) or a “weak binder” (WB) on either of MHC-I or MHC-II. Cf. E on FIG 3. This will constitute a biological behavior that is unprecedented or unusual and not tested. Although the figure displays a usual epitope length (of 3 in the figure), this check needs to be performed for all possible epitope lengths, i.e. 8 to 14 on MHC-I and 13 to 25 on MHC-II. Step 5: Padding the Cuts that introduce a strong or weak binder on either MHC-I or MHC-II or both: (1) If the “Cut” is wide (it the positions are far apart) then any sequence that either, (1 A) silences the Cut (makes it a non-binder) or (1B) extends the epitope to include more from the original protein (padding with the amino acids of the original string) until the cut is silenced (it is a non-binder). (2) If the “Cut” is close (the positions are close) then the original string of the full protein must be used so that the epitopes join up to a consecutive substring of the protein and thereby is similar to what comes out of the full length protein. Cf. the progression between A, B, and C on FIG 3, where more parts of A are added to create longer substrings in B and “pad” the gap when joined in C. • If the said A Priori Polytope after said Padding removes all WB or SB from both MHC-I and MHC-II, the said A Priori Polytope is updated to include the said Padding. • If it cannot be avoided that a substring in the said A Priori Polytope after the said Padding creates a WB or SB in either MHC-I or MHC-II or both, this substring is taken out of the A Priori Polytope, i.e. the said A Priori Polytope is updated to exclude the substring. In this case, we go back to and repeat Step 4, i.e. we need to check the A Priori Polytope again on both MHC-I and on MHC-II. • It is considered to use the substring thus taken out as a separate Polytope and thus as a separate protein in the vaccination, provided it passes the subsequent Step 6. Step 6: If there are “strong binders” on MHC-I that have been selected for the A Priori Polytope (these SBs on MHC-I will most likely be associated with epitopes embedded in the SB epitopes on MHC-II, since the length of epitopes is shorter in most cases on MHC-I than on MHC-II, and we have changed or removed those SB epitopes that come from “Cuts” in the steps above), these epitopes on MHC-II must be thrown out, i.e. the A Priori Polytope is updated to not include the epitopes that constitute SBs on MHC-II, if the said Epitopes contain (or are associated with) epitopes that are SBs on MHC-I. • If this introduces a new cut, repeat Step 4, i.e. we need to check the A Priori Polytope again on both MHC-I and on MHC-II. • If this results in no epitopes left in the polytope then either (1) leave them in (and accept the side effect of it triggering an immune response on MHC-I) or (2) include the “weak binders” on MHC-II. We prefer (1) since there are likely no TCR that match anyhow. [000110] The vaccine is manufactured using the selected epitopes or concatenated epitopes or the Polytope sequence as the active ingredient, e.g. converted to mRNA. If converted into mRNA, it is administered (typically injected) such that the human body will generate a protein similar to the epitope or the concatenated epitopes or the Polytope in e.g. an APC that expresses MHC-II and thus make the immune system react to this protein by e.g. generating CD4+ T cells that can also attach to the cancer and kill it. [000111] The vaccine may need to be repeated in order to create the desired effect (of either prevention or treatment). [000112] The effect of the vaccine may be monitored and assessed to see if (in case of prevention) CD4+ CTLs or antibodies are produced or (in case of treatment) the cancer cells are furthermore being killed by the immune system. The dose of the vaccination may be adjusted according to this monitoring or assessment. Identification of sequences: [000113] The Sequence Catalog comprising sequences representing selected concatenated epitopes for MHC-II binding in multiple MHC-II alleles for each TAA consists of Original and Shortened sequences as follows: • Original: Derived from the substrings of a TAA, where epitopes are triggered by (are strong binders, provided the human has one of) multiple MHC-II alleles, and where the likelihood or world population share of the said MHC-II alleles is high, the said epitopes being concatenated into substrings where the concatenations are then regarded as “hotspots” of said TAA • Shortened: Original sequences that are shortened, if they after shortening are still longer than 18 amino acids, and if by shortening them epitopes that are triggered by one or more MHC-I allele appearing with a high likelihood or share in the world population are avoided. [000114] Each sequence in the Sequence Catalog is either Validated or not yet validated: It is Validated, if that sequence contains one or several epitopes that have been empirically proven to present and become immunogenic (attract T cells) on the cells of a human. Often a Validation is associated with coupling certain alleles to the validation, but this invention choses to rely on the predictions of URL MHC-I and URL MHC-II to produce the correct coupling between the epitope and the alleles required to present it. [000115] Auto-generation of original sequences • Original: Derived from the substrings of a TAA, where epitopes are triggered by (are strong binders, provided the human has one of) at least a threshold number of alleles, said threshold number specific for each of DP, DQ, and DR, and where the likelihood or world population share of the said alleles within either DP, DQ, or DR is at least a threshold likelihood, the said threshold likelihood specific for each of DP, DQ, and DR, the said epitopes being concatenated into substrings that are then regarded as “hotspots” of said TAA • Shortened: Original sequences that are shortened, if they after shortening are still longer than a threshold number of amino acids long, and if by shortening them epitopes that are triggered by one or more MHC-I alleles appearing with a likelihood or share in the world population of a certain percentage are avoided. [000116] The purpose of shortening the original sequences is to reduce the likelihood that the said shortened sequence will become de-selected due to an MHC-I allele that is present in a given human subject, while maintaining as much of or the entire likelihood that the MHC-II epitopes of the said shortened sequence is activated by the MHC-II alleles of the said given human subject compared to the said original sequence, in which case the said shortened sequence may be equally effective in eliciting the MHC-II immune response as the said original sequence, but will not get knocked out or deselected so often as the said original sequence. [000117] The auto-generated Shortened sequences may become further shortened -into another Shortened sequence - by the automatic generation, if they meet the said requirements for shortening. [000118] Sequences in the Sequence Catalog may be combined or joined as follows, if (1) they are equal (if they start and end in the same position of the TAA) (in which case the identical sequences are only represented once in the Sequence Catalog) or (2) if they are almost equal, subject to an algorithm that justifies this (if it does not create or re-create a situation that would lead to it being shortened etc.) (in which case the sequences are concatenated), [000119] Sequences in the Sequence Catalog may be joined with spacers (where each sequence retains the full number of amino acids), if they are triggered by virtually the same alleles, and therefore in most cases would have been selected together anyway. Joining them with a spacer will avoid that they are administered separately as separate injections of the vaccine and instead allow them to be administered as one injection. Selection of sequences from the sequence catalog: [000120] The selection of sequences from the said Sequence Catalog is based on the following elements • Any sequence must contain epitopes that are triggered by one or several of the MHC-II alleles of the human. This is referred to as the MHC-II List of Sequences • Any sequence must not contain any epitopes that are triggered by any of the MHC.I alleles of the human (this is referred to as “knock-out” of sequences from the said “MHC-II List of Sequences” leading to the “Net Sequence List”) Physiological limits, ordering, and repetition: [000121] The invention may adopt a limit on the number of separate vaccines, where this number is calculated based on personal and clinical measurements and parameters. This limit is referred to as the “physiological limit”. [000122] The invention may order sequences and / or repeat some sequences (the “good ones”, e.g. those that are validated), observing the said Physiological Limit in order to focus the immune response. Adjuvants: [000123] The invention uses adjuvants to facilitate the functionality. These adjuvants are either “in string adjuvants”, where the adjuvant is attached to the sequences with an optional spacer, or they are separate active ingredients that are administered along with the vaccine. [000124] An example of an “in string” adjuvant can be seen in Table 4 below, where the “Invariant Chain” is attached to the string in front of the sequences that otherwise constitute the string (in this figure from the TAA CEACAM5). Table 4 Invariant Chain (li) only last part shown Spa cer CEACAM5 seq 1A Spa cer CEACAM5 seq 5A SEQ1 ...SSGLLVTKQ.DLGPVPM HHC TIESTPFNVAEGKEVLLL GGS KPSISSNNSKPVEDKDAVA Dosing: [000125] The invention calculates the dose of the Vaccine according to the following elements • Whether sequences are Validated (contain epitopes that are Validated) • How many epitopes are certain not to be presented • Personal and clinical conditions (measurements and parameters) Best mode for carrying cut the invention [000126] We describe as an example the use of the antigen Cyclin D1 below in a personal vaccine. Using a Cyclin D1 polytope as a vaccination agent to trigger an immune reaction on MHC-II of the adaptive immune system, either as prevention of, or as treatment of, a cancer of the types either (1) breast cancer, (2) prostate cancer, or (3) melanoma according to Table 2.Other TAAs according to the invention may also be used. Personal Vaccine: [000127] The epitopes or concatenated epitopes or Polytope is determined by the following steps, which are a special case of the aforementioned Steps 1 - 6 - which Steps are referenced and detailed for implementation with Cyclin D1 in the following: Step 1: A database table is constructed containing the binding properties of all epitopes of Cyclin D1 on MHC-II (epitopes of the length 15 amino acids, varying from 13 to 25, out of the full length of Cyclin D1, which is 295) on all alleles (or haplotypes) of MHC-II. This includes identifying any epitope as one of (1) a non-binder, (2) a “weak binder” (WB), or (3) a “strong binder” (SB). Across all epitopes with the length of 15, using the service on the URL MHC-II with a selection of alleles that constitute most of the world’s population according to the frequencies on the URL “https: / / allelefrequencies.net / hla.asp”, we get the following count of “strong binders”: Pos Epitope (of length 15) Count of SB 10 VETIRRAYPDANLLN 11 11 ETIRRAYPDANLLND 28 12 TIRRAYPDANLLNDR 41 13 IRRAYPDANLLNDRV 11 18 PDANLLNDRVLRAML 1 19 DANLLNDRVLRAMLK 2 22 LLNDRVLRAMLKAEE 2 23 LNDRVLRAMLKAEET 5 24 NDRVLRAMLKAEETC 2 25 DRVLRAMLKAEETCA 2 47 CVQKEVLPSMRKIVA 3 48 VQKEVLPSMRKIVAT 3 49 QKEVLPSMRKIVATW 3 55 SMRKIVATWMLEVCE 3 56 MRKIVATWMLEVCEE 11 57 RKIVATWMLEVCEEQ 2 79 PLAMNYLDRFLSLEP 2 84 YLDRFLSLEPVKKSR 1 85 LDRFLSLEPVKKSRL 2 86 DRFLSLEPVKKSRLQ 5 87 RFLSLEPVKKSRLQL 3 88 FLSLEPVKKSRLQLL 2 104 ATCMFVASKMKETIP 12 105 TCMFVASKMKETIPL 11 108 FVASKMKETIPLTAE 2 109 VASKMKETIPLTAEK 16 110 ASKMKETIPLTAEKL 19 111 SKMKETIPLTAEKLC 9 112 KMKETIPLTAEKLCI 6 116 TIPLTAEKLCIYTDN 2 119 LTAEKLCIYTDNSIR 6 120 TAEKLCIYTDNSIRP 8 121 AEKLCIYTDNSIRPE 20 122 EKLCIYTDNSIRPEE 6 124 LCIYTDNSIRPEELL 7 125 CIYTDNSIRPEELLQ 10 126 IYTDNSIRPEELLQM 7 127 YTDNSIRPEELLQME 17 128 TDNSIRPEELLQMEL 20 129 DNSIRPEELLQMELL 14 133 RPEELLQMELLLVNK 4 134 PEELLQMELLLVNKL 3 135 EELLQMELLLVNKLK 17 144 LVNKLKWNLAAMTPH 6 145 VNKLKWNLAAMTPHD 16 146 NKLKWNLAAMTPHDF 1 148 LKWNLAAMTPHDFIE 2 149 KWNLAAMTPHDFIEH 2 152 LAAMTPHDFIEHFLS 4 153 AAMTPHDFIEHFLSK 13 154 AMTPHDFIEHFLSKM 13 155 MTPHDFIEHFLSKMP 4 159 DFIEHFLSKMPEAEE 2 160 FIEHFLSKMPEAEEN 3 161 IEHFLSKMPEAEENK 7 162 EHFLSKMPEAEENKQ 2 173 ENKQIIRKHAQTFVA 1 188 LCATDVKFISNPPSM 5 189 CATDVKFISNPPSMV 16 190 ATDVKFISNPPSMVA 40 191 TDVKFISNPPSMVAA 17 192 DVKFISNPPSMVAAG 6 193 VKFISNPPSMVAAGS 1 198 NPPSMVAAGSVVAAV 29 199 PPSMVAAGSVVAAVQ 63 200 PSMVAAGSVVAAVQG 79 201 SMVAAGSVVAAVQGL 42 202 MVAAGSVVAAVQGLN 18 205 AGSVVAAVQGLNLRS 1 206 GSVVAAVQGLNLRSP 2 214 GLNLRSPNNFLSYYR 2 218 RSPNNFLSYYRLTRF 1 219 SPNNFLSYYRLTRFL 1 220 PNNFLSYYRLTRFLS 1 247 CQEQIEALLESSLRQ 2 248 QEQIEALLESSLRQA 6 249 EQIEALLESSLRQAQ 1 256 ESSLRQAQQNMDPKA 1 262 AQQNMDPKAAEEEEE 1 263 QQNMDPKAAEEEEEE 9 264 QNMDPKAAEEEEEEE 15 265 NMDPKAAEEEEEEEE 38 266 MDPKAAEEEEEEEEE 19 267 DPKAAEEEEEEEEEV 8 According to Step 1 we narrow that down based on a particular combination of MHC-II alleles, e.g. the combination DPA1_0202 + DPB1_0501 + DQA1_0501 + DQB1_0301 + DRB1_0701, which will give us 8 “strong binders” cf. Step 3 below. We can see from the above list, that the result of narrowing it down will be very different for different allele combinations. We estimate that about 0.3% of the world’s population will have an allele combination on MHC-II that gives no “strong binders” for Cyclin D1 on MHC-II. Step 2: Selection of those epitopes (by e.g. position in the sequence of the full length Cyclin D1 protein of 295) that constitute “strong binders” (SBs) with the specific combination of alleles for that person. The “strong binders” may constitute substrings that are consecutive epitopes that together are longer than the length of the individual epitopes. • If there are no “strong binders” for the specific allele combination, something which will occur in approx. 0.3% of cases, then we include the WBs in this selection. Step 3: Construction of an “a priori polytype” by appending the epitopes above - marking the “cuts” i.e. the joining points of epitopes in the polytope. For the allele / haplotype combination DPA1_0202 + DPB1_0501 + DQA1_0501 + DQB1_0301 + DRB1_0701 we get Pos Epitope Distance Append 85 LDRFLSLEPVKKSRL LDRFLSLEPVKKSRL 86 DRFLSLEPVKKSRLQL 1 QL 197 SNPPSMVAAGSVVAAV 111 SNPPSMVAAGSVVAAV 199 PPSMVAAGSVVAAVQ 2 Q 200 PSMVAAGSVVAAVQG 1 G 201 SMVAAGSVVAAVQGL 1 L 202 MVAAGSVVAAVQGLN 1 N 206 GSVVAAVQGLNLRSP 4 LRSP Where the nuclear acids in the column “Append” make up the sequence of the A Priori Polytope. The polytope above has one Cut, positioned between the epitope that begins in the Position (Pos) 86 and epitope that begins in the Position 197. Step 4: Check on both MHC-I and MHC-II whether the said A Priori Polytope, focusing on the epitopes that are now created around the Cuts, will trigger a “strong binder” (SB) or a “weak binder” (WB) on either of MHC-I or MHC-II. This check needs to be performed for all possible epitope lengths, i.e. 8 to 14 on MHC-I and 13 to 25 on MHC-II. Step 5: Padding the cuts that introduce a strong or weak binder on either MHC-I or MHC-II or both: (1) If the “Cut” is wide (if the positions are far apart) then any sequence that either, (1 A) silences the cut (makes it a non-binder) or (1B) extends the epitope to include more from the original protein (padding with the amino acids of the original string) until the cut is silenced (it is a non-binder). (2) If the Cut is close (the positions are close) then the original string of the full protein must be used so that the epitopes join up to a consecutive substring of the protein and thereby is similar to what comes out of the full length protein. Cf. the progression between A, B, and C on FIG 3, where more parts of A are added to create longer substrings in B and “pad” the gap when joined in C. • If the said A Priori Polytope after said Padding removes all WB or SB from both MHC-I and MHC-II, the said A Priori Polytope is updated to include the said Padding. • If it cannot be avoided that a substring in the said A Priori Polytope after the said Padding creates a WB or SB in either MHC-I or MHC-II or both, this substring is taken out of the A Priori Polytope, i.e. the said A Priori Polytope is updated to exclude the substring. In this case, we go back to and repeat Step 4, i.e. we need to check the A Priori Polytope again on both MHC-I and on MHC-II. Step 6: If there are “strong binders” on MHC-I that have been selected for the A Priori Polytope, the A Priori Polytope is updated to not include the epitopes that constitute SBs on MHC-II, if the said Epitopes contain (or are associated with) epitopes that are SBs on MHC-I. Then to follow the example above the allele / haplotype combination on MHC-II DPA1_0202 + DPB1_0501 + DQA1_0501 + DQB1_0301 + DRB1_0701 and for the allele combination on MHC-I A_0201 + B_0702 + C_0701 we get Pos Epitope Distance Append 197 SNPPSMVAAGSVVAAV 111 SNPPSMVAAGSVVAAV 199 PPSMVAAGSVVAAVQ 2 Q 200 PSMVAAGSVVAAVQG 1 G 201 SMVAAGSVVAAVQGL 1 L 202 MVAAGSVVAAVQGLN 1 N Where the nuclear acids in the column “Append” make up the sequence of the A Priori Polytope. • If this introduces a new cut, repeat Step 4, i.e. we need to check the A Priori Polytope again on both MHC-I and on MHC-II. • If this results in no epitopes left in the polytope then leave them in (and accept the side effect of it triggering an immune response on MHC-I) [000128] The vaccine is manufactured using the above Polytope sequence as the active ingredient, converted to mRNA. It can be done as an mRNA vaccine or a SAM vaccine that makes dendritic cells (“DC” - a subset of the APCs) produce a protein similar to the above Polytope, such that the MHC-II expressed on the said DCs will activate the immune system e.g. by making it produce CD4+ T cells that can also react on the cancer cells. [000129] It may be implemented such that a reduced set of vaccines will meet the requirements of most of the world’s population - without meeting the optimal combination of SBs on MHC-II for a particular allele combination, but not being excessive in length outside the SBs on MHC-II, and not invoking any WBs or SBs on either of MHC-I or MHC-II from the Cuts, and not invoking any SBs on MHC-I. This will mean that we can pre-approve those vaccines having specified sequences together with their allele combinations instead of relying on an approval of the above method of Step 1 - 6. Identification of sequences: [000130] Auto-generation of original sequences • Original: Derived from the substrings of a TAA, where epitopes are triggered by (are strong binders, provided the human has one of) at least, for DP and DQ: 6 alleles, for DR 4 alleles, and where the likelihood or world population share of the said alleles within either DP, DQ, or DR is at least 1%, the said epitopes being concatenated into substrings that are then regarded as “hotspots” of said TAA • Shortened: Original sequences that are shortened, if they after shortening are still longer than 18 amino acids long, and if by shortening them epitopes that are triggered by one or more MHC-I alleles appearing with a likelihood or share in the world population of 10% are avoided. [000131] The auto-generated Shortened sequences may become further shortened -into another Shortened sequence - by the automatic generation, if they meet the said requirements for shortening. [000132] The following Table 5 provides a brief selection for a few sequences based on the TAA CEACAM5 of an overview for all sequences in the sequence catalog of how likely a sequence is to be selected for a human subject - given a total likelihood from the share in the world population - broken down in MHC-II and MHC-I, and further into the genes (of MHC-II: DP, DQ, and DR; for MHC-I: A, B, and C): Table 5 Sequence DO. lliii MHC-I! Total B MHC-I Total Net Total CEACAM5 9 22% 43% 9% 60% 36% 28% 23% 64% 21% CEACAM5 10 0% 28% 16% 40% 13% 25% 23% 49% 20% CEACAM5 14 11% 33% 6% 45% 26% 19% 7% 45% 25% CEACAM5 19 Vai 8% 17% 24% 42% 7% 2% 47% 13% CEACAM5 20Val 1% 24% 12% 33% 10% 24% 5% 35% 21% [000133] Sequences in the Sequence Catalog may be combined or joined as follows, if (1) they are equal (if they start and end in the same position of the TAA) (in which case the identical sequences are only represented once in the Sequence Catalog) or (2) if they are almost equal, subject to an algorithm that justifies this (if it does not create or re-create a situation that would lead to it being shortened etc.) (in which case the sequences are concatenated), [000134] Sequences in the Sequence Catalog may be joined with spacers (where each sequence retains the full number of amino acids), if they are triggered by virtually the same alleles, and therefore in most cases would have been selected together anyway. Joining them with a spacer will avoid that they are administered separately as separate injections of the vaccine and instead allow them to be administered as one injection. Selection of sequences: [000135] The selection is based on a query in SQL, which takes as input • The alleles of MHC-I and MHC-II (22 in total for the 11 genes: (“HLA-“ omitted): (MHC-I:) A, B, C, (MHC-II:) DPA1, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5) • The TAAs that the tumor expresses (listed as a range of Identities) An example could look like this: “SELECT *from mol_SB_AfterKnockOutMultipleAntigens_4 ('NP_444284_1_G1_','NP_001018016_1_','NP_060884_1_alp','tr_A0A024R0K5_A','NP _937983_2_tel',", -- Cyclin D1, Mucin 1 iso 2, Sialyl Tn iso 1, CEACAM5, TERT ’0202’, ’0103’, - DP A1 ’0101’, ’1101’, - DP B1 -2% 0.1% ’0501’, ’0102’, - DQ A1 ’0201’, ’0502’, - DQ B1 - 7% 2% ’1503’, ’0301’, - DR B1 - 4% 7% ’0101’, ’0108’, - DR B3 ’0101’, ’0107’, - DR B4 ’0101’, ’0102’, - DR B5 ’2402’, ’0201’, - A -10% 25% ’4001’, ’1501’, - B - 5% 7% ’0602’,’1203’ -C - 3% 2% )” Where it is used that if a line starts with or from the point where it has the characters “— “ it is a comment with no influence in SQL- [000136] A comparison of manual and autogenerated sequence selection with personal vaccine is displayed in FIG 14. It is found to be reasonably close, that only 1 in 5 sequences of the optimum personal vaccine (211 -226) will not be covered by a selected sequence for the TAA “Mucin 1” and a selection of alleles, Since any cancer with most alleles has many epitopes sequences, and since there are multiple TAAs in any cancer that displays MHC-II, it is good enough, and we will select a range of sequences for this vaccine. We will hit the physiological limit anyway, in that we will have to prioritize between the sequences selected anyway. Sequence listing XML [000137] The sequence catalog comprises the sequences appearing from the sequence listing. The sequence listing XML is submitted as an xml file is incorporated herein by reference. The sequence listing XML file submitted has the name “Cancer Vaccine based on MHC-II Epitope Selection.xml”, and was created on January 13, 2025, and is 2,738 kilobytes in size. Items [000138] The present invention may be defined as follows [000139]           1. A method for producing a cancer vaccine composition for the treatment or prevention of cancer in a human subject, the method comprising the steps of a) selecting one or more epitopes or concatenated epitopes derived from a tumor associated antigen (TAA), such that the selected epitopes bind to MHC-II in the subject, thereby providing pool of epitopes and concatenated epitopes binding to MHC-II in the subject, b) removing, from the pool of epitopes and concatenated epitopes selected in step a), epitopes and concatenated epitopes comprising an epitope binding to MCH-I in the subject, thereby providing a pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject, c) optionally combining one or more of the epitope(s) and concatenated epitopes provided in step b into a polytope comprising the one or more selected epitopes and concatenated epitopes, d) optionally providing a molecule carrying information capable of facilitating the in vivo production of the one or more epitope and concatenated epitopes provided in step b or the polytope provided in step c, e) combining the one or more epitopes and concatenated epitopes selected from the pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject provided in step b, or a polytope provided in step c, or the information carrying molecules provided in step d, with suitable pharmaceutically acceptable excipients. [000140]          2. Method according to item 1, wherein the epitopes are concatenated epitopes. [000141]          3. Method according to item 2, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing. [000142]          4. Method according to item 3, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321,342, 350, 354, 355, 356, 358, 359, 360, 361,362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581,582, 620, 621,622, 623, 624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575 and 1607. [000143]          5. Method according to any of the above items, wherein steps a) and b) are accomplished by selecting an appropriate TAA, preferably a TAA as provided in the present description, and analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes by use of an algorithm which predicts the behavior of the immune system for the respective TAA as well as for any sequence of epitopes that are considered to make up the respective TAA, given data on the gene alleles of the subject. [000144]          6. Method according to item 5 wherein analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes or concatenated epitopes is accomplished by use of appropriate algorithms which are available for computing a binding probability for each epitope of the TAA for binding to MHC-II and MHC-I. [000145]          7. Method according to item 6 wherein the appropriate algorithm is provided on the URL “https: / / services.healthtech.dtu.dk / services / NetMHCpan-4.1 / ”, or as a subsequently improved version thereof, for MHC-I, and on the URL “https: / / services.healthtech.dtu.dk / services / NetMHCIIpan-4.3 / ”, or as a subsequently improved version thereof, for MHC-II. [000146]          8. Use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen, wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC-II) in the subject, and wherein the epitopes or concatenated epitopes are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC-I) in the subject. [000147]          9. Use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in the subject, wherein the subject is characterized in having a genotype facilitation the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject. [000148]           10. Use according to item 8 or 9, wherein the epitopes are concatenated epitopes. [000149]           11. Use according to item 10, wherein the concatenated epitopes are the concatenated epitopes provided in the sequence listing. [000150]           12. Use according to item 11, wherein the concatenated epitopes are the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321,342, 350, 354, 355, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581,582, 620, 621,622, 623, 624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551,1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575, 1607. [000151]           13. A cancer vaccine comprising one or more specifically selected epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), said selected epitope(s) or concatenated epitopes activating an immune response via the Major Histocompatibility Complex II (MHC II) in a subject, said epitopes being characterized by a) consisting of more than 13 amino acids but less than 25 amino acids, preferably 15 amino acids. [000152]           14. Vaccine according to item 13, wherein the epitopes are one or more concatenated epitopes of a tumor associated antigen (TAA) comprising each epitope or concatenated epitope consisting of no more than XX% of the amino acids of the TAA. [000153]           15. Vaccine according to item 14, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing. [000154]           16. Vaccine according to item 15, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321,342, 350, 354, 355, 356, 358, 359, 360, 361,362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581,582, 620, 621,622, 623, 624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575, 1607. [000155]           17. Vaccine according to any of items 13-16 for use in the treatment or preventive treatment of cancer in a subject having a genotype facilitation the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject. [000156]           18. Library or sequence catalog of cancer vaccine epitopes or concatenated epitopes derived from a tumor associated antigen (TAA) wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in a human subject. [000157]           19. Library or sequence catalog according to item 18, wherein the epitopes are concatenated epitopes. [000158]          20. Library or sequence catalog according to item 19, wherein the library or sequence catalog comprises one or more of the concatenated epitopes provided in the sequence listing. [000159]          21. Library or sequence catalog according to item 20, wherein the library or sequence catalog comprises one or more of the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51,101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281,282, 283, 284, 301,316, 318, 319, 320, 321, 342, 350, 354, 355, 356, 358, 359, 360, 361,362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421,422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581,582, 620, 621,622, 623, 624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561,1562, 1575, 1607. [000160]          22. Library or sequence catalog according to items 18-21 wherein the epitopes or concatenated epitopes are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC I) in a human subject. [000161]          23. A concatenated epitope comprising a peptide sequence according to the sequence listing or a derivative thereof wherein the sequence is shortened by 1,2, 3, 4 or 5 amino acids in the N-terminal and / or by 1,2, 3, 4 or 5 amino acids in the C-terminal part of the concatenated epitope. [000162]          24. A concatenated epitope further comprising an adjuvant sequence. [000163]           Preferably, the cancer to be treated is selected among breast cancer (BC), prostate cancer (PCa), melanoma, colorectal cancer, ovarian cancer, classic Hodgkin lymphoma, glioma, and non-small cell lung cancer. [000164]           Preferably, the tumor associated antigen is selected among Cyclin D1 (CCND1), Mucin-1 (MUC1), Carcinoembryonic antigen (CEA), Human Epidermal Receptor 2 (HER2 or ERBB2), Telomerase Reverse Transcriptase (TERT), Wilms Tumor Gene (WT-1), Sialyl-Tn, Myc proto-oncogene protein (MYC), Prostate-specific membrane antigen (PSMA), Prostatic Acid Phosphatase (PAP), Prostate Specific Antigen (PSA), and Cancer / testis antigen 1 (NY-ESO-1). Carcinoembryonic antigen (CEACAM5) is particularly preferred. [000165]          The present invention may alternatively be defined as follows [000166]           1. A method for generating an active ingredient consisting of one or several proteins in a vaccine that prevents or treats human cancers that express MHC-II in full or in part - referred to as “MHC-H” in the following - on the cell surface by (1) activating the MHC-II part of the adaptive immune system to discover the cancer by maximizing the likelihood of displaying, as a consequence of injecting the said Vaccine, some of a first set of epitopes, that when concatenated (without repeating the amino acids that make up the said Epitopes), are similar to the said Active Ingredient, (2) so that the displayed epitopes of said First Set of Epitopes are also substrings of an antigen produced by the said Cancer, which said Epitopes the said Cancer may display on MHC-II, and (3) while not activating the MHC-I part of the adaptive immune system by maximizing the likelihood that no part of the said Active Ingredient when deriving any second set of epitopes, that when concatenated (without repeating the amino acids that make up the said Epitopes) make up the said Active Ingredient, will display on MHC-I, thereby minimizing any undesired side effects in the human as well as minimizing the likelihood of autoimmune disorders as a consequence of injecting the said Vaccine, (4) while maximizing the likelihood that no element in a third set of epitopes, of either the said First Set of Epitopes or Second Set of Epitopes, that are not parts of said Antigen (because the epitopes of said Third Set of Epitopes span joins or cuts in the said Antigen, so that the said Epitopes do not exist in the said Antigen) will display on MHC-I nor on MHC-II, (5) basing the specification of the said Active Ingredient on an algorithm that predicts the behavior of the immune system for the said Antigen as well as for any sequence of epitopes that are considered to make up the said Active Ingredient, given data on the gene alleles of the said Human, in terms of computing a binding probability for each epitope of the said First Set of Epitopes for it to bind to MHC-II and in terms of computing a binding probability for each epitope of the said Second Set of Epitopes for it to bind to MHC-I. [000167]          2. A method according to item 1 where the said Cancer that expresses MHC-II in full or in part on the cell surface is one of Breast cancer (BC), prostate cancer (PCa), melanoma, colorectal cancer, ovarian cancer, classic Hodgkin lymphoma, glioma, and non-small cell lung cancer. [000168]           Item 3. A method according to item 1 where the said Antigen besides being produced by the said Cancer is also present in some of the non-cancerous cells of the said human, which Non-Cancerous Cells except for Antigen Presenting Cells (APCs) do not express MHC-II, and the said Antigen is therefore a Tumor Associated Antigen. [000169]           Item 4. A method according to item 1 where the said Active Ingredient is one protein, said Protein called a Polytope. [000170]           Item 5. A method according to item 1 where the epitopes in the said First Set of Epitopes have a length (number of amino acids) of one of 13,14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, and 25 amino acids, and the epitopes in the said Second Set of Epitopes have a length (number of amino acids) of one of 8,9,10,11,12,13, and 14 amino acids. [000171]           Item 6. A method according to item 1 where the said Algorithm classifies the said Binding Probabilities for an epitope to bind to MHC-I as well as to MHC-II into one of (1) a non-binder, (2) a weak binder (WB), and a strong binder (SB), such that “maximizing the likelihood of an epitope of the said First Set of Epitopes to bind to MHC-H” is implemented by selecting the said Epitope as an SB on MHC-H, and such that “maximizing the likelihood of an epitope of the said Second Set of Epitopes not to bind to MHCT is implemented by selecting the said Epitope as one of (1) a Non-Binder and (2) a WB on MHC-I, and such that “maximizing the likelihood of an epitope of the said Third Set of Epitopes not to display on MHC-I nor on MHC-H” is implemented by selecting the said Epitope as a Non-Binder on both MHC-I and on MHC-II. [000172]           Item 7. A method according to item 1 where said Algorithm is implemented as the combination of the services in URL MHC-I, or as a subsequently improved version thereof, for MHC-I, and as URL MHC-II, or as a subsequently improved version thereof, for MHC-II, modified to take into account of the situation that it may be that not all of MHC-II is expressed by the said Cancer. [000173]           Item 8. A method according to item 6 where, if after selecting among the said First Set of Epitopes to bind to MHC-II as an SB has as a consequence that the selection is empty (if there are no SB on MHC-II), then “maximizing the likelihood of an epitope of the said First Set of Epitopes to bind to MHC-H” is implemented by selecting the said Epitope as a WB on MHC-H. [000174]           Item 9. A method according to item 6 where, if after selecting among the said Second Set of Epitopes to bind to MHC-I as an SB has as a consequence that the said Active Ingredient is empty (if there are no binders left for MHC-H after removing the SB of MHC-I), then it is implemented to not enforce the requirement to identify any said Second Set of Epitopes and then flag this situation (allowing the method to go on without removing the epitopes that may bind to MHC-I, since it is likely that there are a limited number of CD8+ T cells that bind to these epitopes in MHC-I due to the T cell selection, but with a warning that unwanted side effects or auto-immune disorders may occur). [000175]          Item 10. A method according to item 4 where the said Polytope consists of only consecutive epitopes with the Third Set of Epitopes is empty (so that there are no “cuts” in the said Polytope). [000176]           Item 11. A method according to item 3 where the said Tumor Associated Antigen is Cyclin D1 with the gene code CCND1 and as defined in the sequence number 1 named “Cyclin D1”one or several of Cyclin D1 (CCND1), Mucin-1 (MUC1), Mucin 16, Carcinoembryonic antigen (CEA - either in the form of CEACAM5, or in the form of CEACAMx, where x is 1,3, 4, 6, 7, 8,16,18,19, 20, or 21), Human Epidermal Receptor 2 (HER2 or ERBB2), Telomerase Reverse Transcriptase (TERT), Wilms Tumor Gene (WT-1), Sialyl-Tn, Myc protooncogene protein (MYC), Prostate-specific membrane antigen (PSMA), Prostatic Acid Phosphatase (PAP), Prostate Specific Antigen (PSA), Cancer / testis antigen 1 (NY-ESO-1), Melanoma antigen preferentially expressed in tumors (PRAME), Melanoma-associated antigen 1 (MAGEA1), Melanoma-associated antigen 3 (MAGEA3), Prostate stem cell antigen (PSCA), B-lymphocyte antigen CD19 (CD-19), Cellular tumor antigen p53 (TP-53), GTPase KRas (KRAS), Keratin, type I cytoskeletal 19 (Cyfra21-1), Cellular retinoic acid-binding protein 1 (CRABP1), Cellular retinoic acid-binding protein 2 (CRABP2), Folate receptor (FOLR1), Kallikrein-10 (KLK10), Baculoviral IAP repeat-containing protein 5 (BIRC5 or Survivin), Insulin, Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), Epidermal growth factor receptor (EGFR), Protein LYRIC (Metadherin), Tumor protein D52, Ephrin type-A receptor 2 (EphA2), Tyrosinase, or Alpha-fetoprotein (AFP). [000177]           Item 12. A method according to item 1 where the said Vaccine is produced and administered to the body of the human as one of mRNA vaccine, SAM: Self Amplifying mRNA vaccine, LNP mRNA: Lipid nanoparticles mRNA vaccine, Virus Vector vaccine, DC vaccine, and ISV: In situ vaccine. [000178]           Item 13. A method according to item 1 where the said Vaccine is combined with a treatment that enhances MHC-II, e.g. a “CIITA treatment” (CIITA is the main transcription factor co-activator of MHC-II) or an “IFN-gamma” treatment. [000179]           Item 14. A method according to item 1 where the said Active Ingredient is combined with other active ingredients in the said Vaccine. [000180]           Item 15. A method according to item 1 where the said Vaccine is combined with a treatment that targets other parts of the T cells, e.g. checkpoint inhibition treatment that targets either of the receptors PD-1 or CTLA-4 on the T cell. [000181]           Item 16. A method according to item 1 where the said Vaccine is administered more than once, and the amount of the said Active Ingredient in the non-first injections is computed adaptively based on measurements of (a) the immune response in terms of e.g. one of or a combination of (1) the expression of the epitopes on MHC-II, (2) the amount of CD4+ cells generated, and, if it is used to treat and not prevent cancer, (3) the amount of cancer cells of a tumor that are killed; and (b) side effects happening as a consequence of the said Vaccine. [000182]           Item 17. A method according to item 1 where the said Vaccine is manufactured and approved with different Active Ingredients, such that there exists a mapping method of allele combinations to a limited set of Vaccines, each with different Active Ingredients, such that the said term “Maximizing The Likelihood” is implemented as a trade-off versus limiting the amount of elements in the said Limited Set of Vaccines, such that all the said vaccines in the Limited Set of Vaccines can be approved while their effects are not severely reduced. [000183]           Item 18. A method according to item 17 where the said Limited Set of Vaccines is a catalog consisting of [a subset of the sequences in the XML file] or a combination of them with a spacer [as in the 3rd set of epitopes] is put in between where said Spacers do not present any epitopes given the MHC-I and MHC-II alleles of the patient. [We have not mentioned here that the catalog is derived by (1) “original” sequences and (2) “shortened” sequences (based on the “original” sequences; the next item says how to auto-generate them] [000184]           Item 19. A method according to item 18 where the said Limited Set of Vaccine is constructed in part by a computerized generation method of (1) “original sequences” based on [“hotspots” of] MHC-II as follows (A) Triggered by at least a threshold number of alleles of DP, DQ, and DR, respectively (B) The sum of the likelihood of said alleles in the world population is at least a threshold number (C) [concatenated for as long as there are no gaps in the string, adopting these criteria] and (2) “shortened sequences” based on the said Original Sequences to increase the likelihood of avoiding an epitope triggered by one or more MHC-I alleles as follows (D) After shorting the length of the sequence is at least a threshold number (E) The likelihood of the MHC-I allele that trigger the epitope that is cut out wholly or in part of the sequence is at least a threshold number where the step in (2) may be repeated if the provisions in (E) and (D) are still valid for the resulting sequence. [000185]           Item 20. A method according to item 19 where the said Threshold Numbers of (1) are (A) For DP at least 6, for DQ at least 6, and for DR at least 4 (B) The sum of the likelihood of said alleles in the world population is at least 1% and where the said Threshold Numbers of (2) are (D) After shorting the length of the sequence is at least 19 amino acids (E) The likelihood of the MHC-I allele that trigger the epitope that is cut out wholly or in part of the sequence is at least 10%. [000186]           Item 21. A method according to item 20 where the said Sequences in the Catalog are merged (meaning joined without repeating the Amino Acids), if they satisfy both of the following criteria (1) [They overlap almost completely] and (2) They are triggered by almost the same MHC-II and MHC-I alleles [000187]          Item 22. A method according to item 1 where the said Vaccine is administered such that it is measured, which epitopes in the said Vaccine are immunogenic (meaning presented and attracting T cells) referring to said Immunogenic Epitopes as Validated. [000188]           Item 23. A method according to item 17 where the dose of said Vaccine takes into account whether (1) the sequence contains one or more validated epitopes, (2) the number of epitopes that may become presented in the injected vaccine sequences but are not validated, and (3) the number of epitopes that with certainty [or high likelihood] will not get presented, as well as (4) personal and clinical parameters and measurements. [000189]          Item 24. A method according to item 17 where the said Vaccine has a limit to [on] the number of sequences administered as individual vaccines taking into account physiological limits that are calculated personally based on personal and clinical parameters or measurements. [000190]          Item 25. A method according to item 17 [and item 24] where the said Vaccine adopts an algorithm that determines the ordering of the said Limited Number of Vaccines [sequences] and where some of the elements in the said Limited Number of Vaccines are repeated more than once in the said Vaccine (possibly repeating the “good ones” e.g. those that contain Validated epitopes). [000191]           Item 26. A method according to item 1 where the said Active Ingredient is extended either at the beginning, at the end, or at [points in the joins between epitopes - unlikely scenario] with adjuvants furthering one or several of the following: (1) the process of getting the protein into the MHC-II loading compartment (MlIC), (2) avoidance of MHC-I contamination in the APC (because it takes up other epitopes than those from the vaccine), (3) the presentation of epitopes to T cells, (4) the activation process of the T cells and other cells of the immune system, hereunder rendering the CD4+ T Cells cytotoxic, or (5) the effector process killing the cancer. [000192]           Item 27. A method according to item 14 where the said other Active Ingredients are adjuvants furthering one or several of the following: (1) the process of getting the protein into the MHC-II loading compartment (MIIC), (2) avoidance of MHC-I contamination in the APC (because it takes up other epitopes than those from the vaccine), (3) the presentation of epitopes to T cells, (4) the activation process of the T cells and other cells of the immune system, hereunder rendering the CD4+ T Cells cytotoxic, or (5) the effector process killing the cancer. [000193]           Item 28. A method according to item 23 (point 1 below), item 26 (point 2), and item 27 (point 3) where the data on (1) dosing algorithm including the relative weight of validated epitopes, (2) the formula determining the limit to the number of vaccines administered, (3) the ordering and repeating logic (1), (2), and (3) referred to as “master data”, the master data being re-evaluated and assigned a version reference, and where the method runs on different versions of said Master Data with the said Reference made [clear], [Different master data may be approved in different countries or regions]

Claims

1. Method for producing a cancer vaccine composition for the treatment or prevention of cancer in a human subject, the method comprising the steps ofa. selecting one or more epitopes or concatenated epitopes derived from a tumor associated antigen (TAA), such that the selected epitopes bind to MHC-II in the subject, thereby providing pool of epitopes and concatenated epitopes binding to MHC-II in the subject,b. removing, from the pool of epitopes and concatenated epitopes selected in step a), epitopes and concatenated epitopes comprising an epitope binding to MHC-I in the subject, thereby providing a pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject,c. optionally combining one or more of the epitope(s) and concatenated epitopes provided in step b into a polytope comprising the one or more selected epitopes and concatenated epitopes,d. optionally providing an mRNA molecule capable of facilitating the in vivo production of the one or more epitope and concatenated epitopes provided in step b or the polytope provided in step c,e. combining the one or more epitopes and concatenated epitopes selected from the pool of epitopes and concatenated epitopes binding to MHC-II and not binding to MHC-I in the subject provided in step b, or a polytope provided in step c, or the information carrying molecules provided in step d, with suitable pharmaceutically acceptable excipients.

2. The method according to claim 1, wherein the epitopes are concatenated epitopes.

3. The method according to claim 2, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing.

4. The method according to claim 3, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281, 282, 283, 284, 301, 316, 318, 319, 320, 321, 342,350, 354, 355, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 379,380, 394, 405, 406, 407, 408, 412, 413, 421, 422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581, 582, 620, 621, 622, 623,624, 625, 626, 627, 629, 631, 803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575 and 1607.

5. The method according to any of the above claims 1-4, wherein steps a) and b) are accomplished by selecting an appropriate TAA, preferably a TAA as provided in the present description, and analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes by use of published data on peptides and alleles which predict the behavior of the immune system for the respective TAA as well as for any sequence of epitopes that are considered to make up the respective TAA, given data on the gene alleles of the subject.

6. The method according to claim 5 wherein analyzing the respective TAA for likely MHC-II and MHC-I binding epitopes or concatenated epitopes is accomplished by use of appropriate algorithms which are available for computing a binding probability for each epitope of the TAA for binding to MHC-II and MHC-I.

7. The method according to claim 6 wherein the appropriate algorithm is provided on the URL “https: / / services.healthtech.dtu.dk / services / NetMHCpan-4.1 / ”, or as a subsequently improved version thereof, for MHC-I, and on the URL “https: / / services.healthtech.dtu.dk / services / NetMHCIIpan-4.3 / ”, or as a subsequently improved version thereof, for MHC-II.

8. Use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen, wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC-II) in the subject, and wherein the epitopes or concatenated epitopes are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC-I) in the subject.

9. Use for the treatment or preventive treatment of cancer in a subject of one or more epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in the subject, wherein the subject is characterized in having a genotype facilitation the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject.

10. The use according to any of claims 8 or 9, wherein the epitopes are concatenated epitopes.

11. The use according to claim 10, wherein the concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing.

12. The use according to claim 11, wherein the concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281, 282, 283, 284, 301, 316, 318, 319, 320, 321, 342, 350, 354, 355,356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 379, 380, 394, 405,406, 407, 408, 412, 413, 421, 422, 424, 425, 426, 427, 428, 429, 430, 431, 432, 436, 437,438, 439, 440, 469, 495, 498, 499, 500, 580, 581, 582, 620, 621, 622, 623, 624, 625, 626,627, 629, 631, 803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495,1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575, 1607.

13. Cancer vaccine comprising one or more specifically selected epitope(s) or concatenated epitopes derived from a tumor associated antigen (TAA), said selected epitope(s) or concatenated epitopes activating an immune response via the Major Histocompatibility Complex II (MHC II) in a subject, said epitopes being characterized by consisting of more than 13 amino acids but less than 25 amino acids, preferably 15 amino acids.

14. The vaccine according to claim 13, wherein the epitopes are one or more concatenated epitopes of a tumor associated antigen (TAA) comprising each epitope or concatenated epitope consisting of no more than 25% of the amino acids of the TAA.

15. The vaccine according to claim 14, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing.

16. The vaccine according to claim 15, wherein the one or more concatenated epitopes are selected among the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281, 282, 283, 284, 301, 316, 318, 319, 320, 321, 342,350, 354, 355, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 379,380, 394, 405, 406, 407, 408, 412, 413, 421, 422, 424, 425, 426, 427, 428, 429, 430, 431,432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581, 582, 620, 621, 622, 623,624, 625, 626, 627, 629, 631,803, 805, 806, 807, 895, 896, 897, 904, 905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551,1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575, 1607.

17. The vaccine according to any of claims 13-16 for use in the treatment or preventive treatment of cancer in a subject having a genotype facilitating the non-binding of the specifically selected epitope(s) or concatenated epitopes to the Major Histocompatibility Complex I (MHC I) in the subject.

18. Library or sequence catalog of cancer vaccine epitopes or concatenated epitopes derived from a tumor associated antigen (TAA) wherein the epitopes or concatenated epitopes are specifically selected to activate an immune response via the Major Histocompatibility Complex II (MHC II) in a human subject.

19. The library or sequence catalog according to claim 18, wherein the epitopes are concatenated epitopes.

20. The library or sequence catalog according to claim 19, wherein the library or sequence catalog comprises one or more of the concatenated epitopes provided in the sequence listing.

21. The library or sequence catalog according to claim 20, wherein the library or sequence catalog comprises one or more of the concatenated epitopes provided in the sequence listing as sequence 2, 3, 4, 5, 6, 7, 8, 9, 18, 23, 29, 30, 33, 34, 43, 46, 47, 48, 49, 50, 51, 101, 105, 106, 108, 173, 174, 176, 177, 178, 179, 180, 279, 280, 281, 282, 283, 284, 301, 316, 318,319, 320, 321, 342, 350, 354, 355, 356, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367,368, 369, 370, 379, 380, 394, 405, 406, 407, 408, 412, 413, 421, 422, 424, 425, 426, 427,428, 429, 430, 431, 432, 436, 437, 438, 439, 440, 469, 495, 498, 499, 500, 580, 581, 582,620, 621, 622, 623, 624, 625, 626, 627, 629, 631, 803, 805, 806, 807, 895, 896, 897, 904,905, 906, 1468, 1475, 1478, 1495, 1502, 1503, 1504, 1505, 1536, 1551, 1552, 1553, 1554, 1558, 1559, 1560, 1561, 1562, 1575, 1607.

22. The library or sequence catalog according to any of claims 18-21 wherein the epitopes or concatenated epitopes are specifically selected not to activate an immune response via the Major Histocompatibility Complex I (MHC I) in a human subject.

23. Concatenated epitope comprising a peptide sequence according to the sequence listing or a derivative thereof wherein the sequence is shortened by 1,2, 3, 4 or 5 amino acids in theN-terminal and / or by 1, 2, 3, 4 or 5 amino acids in the C-terminal part of the concatenated epitope.

24. The concatenated epitope according to claim 23 further comprising an adjuvant sequence.

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