product

Abstract

The present invention relates to novel polypeptides, polynucleotides encoding the polypeptides, and compositions comprising the polypeptides or polynucleotides. The present invention also relates to the use of the polypeptides, polynucleotides, and compositions for the treatment, prevention, and diagnosis of cancer, in particular colorectal cancer.

Description

Technical Field

[0001] This invention relates to novel polypeptides, polynucleotides encoding said polypeptides, and compositions comprising said polypeptides or polynucleotides. The invention also relates to the use of said polypeptides, polynucleotides, and compositions for the treatment, prevention, and diagnosis of cancer, particularly colorectal cancer. Background Technology

[0002] Tumor-associated antigens (TAAs) have been proposed as a potential source of neoantigens for cancer therapy. However, clinical trials have shown significant adverse events when TAA-based neoantigens are administered, such as neurotoxicity and respiratory toxicity associated with anti-MAGE-A3 TCR gene and CEACAM5-specific CAR T-cell therapies, leading to the abandonment of TAA-based cancer treatments. This invention reveals a potential new class of molecules to further expand the number of public neoantigens and broaden the library of potential off-the-shelf antigen-targeted therapies for colorectal cancer. These new molecules are expressed from large non-coding regions of the genome, such as from long non-coding RNAs (lncRNAs). Summary of the Invention

[0003] The inventors have identified the presence of a group of lncRNAs (which may be referred to herein as camyoRNAs) specifically expressed in cancer tissues, particularly colorectal cancer tissues. The inventors have also identified smORFs (small open reading frames) included within said lncRNAs, which are translated into proteins (which may be referred to herein as “camyo peptides”) in cancer tissues, particularly colorectal cancer tissues. These translated proteins are also described for the first time herein as being processed in cells and presented by the major histocompatibility complex (MHC) in the form of immunogenic peptide fragments. These peptides may be referred to herein as “camyo epitopes”. Cancer-specific lncRNAs and polypeptides derived therefrom represent potent candidates for the treatment and diagnosis of colorectal cancer, with little or no off-target effects.

[0004] Unlike tumor-specific antigens (TSAs), cameo peptides and cameo epitopes are not limited to recurrent mutations within the host gene. Due to the tumor-specific expression profiles of their derived cameoRNAs, any immunogenic peptide derived from translated smORFs can be targeted as a TAA (tumor-associated antigen) in colorectal cancer therapy, thus significantly expanding the potential pool of new antigens for targeting via immunotherapy. They can also serve as biomarkers for diagnosing colorectal cancer. Furthermore, the workflow for validating the presence of cameoRNA-derived TAAs is faster and simpler because it involves differential expression analysis of cameoRNAs in normal and colorectal cancer groups based on direct RNA sequencing, eliminating the need for variant determination. Using cameoRNA-based TAAs can increase the efficiency of “off-the-shelf” therapies (i.e., immunotherapies that are generally available to all cancer patients, as opposed to immunotherapies tailored to specific patients with specific antigen variants) by increasing population coverage and the number of targetable antigens per patient. The camyoRNA, camyo peptide, and camyo epitope described in this article are specific to colorectal cancer, and their expression profiles are similar to those of TAAs encoding proteins well-known in the art, thus they are expected to have similar potential as therapeutic vaccine targets.

[0005] Off-the-shelf vaccines targeting camyoRNAs, camyo peptides, and camyo epitopes as described in this article offer several advantages. Compared to personalized vaccines, the development cost per patient is significantly lower because they only require one production run and patient selection can be performed rapidly and cost-effectively via, for example, direct multiplex quantitative PCR (qPCR) analysis. Furthermore, the tumor-specific properties of camyoRNAs may be associated with their role in tumor initiation and progression. This, combined with the large number of camyoRNAs present in any given patient, should, when targeted as part of a vaccine, reduce the chance of immune evasion.

[0006] In summary, the inventors have discovered that a population of lncRNAs is overexpressed in colorectal cancer cells relative to healthy cells. The polypeptides encoded by these lncRNAs represent tumor neoantigens, which have been identified as being presented by the MHC and are immunogenic. Therefore, the inventors have advantageously determined that these polypeptides can be used in a therapeutic setting to induce an antitumor immune response in colorectal cancer, for example, by formulation, administration, and administration of cancer vaccines. Therefore, the present invention relates to novel polypeptides capable of eliciting an antitumor immune response in subjects. The same group of lncRNAs, and the polypeptides encoded by them, can also be used as markers for the diagnosis of colorectal cancer in subjects.

[0007] This invention provides polypeptides encoded by open reading frames in long non-coding RNA (lncRNA) genes, wherein the lncRNA is overexpressed in colorectal cancer cells relative to healthy cells, preferably wherein the lncRNA is defined as any of SEQ ID NO: 1 to 18 (the sequence of which is also provided by this invention and may be referred to herein as an exemplary “camyoRNA” associated with colorectal cancer). The polypeptide may comprise a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, comprising any polypeptide sequence defined as SEQ ID NO: 19 to 97 (the sequence of which may be referred to herein as an exemplary “camyo peptide” associated with colorectal cancer). The polypeptide may comprise or consist of any polypeptide sequence defined as SEQ ID NO: 98 to 611 (the sequence of which may be referred to herein as an exemplary “camyo epitope” associated with colorectal cancer – this term indicates that it is an immunogenic epitope of the cameo peptide).

[0008] This invention also provides: - A polynucleotide encoding one or more of the said polypeptides; and a carrier and / or cell comprising the said polynucleotide; - A composition comprising any of the said polypeptides, polynucleotides, cells or carriers, and optionally one or more of pharmaceutically acceptable carriers, preservatives or diluents; - A method for treating colorectal cancer in an individual, comprising administering the polypeptide, polynucleotide, cell, carrier, or composition to the individual. Attached Figure Description

[0009] Figure 1 The cumulative distribution of the 10 most highly expressed camyoRNAs is shown in the CRC (thick line), the 6 known TAAs (dotted lines), and the TAAs included in the PolyPEPI1018 multi-target vaccine known in the art (dashed lines). The figure shows the percentage of cancer samples expressing a large number of targets. For example, 50% of cancer samples express 5 or more camyoRNAs.

[0010] Figure 2 CRC stage-specific expression coverage. Each column represents the mean expression coverage (%) of stage I, II, III, and IV CRC samples obtained from the TCGA-COAD age-matched group. Green indicates the mean coverage of the entire COAD-TCGA cohort.

[0011] Figure 3 This invention preferably describes the expression analysis of camyoRNAs in the vaccine composition. This figure shows a box plot of each camyoRNA, illustrating their expression levels (TPM) in tumor samples, healthy transverse colon samples, and healthy sigmoid colon samples.

[0012] Figure 4 Translational levels of camyo peptides and known TAAs. The heatmap values ​​represent the translational levels of each camyo peptide and a set of known TAAs across a group of proteomic samples from healthy colon tissue.

[0013] Figure 5 : The number of MS spectra matching any peptide produced by the preferred vaccine composition described in this invention. The x-axis represents 6 samples; PBMCs from 2 healthy donors electroporated with short constructs (S2), long constructs (L6), or no constructs (simulated).

[0014] Figure 6 Homology analysis of the human proteome and other animal species. After comparison with reference proteomes of A) humans, B) dogs, macaques, mice, rats, and pigs, the minimum logarithmic order of each of the 73 camyo epitopes (blue), 12 known TAAs (red), and (positive control) species-specific sequences (green) was analyzed. 10 BLASTp E value.

[0015] Figure 7 The response of granzyme B, interferon-γ, and interleukin II to camyo epitope stimulation in five healthy donors.

[0016] Figure 8 : Individual healthy donor response to camyo epitopes and TAA. Each column represents the ELISpot response of a healthy donor to a camyo peptide library and positive and negative controls.

[0017] Sequence Description

[0018] SEQ ID NO: 1-18 are 18 multinucleotide sequences defining lncRNAs, which may be referred to herein as exemplary “camyoRNAs” associated with colorectal cancer.

[0019] SEQ ID NO: 19~97 are polypeptide sequences translated from open reading frames of 18 lncRNAs of SEQ ID NO: 1~18, and their polypeptide sequences may herein be referred to as exemplary “camyo peptides” associated with colorectal cancer.

[0020] SEQ ID NO: 98~611 are polypeptide sequences derived from larger polypeptide sequences as defined in SEQ ID NO: 19~97, which may herein be referred to as exemplary “camyo epitopes” associated with colorectal cancer. Detailed Implementation

[0021] It should be understood that different applications of the disclosed products and methods can be adapted to the specific needs of the art. It should also be understood that the terminology used herein is for describing particular embodiments of the invention only and is not intended to be limiting.

[0022] Furthermore, as used in this specification and the appended claims, the singular forms “a,” “an,” and “described” include plural references unless the content expressly indicates otherwise. Thus, for example, reference to “polypeptide” includes “polypeptide,” etc.

[0023] The terms “polypeptide” and “peptide” are used interchangeably herein to refer to polymers of amino acid residues and their variants and synthetic analogs. Therefore, these terms apply to amino acid polymers in which one or more amino acid residues are synthetic non-naturally occurring amino acids, such as corresponding chemical analogs of naturally occurring amino acids, and also to naturally occurring amino acid polymers. Polypeptides may also undergo maturation or post-translational modification processes, which may include, but are not limited to, glycosylation, proteolytic cleavage, lipolysis, signal peptide cleavage, propeptide cleavage, phosphorylation, etc. Peptides can be prepared using recombinant technologies, such as through the expression of recombinant or synthetic polynucleotides. Recombinant peptides are generally substantially free of culture medium, for example, the culture medium constitutes less than about 20% of the volume of the protein preparation, more preferably less than about 10%, and most preferably less than about 5%.

[0024] The term “amino acid” in this disclosure is used in its broadest sense and is intended to encompass organic compounds containing amine (NH2) and carboxyl (COOH) functional groups, as well as the side chains (e.g., R groups) characteristic of each amino acid. In some embodiments, amino acid refers to naturally occurring L-α-amino acids or residues. Commonly used one- and three-letter abbreviations for naturally occurring amino acids are used herein: A=Ala; C=Cys; D=Asp; E=Glu; F=Phe; G=Gly; H=His; I=Ile; K=Lys; L=Leu; M=Met; N=Asn; P=Pro; Q=Gln; R=Arg; S=Ser; T=Thr; V=Val; W=Trp; and Y=Tyr (Lehninger, AL, (1975) Biochemistry, 2d ed., pp. 71-92, Worth Publishers, New York). The general term “amino acid” also includes D-amino acids, inverted amino acids, and chemically modified amino acids, such as amino acid analogs, naturally occurring amino acids that are not typically incorporated into proteins, such as ortholeucine, and chemically synthesized compounds that have characteristic properties of amino acids known in the art, such as β-amino acids. For example, analogs or mimics of phenylalanine or proline, which allow for the same conformational restrictions as natural Phe or Pro, are included within the definition of an amino acid. Such analogs and mimics are referred to herein as “functional equivalents” of the corresponding amino acids. Other examples of amino acids are listed in Roberts and Vellaccio, *The Peptides: Analysis, Synthesis, Biology*, Gross and Meiehofer, eds., Vol. 5, p. 341, Academic Press, Inc., NY 1983, which is incorporated herein by reference.

[0025] The term "protein" is used to describe folded polypeptides that have secondary or tertiary structures. Proteins may consist of a single polypeptide or may comprise multiple polypeptides that are assembled to form a multimer. Multimers may be homo-oligomers or hetero-oligomers. Proteins may be naturally occurring, wild-type proteins, or modified or non-natural proteins. Proteins can differ from wild-type proteins by, for example, the addition, substitution, or deletion of one or more amino acids.

[0026] Protein “variants” include peptides, oligopeptides, polypeptides, proteins, and enzymes that have amino acid substitutions, deletions, and / or insertions relative to unmodified or wild-type proteins and have similar biological and functional activities to the unmodified proteins from which they originate. As used herein, the term “amino acid identity” refers to the degree to which sequences within a comparison window are identical on an amino acid-by-amino acid basis. Therefore, the “sequence identity percentage” is calculated by determining the number of positions in two best-aligned sequences on the comparison window where the same amino acid residues (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gln, Cys, and Met) appear in both sequences to obtain the number of matching positions. This number of matching positions is then divided by the total number of positions in the comparison window (i.e., the window size), and the result is multiplied by 100 to obtain the sequence identity percentage.

[0027] For all aspects and embodiments of the invention, the polypeptide “variant” has at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% complete sequence identity with the specified corresponding amino acid sequence. Sequence identity can also be identity with a fragment or portion of a full-length polynucleotide or polypeptide. Thus, a sequence may have only 50% overall sequence identity with a full-length reference sequence, but the sequence of a specific region, domain, or subunit may share 80%, 90%, or up to 99% sequence identity with the reference sequence.

[0028] The term "wild-type" refers to a gene or gene product isolated from a naturally occurring source. Wild-type genes are the most frequently observed genes in a population and are therefore arbitrarily engineered to be in their "normal" or "wild-type" form. Conversely, the terms "modified," "mutant," or "variant" refer to a gene or gene product that, when compared to a wild-type gene or gene product, exhibits modifications in its sequence (e.g., substitution, truncation, or insertion), post-translational modifications, and / or functional properties (e.g., altered characteristics).

[0029] Methods for introducing or replacing naturally occurring amino acids are well known in the art. For example, at the relevant position of a polynucleotide encoding a mutant monomer, arginine (R) can replace the methionine (ATG) codon by replacing the arginine (CGT) codon with the methionine (R) codon. Methods for introducing or replacing non-naturally occurring amino acids are also well known in the art. For example, non-naturally occurring amino acids can be introduced by including synthetic aminoacyl-tRNA in an IVTT system used to express the mutant monomer. Alternatively, they can be introduced by expressing the mutant monomer in the presence of synthetic (i.e., non-natural) analogs of those specific amino acids in *E. coli* that are auxotrophic for a particular amino acid. They can also be generated by naked linking if the mutant monomer is prepared using partial peptide synthesis. Conservative substitution replaces an amino acid with another amino acid having a similar chemical structure, similar chemical properties, or similar side chain volume. The introduced amino acids may have similar polarity, hydrophilicity, hydrophobicity, basicity, acidity, neutrality, or charge as the amino acid they replace. Alternatively, conservative substitution may introduce another aromatic or aliphatic amino acid to replace a pre-existing aromatic or aliphatic amino acid. Conservative amino acid alterations are well known in the art and can be selected based on the properties of the 20 major amino acids defined in Table 1 below. When amino acids have similar polarity, this can also be determined by referring to the hydrophilicity ranking of the amino acid side chains in Table 2.

[0030] Table 1 – Chemical Properties of Amino Acids

[0031] alanine Aliphatic, hydrophobic, neutral Methionine Hydrophobic and neutral Cysteine Polar, hydrophobic, neutral Asparagine Polar, hydrophilic, neutral Aspartic acid Polar, hydrophilic, charged (-) proline Hydrophobic and neutral glutamic acid Polar, hydrophilic, charged (-) glutamine Polar, hydrophilic, neutral Phenylalanine Aromatic, hydrophobic, neutral Arginine Polar, hydrophilic, charged (+) glycine aliphatic, neutral Serine Polar, hydrophilic, neutral Histidine Aroma group, polar, hydrophilic, charged (+) threonine Polar, hydrophilic, neutral Isoleucine Aliphatic, hydrophobic, neutral Valine Aliphatic, hydrophobic, neutral Lysine Polar, hydrophilic, charged (+) Tryptophan Aromatic, hydrophobic, neutral Leucine Aliphatic, hydrophobic, neutral Tyrosine Aroma, polar, hydrophobic

[0032] Table 2 – Hydrophilicity / Hydrophilicity Scale

[0033] side chain Hydrophilicity Isoleucine 4.5 Valine 4.2 Leucine 3.8 Phenylalanine 2.8 Cysteine 2.5 Methionine 1.9 alanine 1.8 glycine -0.4 threonine -0.7 Serine -0.8 Tryptophan -0.9 Tyrosine -1.3 proline -1.6 Histidine -3.2 glutamic acid -3.5 glutamine -3.5 Aspartic acid -3.5 Asparagine -3.5 Lysine -3.9 Arginine -4.5

[0034] Unless otherwise stated, the nucleic acid sequences in this article are written from left to right in the 5' to 3' direction.

[0035] As used herein, “polynucleotide,” “nucleotide sequence,” “DNA sequence,” or “nucleic acid molecule” refers to a polymeric form of nucleotides of any length, including ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Therefore, this term encompasses double-stranded and single-stranded DNA, as well as RNA. As used herein, the term “polynucleotide” can be a single-stranded or double-stranded covalently linked nucleotide sequence, wherein the 3' and 5' ends of each nucleotide are linked by a phosphodiester bond. Polynucleotides can consist of deoxyribonucleotide bases or ribonucleotide bases. Polynucleotides can be synthesized in vitro or isolated from natural sources. Polynucleotides can also contain modified DNA or RNA, such as methylated DNA or RNA, or RNA that has undergone post-translational modifications, such as 5' capping with 7-methylguanosine, 3' processing such as cleavage and polyadenylation, and splicing. Polynucleotides may also include synthetic nucleic acids (XNAs), such as hexetol nucleic acid (HNA), cyclohexene nucleic acid (CeNA), threonine nucleic acid (TNA), glycerol nucleic acid (GNA), locked nucleic acid (LNA), and peptide nucleic acid (PNA).

[0036] The terms “patient” and “subject” are used interchangeably and generally refer to mammals, preferably humans.

[0037] All publications, patents, and patent applications cited in this article, whether mentioned above or below, are incorporated herein in their entirety.

[0038] polypeptide

[0039] The present invention provides a polypeptide encoded by an open reading frame in a long non-coding RNA gene (lncRNA), wherein the lncRNA is overexpressed in colorectal cancer cells relative to healthy cells, preferably wherein the lncRNA is defined as any one of SEQ ID NO: 1 to 18.

[0040] lncRNAs are known in the art. The inventors have surprisingly discovered for the first time that some lncRNAs are overexpressed in colorectal cancer cells relative to healthy cells, and that polypeptides can be encoded by open reading frames (ORFs) in said cancer cells. Open reading frames, as known in the art, are polynucleotide sequences included in lncRNAs that begin with a start codon and end with a stop codon. Proteins are not typically considered to be translated from lncRNAs. However, the inventors have determined that polypeptides encoded by ORFs in lncRNAs overexpressed in colorectal cancer cells can be presented via the major histocompatibility complex (MHC) and thus elicit an immune response.

[0041] Overexpression of lncRNA in colorectal cancer cells relative to healthy cells can be detected by any suitable method in the art. Preferably, lncRNA expression can be observed in colorectal cancer cells, and its expression level is significantly higher than that in healthy cells. More preferably, expression is substantially not observed in healthy cells. Preferably, lncRNA expression in colorectal cancer cells is determined by the same method as lncRNA expression in healthy cells. Colorectal cancer cells and healthy cells can be derived from the same subject.

[0042] The present invention preferably provides a polypeptide encoded by an open reading frame of an lncRNA as defined by any of SEQ ID NO: 1-5, 7, 8, 11, 12 and 15-17.

[0043] The polypeptide may include at least 6 to 32 amino acids, preferably about 7 to 30 amino acids, and most preferably about 8 to 11 or about 12 to 28 amino acids.

[0044] The peptide is preferably capable of MHC presentation, wherein MHC is expressed on the surface of antigen-presenting cells (APCs). The peptide may be presented by MHC-I or MHC-II, with MHC-I presentation being most preferred. The peptide may include or consist of human leukocyte antigen (HLA) class I restricted epitopes. The peptide can be determined to be MHC-presented by any applicable method in the art, preferably MHC-I. Peptide presentation can be determined by an algorithm utilizing mass spectrometry-derived MHC ligand omics data. Most preferably, peptide presentation can be determined by combining a method utilizing mass spectrometry analysis of derived MHC ligand endogenous data to reliably predict presentation. An exemplary method is disclosed in WO2022 / 013154, the entire contents of which are incorporated herein by reference. This method uses the neoMS algorithm to reliably predict MHC presentation.

[0045] The peptide is preferably immunogenic, i.e., capable of evoking an immune response. An immune response can be detected in at least one individual (or a sample obtained from said individual) after the peptide is administered. The immune response is preferably a T-cell response. The peptide is preferably capable of stimulating CD4+ and / or CD8+ T cells, including CD8+ T cells capable of lysing cancer cells. The immunogenicity of the peptide can be determined by any suitable method in the art. Preferably, the immunogenicity of the peptide can be determined by an algorithm trained using a positive dataset consisting of non-autoimmunogenic peptide sequences and a negative dataset consisting of peptides derived from housekeeping genes and presented via MHCI. Most preferably, the immunogenicity of the peptide can be determined by incorporating an algorithm trained using a positive dataset consisting of non-autoimmunogenic peptide sequences and a negative dataset consisting of peptides derived from housekeeping genes and presented via MHCI. An exemplary method is disclosed in WO2022 / 079255, the entire contents of which are incorporated herein by reference. This method uses the neoIM algorithm to reliably predict immunogenicity.

[0046] Preferably, the algorithm used for presentation and immunogenicity considers a set of alleles common in European and American populations: HLA-I alleles (A*02:10, A*01:01, A*03:01, A*24:02, A*11:01, B*07:02, B*08:01, B*44:02, B*35:01, B*51:01, B*44:03, C*07:01, C*07:02, C*05:01, C*04:01, C*06:02, C*03:04).

[0047] The immunogenicity of a peptide can be further determined using any suitable method, including in vitro methods. For example, a peptide can be identified as immunogenic if it possesses at least one of the following characteristics: (i) It can elicit a pluripotent T-cell response (IFN-γ, IL-2 and / or TNF-α producing cells) in a PBL population of healthy subjects and / or cancer patients, as determined by ELISPOT assay, and / or (ii) It enables in situ detection of cytotoxic T lymphocytes (CTLs) that react with peptides in tumor tissue samples; and / or (iii) It can induce the in vitro growth of specific T cells.

[0048] Methods suitable for determining whether a peptide is immunogenic are also described in the following examples section.

[0049] The polypeptide may include a 6-amino acid sequence, a 7-amino acid sequence, an 8-amino acid sequence, a 9-amino acid sequence, a 10-amino acid sequence, or an 11-amino acid sequence, or variations thereof, including any polypeptide sequence as defined in SEQ ID NO: 19 to 97. Most preferably, the polypeptide may include an 8-amino acid sequence, or variations thereof, including any polypeptide sequence as defined in SEQ ID NO: 19 to 97.

[0050] The polypeptide may have at least 50%, at least 60%, at least 80%, at least 90%, or at least 95% sequence identity with an amino acid sequence of the same length included in any polypeptide sequence as defined in SEQ ID NO: 19 to 97. The polypeptide is preferably an 8-amino acid sequence and has at least 50%, at least 60%, at least 80%, at least 90%, or at least 95% sequence identity with an 8-amino acid sequence included in any polypeptide sequence as defined in SEQ ID NO: 19 to 97. Preferably, when the polypeptide is a variant, it should be capable of being presented by MHC class I molecules and possess immunogenicity.

[0051] The polypeptide preferably includes a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, included in any polypeptide sequence as defined in SEQ ID NO: 20~22, 29, 33~35, 46, 49, 51, 53, 55, 60, 62, 64, 67, 70, 76, 83 and 97.

[0052] The polypeptide may include, consist of, or be a variant of any polypeptide sequence as defined in SEQ ID NO: 98 to 611. A variant may have at least 50%, at least 60%, at least 80%, at least 90%, or at least 95% sequence identity with the amino acid sequence included in any polypeptide sequence as defined in SEQ ID NO: 98 to 611.

[0053] The preferred polypeptides include those listed in SEQ ID NO: 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 197, 200, 201, 209, 212, 215, 218, 222, 229, 216, 101, 103, 113, 122, 1 Any polypeptide sequence defined in 51, 152, 156, 172, 186, 189, 195, 204, 205, 208, 220, 227, 99, 100, 104, 105, 111, 123, 130, 131, 134, 136, 137, 138, 157, 159, 175, 182, 187, 188, 194, 203, 211, 221, and 234, or a polypeptide sequence thereof.

[0054] The polypeptide more preferably includes, or is composed of, any polypeptide sequence as defined in SEQ ID NO: 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 197, 200, 201, 209, 212, 215, 218, 222, 229, 216, 101, 103, 113, 122, 151, 152, 156, 172, 186, 189, 195, 204, 205, 208, 220, and 227. The polypeptide may also include any or more polypeptide sequences as defined in SEQ ID NO: 99, 100, 104, 105, 111, 123, 130, 131, 134, 136, 137, 138, 157, 159, 175, 182, 187, 188, 194, 203, 211, 221 and 234.

[0055] Even more preferably, the polypeptide comprises, or is composed of, any polypeptide sequence as defined in SEQ ID NO: 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 197, 200, 201, 209, 212, 215, 218, 222, 229, 216. The polypeptide may also include any or more polypeptide sequences as defined in SEQ ID NO:101, 103, 113, 122, 151, 152, 156, 172, 186, 189, 195, 204, 205, 208, 220, 227, 99, 100, 104, 105, 111, 123, 130, 131, 134, 136, 137, 138, 157, 159, 175, 182, 187, 188, 194, 203, 211, 221 and 234.

[0056] The polypeptides of the present invention may be in a substantially isolated form. They may be mixed with a carrier, preservative, or diluent (discussed in more detail below) and / or with an adjuvant (also discussed in more detail below) that does not interfere with the intended use, and are still considered substantially isolated. They may also be in a substantially purified form, in which case they typically comprise at least 90%, for example at least 95%, 98%, or 99%, of the protein in the formulation.

[0057] Polynucleotides, carriers and cells

[0058] This invention provides polynucleotides encoding one or more polypeptides of this invention.

[0059] Polynucleotides may encode a single polypeptide of the present invention. Other polynucleotides of the present invention may encode multiple polypeptides of the present invention, optionally wherein the coding sequences of multiple polypeptides are within each other's reading frames, and thus the polynucleotide molecule encodes a polypeptide comprising multiple polypeptides of the present invention in a continuous sequence.

[0060] The polynucleotide preferably encodes 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, or 70 or more polypeptides of the present invention. Preferably, the polynucleotide encodes 34 or more, 50 or more, or 73 or more polypeptides of the present invention. Most preferably, the polynucleotide encodes 34 or more, or 50 or more polypeptides of the present invention.

[0061] The polynucleotide preferably encodes 10 or more, 20 or more, or most preferably 34 or more polypeptides of the present invention, wherein the 34 or more polypeptides include 34 or more polypeptides encoded by open reading frames in lncRNAs as defined by any of SEQ ID NO: 1-5, 7, 8, 11, 12 and 15-17.

[0062] The polynucleotide preferably encodes 10 or more, 20 or more, or most preferably 34 or more polypeptides of the present invention, wherein each of the 34 or more polypeptides comprises a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, and is included in any polypeptide sequence as defined in SEQ ID NO: 20-22, 29, 33-35, 46, 49, 51, 53, 55, 60, 62, 64, 67, 70, 76, 83 and 97.

[0063] The polynucleotide preferably encodes 10 or more, 20 or more, or most preferably 34 or more polypeptides of the present invention, wherein each of the 34 or more polypeptides comprises, or is composed of, a polypeptide sequence as defined in SEQ ID NO: 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 197, 200, 201, 209, 212, 215, 218, 222, 229, 216.

[0064] The polynucleotide preferably encodes 10 or more, 20 or more, 30 or more, 40 or more, or most preferably 50 or more polypeptides of the present invention, wherein the 50 or more polypeptides include 50 or more polypeptides encoded by open reading frames in lncRNAs as defined by any of SEQ ID NO: 1-5, 7, 8, 11, 12 and 15-17.

[0065] The polynucleotide preferably encodes 10 or more, 20 or more, 30 or more, 40 or more, or most preferably 50 or more polypeptides of the present invention, wherein each of the 50 or more polypeptides comprises a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, and is included in any polypeptide sequence as defined in SEQ ID NO: 20-22, 29, 33-35, 46, 49, 51, 53, 55, 60, 62, 64, 67, 70, 76, 83 and 97.

[0066] The polynucleotides preferably encode 10 or more, 20 or more, 30 or more, 40 or more, or most preferably 50 or more polypeptides of the present invention, wherein each of the 50 or more polypeptides includes, as shown in SEQ ID NO: The polypeptide sequences defined as 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 173, 200, 201, 209, 212, 215, 218, 222, 229, 216, 101, 103, 113, 122, 151, 152, 156, 172, 186, 189, 195, 204, 205, 208, 220, and 227, or sequences thereof. The polynucleotide may also encode any or more polypeptides including, or composed of, sequences as defined in SEQ ID NO: 99, 100, 104, 105, 111, 123, 130, 131, 134, 136, 137, 138, 157, 159, 175, 182, 187, 188, 194, 203, 211, 221 and 234.

[0067] The polynucleotide may encode 10 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, or most preferably 73 or more polypeptides of the present invention, wherein the 73 or more polypeptides include 73 or more polypeptides encoded by open reading frames in lncRNAs as defined by any of SEQ ID NO: 1-5, 7, 8, 11, 12 and 15-17.

[0068] The polynucleotide preferably encodes 10 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, or most preferably 73 or more polypeptides of the present invention, wherein each of the 73 or more polypeptides comprises a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, and is included in any of the polypeptide sequences defined as in SEQ ID NO: 20-22, 29, 33-35, 46, 49, 51, 53, 55, 60, 62, 64, 67, 70, 76, 83 and 97.

[0069] The polynucleotides preferably encode 10 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, or most preferably 73 or more polypeptides of the present invention, wherein each of the 73 or more polypeptides includes, for example, SEQ ID NO: 98, 102, 106, 110, 115, 135, 139, 141, 144, 148, 153, 165, 166, 167, 168, 169, 173, 174, 176, 179, 183, 184, 191, 193, 197, 200, 201, 209, 212, 215, 218, 222, 229, 216, 101, 103, 113, 12 2, 151, 152, 156, 172, 186, 189, 195, 204, 205, 208, 220, 227, 99, 100, 104, 105, 111, 123, 130, 131, 134, 136, 137, 138, 157, 159, 175, 187, 188, 194, 203, 211, 221, and 234, or polypeptide sequences defined therein.

[0070] The generation and delivery of immunogenic peptides, enabling their efficient presentation on MHC molecules to elicit a desired immune response in an individual, can be challenging. The polynucleotides of this invention alleviate this problem by providing coding sequences for multiple peptides that conform to each other's reading frames; thus, the polynucleotide molecule encodes peptides comprising multiple peptides of this invention in a continuous sequence. In such polynucleotides, the peptides of this invention can be dispersed at cleavage sites recognized by proteases abundant in antigen-presenting cells (APCs). These methods mimic antigen processing and may potentially lead to more efficient antigen presentation than can be achieved by administering peptide antigens.

[0071] The terms "nucleic acid molecule" and "polynucleotide" are used interchangeably herein and refer to a polymer of nucleotides of any length, deoxyribonucleic acid or ribonucleic acid, or similar substances. Non-limiting examples of polynucleotides include genes, gene fragments, messenger RNA (mRNA), cDNA, recombinant polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. Most preferably, the polynucleotide is a DNA molecule, such as a cDNA molecule or an mRNA molecule.

[0072] When the polynucleotide of the present invention is mRNA, the polypeptide of the present invention is encoded by a nucleotide sequence included in an open reading frame (ORF). The mRNA may include a 5' cap at the 5' end, a 5' untranslated region (UTR) included in the ORF 5', a 3' UTR included in the ORF 3', and / or a 3' tail sequence at the 3' end. The "5' untranslated region (UTR)" is the region directly upstream (i.e., 5') of the start codon (i.e., the first codon of the ribosomally translated mRNA transcript) of the mRNA that does not encode a protein or peptide.

[0073] The “3’ untranslated region (UTR)” is the region directly downstream (i.e., the 3’) of an mRNA that does not encode a protein or peptide, and is the stop codon (i.e., the codon of the mRNA transcript that signals the termination of translation).

[0074] An open reading frame (ORF) is a continuous extension of DNA that begins with a start codon and ends with a stop codon, encoding proteins or peptides. The start codon is typically translated as methionine, most commonly ATG, although substitutions such as TTG, GTG, and CTG are also possible. When located at the beginning of the ORF, the substituted start codon is still translated as methionine, even if the codon encodes a different amino acid. The stop codon is usually chosen from TAA, TAG, or TGA.

[0075] A 5' cap is a specially modified nucleotide at the 5' end of some primary transcripts, such as messenger RNA, that promotes stability and translation. It typically consists of a guanine nucleotide linked to mRNA via an unusual 5'-5' triphosphate bond. This guanosine is immediately methylated at the 7-position after being capped by a methyltransferase in vivo. Therefore, it can be referred to as a 7-methylguanine cap, abbreviated as m7G. The preferred 5' cap is m7G(5')ppp(5')NlmpNp.

[0076] The 3' tail sequence is a polyA tail, a polyA-G tetrad, and / or a stem-loop sequence. The length of the 3' tail sequence is typically between 40 and 200 nucleotides. In some embodiments, the 3' tail sequence is a polyA tail. A "polyA tail" is a region of mRNA located downstream of the 3' UTR, such as directly downstream (i.e., 3'), containing multiple consecutive adenosine monophosphates (ATPs). A polyA tail can contain 10 to 300 ATPs. For example, a polyA tail can contain 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, or 300 ATPs. In some implementations, the polyA tail contains 50 to 250 adenosine monophosphates. In relevant biological environments (e.g., in cells, in vivo, etc.), the polyA tail functions to protect mRNA from enzymatic degradation, for example, in the cytoplasm, and to aid in transcription termination, mRNA export from the nucleus, and translation.

[0077] When the polynucleotide of the present invention is mRNA, it can be provided as an mRNA vaccine. The mRNA vaccine can be formulated as a lipid nanoparticle composition, for example, a lipid nanoparticle composition comprising mRNA encoding the polypeptide of the present invention and ionizable lipids.

[0078] The polynucleotides of this invention can be provided in isolated or substantially isolated form. Substantially isolated means that the polypeptide can be substantially, but not completely, isolated from any surrounding culture medium. The polynucleotides can be mixed with a vector or diluent that does not interfere with their intended use and are still considered substantially isolated. The nucleic acid sequence “encoding” the selected polypeptide is a nucleic acid molecule that, when placed under the control of appropriate regulatory sequences, such as in an expression vector, is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo. The boundaries of the coding sequence are defined by a start codon at the 5' (amino) end and a translation stop codon at the 3' (carboxyl) end. For the purposes of this invention, such nucleic acid sequences may comprise, but are not limited to, cDNA from viral, prokaryotic, or eukaryotic mRNA, genomic sequences from viral or prokaryotic DNA or RNA, or even synthetic DNA sequences. The transcription termination sequence may be located at the 3' end of the coding sequence.

[0079] The polynucleotides of this invention can function as mRNA, but differ from wild-type mRNA in function and / or structural characteristics. The mRNA cancer vaccine of this invention can be encoded by in vitro translated (IVT) polynucleotides. As used herein, “in vitro transcription template (IVT)” refers to deoxyribonucleic acid (DNA) suitable for IVT reactions to produce messenger RNA (mRNA). In some embodiments, the IVT template encodes a 5' untranslated region containing an open reading frame and encodes a 3' untranslated region and a polyA tail. The specific nucleotide sequence composition and length of the IVT template will depend on the target mRNA encoded by the template.

[0080] Polynucleotides may also encode polypeptide sequences known in the art for enhancing T cell activation, particularly in cancer vaccines. Those skilled in the art are familiar with example polypeptide sequences suitable for enhancing T cell activation. Therefore, the polynucleotides of the present invention may, for example, include sequences encoding LAMP1 and / or DC-LAMP domains.

[0081] Polynucleotides can be synthesized using methods well known in the art, such as those described in Sambrook et al. (1989, Molecular Cloning - a laboratory manual; Cold Spring Harbor Press). The nucleic acid molecules of the present invention can be provided in the form of expression cassettes containing a control sequence effectively linked to an insert sequence, thereby allowing the polypeptides of the present invention to be expressed in vivo. These expression cassettes are typically provided within a vector (e.g., a plasmid or recombinant viral vector). Such expression cassettes can be administered directly to a host subject. Alternatively, a vector comprising the polynucleotides of the present invention can be given to a host subject. Preferably, a gene vector is used to prepare and / or administer the polynucleotides. Suitable vectors can be any vector capable of carrying a sufficient amount of genetic information and allowing the expression of the polypeptides of the present invention.

[0082] mRNA can be prepared using any suitable technique and any suitable synthetic route known in the art. IVT is preferred. In vitro transcription (IVT) allows for template-guided synthesis of RNA molecules of virtually any sequence. RNA molecules that can be synthesized using IVT range in size from short oligonucleotides to long nucleic acid polymers of several thousand bases. In vitro transcription (IVT) can synthesize large quantities of RNA transcripts (e.g., from micrograms to milligrams) (Beckert et al, Synthesis of RNA by in vitro transcription, Methods Mol Biol. 703:29-41 (2011); Rio et al. RNA: A Laboratory Manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2011, 205-220.; Cooper, Geoffery M. The Cell: A Molecular Approach. 4th ed. Washington DC: ASM Press, 2007. 262-299). Typically, IVT utilizes a DNA template characterized by a promoter sequence upstream of the target sequence. The most common promoter sequences are phage-derived (e.g., T7, T3, or SP6 promoter sequences), but many other promoter sequences are tolerated, including those designed de novo. Transcription of the DNA template is generally best achieved using an RNA polymerase corresponding to a specific phage promoter sequence. Exemplary RNA polymerases include, but are not limited to, T7 RNA polymerase, T3 RNA polymerase, or SP6 RNA polymerase. IVT is typically initiated from dsDNA, but can be performed on a single strand. Suitable methods include, for example, those listed in WO2017 / 020026 (whose citation is incorporated herein by reference).

[0083] Therefore, the present invention comprises expression vectors including such polynucleotide sequences. Thus, the vector can encode a single polypeptide of the present invention. Therefore, other vectors of the present invention can encode multiple polypeptides of the present invention, optionally wherein the coding sequences of the multiple polypeptides are within each other's reading frames, thus the vector encodes polypeptides comprising multiple polypeptides of the present invention with consecutive sequences. The vector is preferably a viral vector.

[0084] Such expression vectors are routinely constructed in the field of molecular biology and may include, for example, plasmid DNA and appropriate initiators, promoters, enhancers, and other elements, such as polyadenylation signals, which may be necessary and oriented correctly to allow expression of the peptides of the present invention. Other suitable vectors will be apparent to those skilled in the art. Further examples in this regard can be found in Sambrook et al. (1989, Molecular Cloning - a laboratory manual; Cold Spring Harbor Press).

[0085] The present invention also provides a cell comprising a polynucleotide or viral vector as described herein. The cell may be a dendritic cell (DC), wherein the DC has been matured in vitro, wherein maturation includes transfection with a polynucleotide as described herein or infection with a viral vector of the present invention. Methods for DC maturation are well known in the art. When such cells are intended to be given to a patient in any of the treatments provided herein, it is preferred that the cells be genetically homologous to the patient.

[0086] Other cells used in this invention include prokaryotic cells, such as bacterial cells, such as *Escherichia coli*. Such prokaryotic cells can be engineered and cultured using conventional methods to produce the polypeptides of this invention.

[0087] The present invention also provides a cell, wherein the cell is a CAR-T cell, and wherein the cell includes a cell surface receptor generated against one or more of the polynucleotides of the present invention. Methods for modifying patient-derived T cells to express cell surface receptors against antigens (such as the peptides of the present invention) are known in the art. Therefore, CAR-T cells may include receptors capable of binding one or more peptides of the present invention. When such cells are intended to be given to a patient in any of the treatment methods provided herein, it is preferable that the cells are syngeneically homologous to the patient.

[0088] The present invention also provides a T cell that generates one or more polypeptides of the present invention.

[0089] Compositions including peptides, polynucleotides, or cells

[0090] The present invention provides a composition comprising the polypeptide of the present invention, the polynucleotide of the present invention, the carrier of the present invention, or the cell of the present invention, as well as a pharmaceutically acceptable carrier.

[0091] The composition may, for example, include at least two, at least three, at least four, at least five, at least six, at least seven, or at least eight different polypeptides of the present invention and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0092] The composition may, for example, include at least two, at least three, at least four, at least five, at least six, at least seven, or at least eight different polynucleotides of the present invention and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0093] The carrier, preservative, and excipients must be "acceptable," meaning compatible with the other components of the composition and harmless to the subject administering the composition. Typically, all components and the final composition are sterile and pyrogen-free. The composition may be a pharmaceutical composition. The composition may also preferably include an adjuvant.

[0094] An adjuvant is any substance incorporated into a composition that enhances or otherwise alters the immune response elicited by the composition. Adjuvants, broadly defined, are substances that promote an immune response. Adjuvants may also preferably have a storage effect, as they also result in a slow and sustained release of the active agent from the site of administration. An overview of adjuvants can be found in Goding, Monoclonal Antibodies: Principles & Practice (2). nd Available on pages 61-63 of the edition (1986).

[0095] The adjuvant may be selected from the group consisting of: AlK(SO4)2, AlNa(SO4)2, AlNH4(SO4)2, silicon dioxide, alum, Al(OH)3, Ca3(PO4)2, kaolin, carbon, aluminum hydroxide, muramyl dipeptide, N-acetylmuramyl-L-threonyl-D-isoglutamine (thr-DMP), N-acetylnormuramyl-L-alanyl-D-isoglutamine (CGP 11687, also known as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutamine-L-alanine-2-(1',2'-dipalmitoyl-sn-glycerol-3-hydroxyphosphoryloxy)ethylamine (CGP). RIBI (MPL+TDM+CWS) in 19835A (also known as MTP-PE), 2% squalene / Tween-80® emulsion, lipopolysaccharides and their various derivatives, including lipid A, Freund's complete adjuvant (FCA), Freund's incomplete adjuvant, Merck adjuvant 65, polynucleotides (e.g., polyIC and polyAU acid), Mycobacterium tuberculosis wax D, substances found in tuberculosis, Corynebacterium breve, Bordetella pertussis, and Brucella members, Titermax, ISCOMS, Quil A, ALUN (see US58767 and 5,554,372), lipid A derivatives, cholera toxin derivatives, HSP derivatives, LPS derivatives, synthetic peptide matrix or GMDP, interleukin-1, interleukin-2, Montanide ISA-51, and QS-21. Several saponin extracts have been suggested for use as adjuvants in immunogenic compositions. Granulocyte-macrophage colony-stimulating factor (GM-CSF) can also be used as an adjuvant.

[0096] Preferred adjuvants used in this invention include oil / surfactant-based adjuvants, such as Montanide adjuvant (available from Seppic, Belgium), preferably Montanide ISA-51. Other preferred adjuvants are bacterial DNA-based adjuvants, such as adjuvants containing CpG oligonucleotide sequences. Other preferred adjuvants are viral dsRNA-based adjuvants, such as poly I:C. GM-CSF and imidazoquinone are also examples of preferred adjuvants.

[0097] The preferred adjuvant is Montanide ISA adjuvant. The preferred Montanide ISA adjuvants are Montanide ISA 51 or Montanide ISA 720.

[0098] In Goding, Monoclonal Antibodies: Principles & Practice (2 ndPages 61-63 of the 1986 edition also note that conjugation with an immunogenic carrier is recommended when the target antigen is of low molecular weight or poor immunogenicity. Therefore, the peptides of the present invention can be conjugated with a carrier. The carrier can exist independently of the adjuvant. The function of the carrier can be, for example, to increase the molecular weight of the peptide fragment to increase activity or immunogenicity, impart stability, increase biological activity, or increase serum half-life. Furthermore, the carrier can facilitate the presentation of the peptide or fragment thereof to T cells. Therefore, in the composition, the peptide can be bound to a carrier, such as those listed below.

[0099] The carrier can be any suitable carrier known to those skilled in the art, such as commonly used carrier proteins or antigen-presenting cells like dendritic cells (DCs). Carrier proteins include keyhole hemocyanin, serum proteins such as transferrin, bovine serum albumin, human serum albumin, thyroglobulin or ovalbumin, immunoglobulins, or hormones such as insulin or palmitic acid. Alternatively, the carrier protein can be tetanus toxoid or diphtheria toxoid. Alternatively, the carrier can be a dextran, such as agarose. The carrier must be physiologically acceptable and safe for humans.

[0100] If the composition includes excipients, they must be "pharmaceutical acceptable," meaning they are compatible with the other components of the composition and harmless to the recipient. Excipients may include auxiliary substances such as wetting agents or emulsifiers, pH buffers, etc. These excipients and auxiliary substances are generally agents that do not induce an immune response in the individual receiving the composition and can be administered without excessive toxicity. Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethylene glycol, hyaluronic acid, glycerin, and ethanol. Pharmaceutically acceptable salts may also be included, such as inorganic acid salts such as hydrochloride, hydrobromide, phosphate, sulfate, etc.; and salts of organic acids such as acetate, propionate, malonate, benzoate, etc. For a detailed discussion of pharmaceutically acceptable excipients, carriers, and auxiliary substances, see Remington's Pharmaceutical Sciences (Mack Pub.Co., NJ1991).

[0101] Suitable compositions can be formulated using standard pharmaceutical formulation chemistry and methods, all of which are readily available to those skilled in the art. Such compositions can be prepared, packaged, or marketed in forms suitable for rapid, concentrated administration or continuous administration. Injectable compositions can be prepared, packaged, or marketed in unit dosage forms, such as in ampoules or optional multi-dose containers containing preservatives. Compositions comprise, but are not limited to, suspensions, solutions, emulsions in oily or aqueous media, pastes, and implantable, sustained-release, or biodegradable formulations. In one embodiment of the composition, the active ingredient is provided in dry (e.g., powder or granules) form for reconstitution with a suitable media (e.g., sterile, pyrogen-free water) prior to administration of the reconstituted composition. Compositions can be prepared, packaged, or marketed as sterile injectable aqueous or oily suspensions or solutions. This suspension or solution can be formulated according to known techniques and may include additional components such as adjuvants, excipients, and excipients as described herein, in addition to the active ingredient. Such sterile injectable formulations can be prepared using non-toxic, parenteral-acceptable diluents or solvents, such as water or 1,3-butanediol. Other acceptable diluents and solvents include, but are not limited to, Ringer's solution, isotonic sodium chloride solution, and fixed oils such as synthetic monoglycerides or diglycerides. Other useful compositions include those containing active ingredients in microcrystalline form, in liposome formulations, or as components of biodegradable polymer systems. Compositions for sustained release or implantation may include pharmaceutically acceptable polymers or hydrophobic materials, such as emulsions, ion exchange resins, slightly soluble polymers, or slightly soluble salts. Alternatively, the active ingredient of the composition may be encapsulated, adsorbed onto a particulate carrier, or bound to a particulate carrier. Suitable particulate carriers include those derived from polymethyl methacrylate polymers, as well as PLG microparticles derived from poly(lactide) and poly(lactide-co-glycolic acid). See, for example, Jeffery et al. (1993) Pharm. Res. 10:362-368. Other particulate systems and polymers may also be used, such as polymers like polylysine, polyarginine, polyornithine, spermine, spermidine, and conjugates of these molecules.

[0102] The compositions of the present invention may be polynucleotide vaccines, preferably wherein the polynucleotide is DNA or mRNA, most preferably wherein the polynucleotide is mRNA, and the compositions include mRNA (cancer) vaccines.

[0103] mRNA cancer vaccines may be formulated with one or more excipients to: (1) increase stability; (2) increase cell transfection; (3) allow sustained or delayed release (e.g., from a reservoir formulation); (4) alter biodistribution (e.g., targeting specific tissues or cell types); (5) increase the translation of encoded proteins in vivo; and / or (6) alter the release profile of encoded proteins (antigens) in vivo. In addition to conventional excipients such as any and all solvents, dispersion media, diluents or other liquid media, dispersing or suspending agents, surfactants, isotonic agents, thickeners or emulsifiers, and preservatives, the excipients of the present invention may comprise, but are not limited to, lipids, liposomes, lipid nanoparticles, polymers, lipid complexes, core-shell nanoparticles, peptides, proteins, cells transfected with mRNA cancer vaccines (e.g., for transplantation into subjects), hyaluronidase, nanoparticle mimics, and combinations thereof.

[0104] The mRNAs and / or compositions disclosed herein may contain stabilizing elements. Naturally occurring eukaryotic mRNA molecules have been found to contain stabilizing elements, including, but not limited to, the 5' and 3' UTRs, 5' caps, and 3' tails discussed elsewhere herein. Other stabilizing elements that may be included in the mRNAs disclosed herein may include, for example, histone stem-loops. In some embodiments, the histone stem-loop is typically derived from histone genes and comprises intramolecular base pairings of two adjacent partially or completely inversely complementary sequences separated by spacers consisting of short sequences forming a loop. The mRNA may have one or more AU-rich sequences removed. Such sequences may be unstable. RNA vaccines may contain or not contain enhancer and / or promoter sequences, which may be modified or unmodified, or activated or inactivated.

[0105] In a preferred embodiment, the mRNA cancer vaccine may be formulated in a lipid-polycationic complex. The formation of the lipid-polycationic complex may be achieved by methods known in the art and / or as described in U.S. Publication No. 20120178702, the entire contents of which are incorporated herein by reference. As a non-limiting example, the polycation may comprise cationic peptides or polypeptides, such as, but not limited to, polylysine.

[0106] Polyornithine and / or polyarginine and the cationic peptides described in International Publication No. WO2012013326 or US Publication No. US20130142818, each of which is incorporated herein by reference in its entirety. In another embodiment, the mRNA cancer vaccine may be formulated as a lipid-polycationic complex, which may also contain non-cationic lipids, such as, but not limited to, cholesterol or dioleoylphosphatidylethanolamine (DOPE). The liposome formulation may be influenced by, but is not limited to, the selection of the cationic lipid component, the saturation of the cationic lipid, the nature of PEGylation, the proportions of all components, and biophysical parameters such as size. In one example by Semple et al. (Semple et al. Nature Biotech. 2010 28: 172-176; incorporated herein by reference in its entirety), the liposome formulation consisted of 57.1% cationic lipids, 7.1% dipalmitoylphosphatidylcholine, 34.3% cholesterol, and 1.4% PEG-c-DMA. As another example, altering the composition of cationic lipids can more effectively deliver siRNA to various antigen-presenting cells (Basha et al. Mol Ther. 2011 19:2186-2200; cited in full hereto).

[0107] Liposome formulations may comprise about 35% to about 45% cationic lipids, about 40% to about 50% cationic lipids, about 50% to about 60% cationic lipids, and / or about 55% to about 65% cationic lipids. In some embodiments, the lipid-to-mRNA ratio in the liposomes may be from about 5:1 to about 20:1, from about 10:1 to about 25:1, from about 15:1 to about 30:1, and / or at least 30:1. In some embodiments, the proportion of PEG in the lipid nanoparticle (LNP) formulation may be increased or decreased, and / or the carbon chain length of the PEG lipids may be modified from C14 to C18 to alter the pharmacokinetics and / or biodistribution of the LNP formulation. As a non-limiting example, the LNP formulation may contain about 0.5% to about 3.0%, about 1.0% to about 3.5%, about 1.5% to about 4.0%, about 2.0% to about 4.5%, about 2.5% to about 5.0% and / or about 3.0% to about 6.0% of PEG-c-DOMG (R-3-[(comethoxy-poly(ethylene glycol)2000)carbamoyl)]-1,2-dimyristyloxypropyl-3-amine) (also referred to herein as PEG-DOMG) in a lipid molar ratio to cationic lipids, DSPC, and cholesterol. In another embodiment, PEG-c-DOMG may be replaced by PEG lipids, such as, but not limited to, PEG-DSG (1,2-distearyl-sn-glycerol, methoxy polyethylene glycol), PEG-DMG (1,2-dimyristyl-sn-glycerol), and / or PEG-DPG (1,2-dipalmitoyl-sn-glycerol, methoxy polyethylene glycol). The cationic lipid may be selected from any lipid known in the art, such as, but not limited to, DLin-MC3-DMA, DLin-DMA, C12-200 and DLin-KC2-DMA.

[0108] The mRNA cancer vaccine formulation comprising polynucleotides may be nanoparticles comprising at least one lipid. The lipid may be selected from, but is not limited to, DLin-DMA, DLin-K-DMA, 98N12-5, C12-200, DLin-MC3-DMA, DLin-KC2-DMA, DODMA, PLGA, PEG-DMG, PEGylated lipids, and amino alcohol lipids. Alternatively, the lipid may be a cationic lipid, such as, but not limited to, DLin-DMA, DLin-D-DMA, DLin-MC3-DMA, DLin-KC2-DMA, DODMA, and amino alcohol lipids. The amino alcohol cationic lipid may be a lipid described in and / or prepared by the method described in U.S. Patent Publication No. US20130150625, the entire contents of which are incorporated herein by reference. As non-limiting examples, the cationic lipid may be 2-amino-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-{[(9Z,2Z)-octadec-9,12-dien-1-yloxy]methyl}prop-1-ol (compound 1 in US20130150625); 2-amino-3-[(9Z)-octadec-9-en-1-yloxy]-2-{[(9Z)-octadec-9-en-1-yloxy]methyl}prop-1-ol (compound 2 in US20130150625); -amino-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-[(octoxy)methyl]prop-1-ol (compound 3 in US20130150625); and 2-(dimethylamino)-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-{[(9Z,12Z)-octadec-9,12-dien-1-yloxy]methyl}prop-1-ol (compound 4 in US20130150625); or any pharmaceutically acceptable salt or stereoisomer thereof.

[0109] Lipid nanoparticle formulations typically include lipids, particularly ionizable cationic lipids, such as 2,2-dilinoleo-4-dimethylaminoethyl-[1,3]-dioxacyclopentane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), or 9-((4-(dimethylamino)butyryl)oxy)heptadecanoic acid di((Z)-non-2-en-1-yl) ester (L319), and also include neutral lipids, sterols, and molecules that can reduce particle aggregation, such as PEG or PEG-modified lipids. The lipid nanoparticle formulation may consist essentially of: (i) at least one lipid selected from the group consisting of 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319); (ii) neutral lipids selected from DSPC, DPPC, POPC, DOPE, and SM; (iii) sterols, such as cholesterol; and (iv) PEG lipids, such as PEG-DMG or PEG-cDMA, in a molar ratio of about 20-60% cationic lipids: 5-25% neutral lipids: 25-55% sterols: 0.5-15% PEG-lipids. The formulation may contain, on a molar basis, about 25% to about 75% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxacyclopentane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), for example, on a molar basis, about 35% to about 65%, about 45% to about 65%, about 60%, about 57.5%, about 50%, or about 40%.

[0110] The formulation may contain, in molar amounts, about 0.5% to about 15% of neutral lipids, such as about 3% to about 12%, about 5% to about 10%, or about 15%, about 10%, or about 7.5% in molar amounts. Exemplary neutral lipids include, but are not limited to, DSPC, POPC, DPPC, DOPE, and SM. The formulation may contain, in molar amounts, about 5% to about 50% of sterols (e.g., about 15% to about 45%, about 20% to about 40%, about 40%, about 38.5%, about 35%, or about 31% in molar amounts). An exemplary sterol is cholesterol. The formulation may contain, in molar amounts, about 0.5% to about 20% of PEG or PEG-modified lipids (e.g., about 0.5% to about 10%, about 0.5% to about 5%, about 1.5%, about 0.5%, about 3.5%, or about 5% in molar amounts). PEG or PEG-modified lipids may include PEG molecules with an average molecular weight of 2,000 Da or less than 2,000 Da, such as about 1,500 Da, about 1,000 Da, or about 500 Da. Exemplary PEG-modified lipids include, but are not limited to, PEG distearate (PEG-DMG) (also referred to herein as PEG-C14 or C14-PEG) and PEG-cDMA (detailed in Reyes et al. J. Controlled Release, 107, 276-287 (2005), the entire contents of which are incorporated herein by reference).

[0111] The formulation may contain, on a molar basis, 25% to 75% of cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 0.5% to 15% of neutral lipids, 5% to 50% of sterols, and 0.5% to 20% of PEG or PEG-modified lipids.

[0112] In one embodiment, the formulation of the present invention comprises, on a molar basis, 35%-65% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 3%-12% of neutral lipids, 15%-45% of sterols, and 0.5%-10% of PEG or PEG-modified lipids.

[0113] The formulation herein may contain, on a molar basis, 45%-65% of cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 5%-10% of neutral lipids, 25%-40% of sterols, and 0.5%-10% of PEG or PEG-modified lipids.

[0114] The formulation herein may contain, on a molar basis, approximately 60% of cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), approximately 7.5% of neutral lipids, approximately 31% of sterols, and approximately 1.5% of PEG or PEG-modified lipids.

[0115] The formulation herein may contain, on a molar basis, approximately 50% of cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), approximately 10% of neutral lipids, approximately 38.5% of sterols, and approximately 1.5% of PEG or PEG-modified lipids.

[0116] The formulation herein may contain, on a molar basis, approximately 50% cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), approximately 10% neutral lipids, approximately 35% sterols, approximately 4.5% or approximately 5% PEG or PEG-modified lipids, and approximately 0.5% targeted lipids.

[0117] The formulation herein may contain, on a molar basis, approximately 40% of cationic lipids selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxacyclopentane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), approximately 15% of neutral lipids, approximately 40% of sterols, and approximately 5% of PEG or PEG-modified lipids.

[0118] In one embodiment, the formulation comprises, on a molar basis, about 57.2% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), about 7.1% of a neutral lipid, about 34.3% of a sterol, and about 1.4% of PEG or PEG-modified lipids.

[0119] The formulation herein may contain, on a molar basis, approximately 57.5% of cationic lipids selected from PEG lipids and of PEG-cDMA (PEG-cDMA is discussed in detail in Reyes et al. (J. Controlled Release, 107, 276-287 (2005), the contents of which are cited in full and incorporated herein by reference), approximately 7.5% of neutral lipids, approximately 31.5% of sterols, and approximately 3.5% of PEG or PEG-modified lipids.

[0120] In a preferred embodiment, the lipid nanoparticle formulation is essentially composed of a lipid mixture, wherein the molar ratio is about 20-70% cationic lipids: 5-45% neutral lipids: 20-55% cholesterol: 0.5-15% PEG-modified lipids; more preferably, the molar ratio is about 20-60% cationic lipids: 5-25% neutral lipids: 25-55% cholesterol: 0.5-15% PEG-modified lipids.

[0121] In a specific embodiment, the lipid molar ratio is approximately 50 / 10 / 38.5 / 1.5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG-modified lipids, such as PEG-DMG, PEG-DSG, or PEG-DPG), 57.2 / 7.11 / 34.3 / 1.4 (mol% cationic lipids / neutral lipids, such as...

[0122] DPPC / Chol / PEG modified lipids, such as PEG-cDMA), 40 / 15 / 40 / 5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG), 50 / 10 / 35 / 4.5 / 0.5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DSG).

[0123] 50 / 10 / 35 / 5 (cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG), 40 / 10 / 40 / 10 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA), 35 / 15 / 40 / 10 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA), or 52 / 13 / 30 / 5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA).

[0124] Exemplary lipid nanoparticle compositions and their preparation methods are found, for example, in Semple et al. (2010) Nat. Biotechnol. 28: 172-176; Jayarama et al. (2012), Angew. Chem. Int. Ed., 51: 8529-8533; and Maier et al. (2013) Molecular Therapy 21, 1570-1578 (each of which is incorporated herein by reference in its entirety).

[0125] The lipid nanoparticle formulations described herein may include cationic lipids, PEG lipids, and structured lipids, and optionally include non-cationic lipids. As a non-limiting example, the lipid nanoparticles may include about 40-60% cationic lipids, about 5-15% non-cationic lipids, about 1-2% PEG lipids, and about 30-50% structured lipids. As another non-limiting example, the lipid nanoparticles may include about 50% cationic lipids, about 10% non-cationic lipids, about 1.5% PEG lipids, and about 38.5% structured lipids. As yet another non-limiting example, the lipid nanoparticles may include about 55% cationic lipids, about 10% non-cationic lipids, about 2.5% PEG lipids, and about 32.5% structured lipids. In one embodiment, the cationic lipid may be any cationic lipid described herein, such as, but not limited to, DLin-KC2-DMA, DLin-MC3-DMA, and L319.

[0126] The lipid nanoparticle formulations described herein may be four-component lipid nanoparticles. The lipid nanoparticles may include cationic lipids, non-cationic lipids, PEG lipids, and structural lipids. As a non-limiting example, the lipid nanoparticles may include about 40-60% cationic lipids, about 5-15% non-cationic lipids, about 1-2% PEG lipids, and about 30-50% structural lipids. As another non-limiting example, the lipid nanoparticles may include about 50% cationic lipids, about 10% non-cationic lipids, about 1.5% PEG lipids, and about 38.5% structural lipids. As yet another non-limiting example, the lipid nanoparticles may include about 55% cationic lipids, about 10% non-cationic lipids, about 2.5% PEG lipids, and about 32.5% structural lipids. In one embodiment, the cationic lipids may be any cationic lipid described herein, such as, but not limited to, DLin-KC2-DMA, DLin-MC3-DMA, and L319.

[0127] The lipid nanoparticle formulations described herein may include cationic lipids, non-cationic lipids, PEG-coated lipids, and structured lipids. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-KC2-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG-coated lipid PEG-DOMG, and approximately 38.5% structured lipid cholesterol. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-MC3-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG-coated lipid PEG-DOMG, and approximately 38.5% structured lipid cholesterol. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-MC3-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG-coated lipid PEG-DMG, and approximately 38.5% structured lipid cholesterol. As another non-limiting example, the lipid nanoparticles comprise approximately 55% cationic lipid L319, approximately 10% noncationic lipid DSPC, approximately 2.5% PEG lipid PEG-DMG, and approximately 32.5% structural lipid cholesterol.

[0128] The relative amounts of the active ingredient, pharmaceutically acceptable excipients, and / or other additives in the pharmaceutical compositions according to this disclosure may vary, depending on the individual attributes, body size, and / or physical condition of the subject to be treated, and also on the route of administration of the composition. For example, the composition may include 0.1% to 99% (w / w) of the active ingredient. For example, the composition may include between 0.1% and 100%, such as between 5% and 50%, between 1% and 30%, between 5% and 80%, or at least 80% (w / w) of the active ingredient.

[0129] mRNA cancer vaccine compositions may include the polynucleotides described herein, formulated in lipid nanoparticles comprising MC3, cholesterol, DSPC and PEG2000-DMG, buffered trisodium citrate, sucrose and water for injection. As a non-limiting example, the composition comprises: 2.0 mg / mL of a drug (e.g., a polynucleotide encoding H10N8 influenza virus), 21.8 mg / mL of MC3, 10.1 mg / mL of cholesterol, 5.4 mg / mL of DSPC, 2.7 mg / mL of PEG2000-DMG, 5.16 mg / mL of trisodium citrate, 71 mg / mL of sucrose, and approximately 1.0 mL of water for injection.

[0130] RNA vaccines can be formulated using one or more liposomes, lipid complexes, or lipid nanoparticles. The pharmaceutical composition of an RNA vaccine may contain liposomes. Liposomes are artificially prepared vesicles that may consist primarily of a lipid bilayer and can be used as delivery carriers for administering nutrients and pharmaceutical formulations. Liposomes can have different sizes, such as, but not limited to, multilayer vesicles (MLVs) with diameters of hundreds of nanometers and containing a series of concentric bilayers separated by narrow aqueous compartments, small single-cell vesicles (SUVs) with diameters less than 50 nm, and large monolayer vesicles (LUVs) with diameters between 50 and 500 nm. Liposome design may include, but not limited to, opsonins or ligands to improve liposome attachment or activation events with unhealthy tissues, such as, but not limited to, endocytosis. Liposomes may contain low or high pH to improve the delivery of pharmaceutical formulations. The formation of liposomes may depend on their physicochemical properties, such as, but not limited to, the encapsulated pharmaceutical formulation and liposome components, the properties of the lipid vesicle dispersion medium, the effective concentration of the encapsulated substance and its potential toxicity.

[0131] Any additional processes involved in the application and / or delivery of vesicles, the optimized size, polydispersity, and shelf life of vesicles for the intended application, and the possibility of batch-to-batch reproducibility and large-scale production of safe and effective liposome products.

[0132] As a non-limiting example, liposomes, such as synthetic membrane vesicles, can be prepared by the methods, apparatus, and devices described in U.S. Patent Publications US20130177638, US20130177637, US20130177636, US20130177635, US20130177634, US20130177633, US20130183375, US20130183373, and US20130183372, the contents of which are incorporated herein by reference in their entirety. The pharmaceutical compositions described herein include, but are not limited to, liposomes, such as DiLa2 liposomes from Marina Biotech (Bothell, WA), 1,2-dilinoleoyloxy-3-dimethylaminopropane (DLin-DMA), 2,2-dilinoleoyl-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), and MC3 (US20100324120, the entire contents of which are incorporated herein by reference); and liposomes capable of delivering small molecule drugs, such as, but not limited to, DOXIL® from Janssen Biotech (Horsham, WA).

[0133] The pharmaceutical compositions described herein include, but are not limited to, liposomes, such as those synthesized from stable plasmid-lipid particles (SPLPs) or stable nucleic acid-lipid particles (SNALPs); which have been reported in the literature and demonstrated to be suitable for the in vitro and in vivo delivery of oligonucleotides (see Wheeler et al. Gene Therapy. 1999 6:271-281; ​​Zhang et al. Gene Therapy. 1999 6: 1438-1447; Jeffs et al. Pharm Res. 2005 22:362-372; Morrissey et al., Nat Biotechnol. 2005 2: 1002-1007; Zimmermann et al., Nature. 2006 441: 111-114; Heyes et al. J Contr Rel. 2005 107:276-287; Semple et al. Nature Biotech. 2010 28: 172-176; Judge et al. J Clin Invest. 2009 119:661-673; de Fougerolles Hum Gene Ther. 2008 19: 125-132; US Patent Publication No. US20130122104; the entire contents of which are incorporated herein by reference. Wheeler et al.'s initial manufacturing method was a detergent dialysis method, which was later improved by Jeffs et al. and termed the spontaneous vesicle formation method. The liposome formulation consists of 3 to 4 lipid components other than polynucleotides.

[0134] For example, liposomes may contain, but are not limited to, 55% cholesterol, 20% distearylphosphatidylcholine (DSPC), 10% PEG-S-DSG, and 15% 1,2-dioleoyloxy-N,N-dimethylaminopropane (DODMA), as described by Jeffs et al. As another example, certain liposome formulations may contain, but are not limited to, 48% cholesterol, 20% distearylphosphatidylcholine (DSPC), 2% PEG-c-DMA, and 30% cationic lipids, wherein the cationic lipids may be 1,2-distearyloxy-N,N-dimethylaminopropane (DSDMA), DODMA, DLin-DMA, or 1,2-dilinoyloxy-3-dimethylaminopropane (DLenDMA), as described by Heyes et al.

[0135] The liposome formulation may include about 25.0% to about 40.0% cholesterol, about 30.0% to about 45.0% cholesterol, about 35.0% to about 50.0% cholesterol, and / or about 48.5% to about 60% cholesterol. In a preferred embodiment, the formulation may include a cholesterol percentage selected from 28.5%, 31.5%, 33.5%, 36.5%, 37.0%, 38.5%, 39.0%, and 43.5%. In some embodiments, the formulation may include about 5.0% to about 10.0% DSPC and / or about 7.0% to about 15.0% DSPC.

[0136] Pharmaceutical compositions may comprise liposomes, which may be formed to deliver polynucleotides encoding at least one immunogen (antigen) or any other target polypeptide. RNA vaccines may be encapsulated in liposomes and / or contained in an aqueous core that may subsequently be encapsulated in liposomes (see International Publications WO2012031046, WO2012031043, WO2012030901 and WO2012006378 and U.S. Patent Publications US20130189351, US20130195969 and US20130202684, the contents of which are incorporated herein by reference in their entirety).

[0137] Liposomes can be formulated for targeted delivery. As a non-limiting example, liposomes can be formulated for targeted delivery to the liver. Liposomes for targeted delivery may include, but are not limited to, the liposomes and methods for preparing liposomes described in U.S. Patent Publication No. US20130195967, the entire contents of which are incorporated herein by reference.

[0138] In another embodiment, a polynucleotide encoding an immunogen (antigen) may be formulated in a cationic oil-in-water emulsion; wherein the emulsion particles include an oil core and cationic lipids that can interact with the polynucleotide to anchor the molecule to the emulsion particles (see International Publication No. WO2012006380; the entire contents of which are incorporated herein by reference).

[0139] RNA vaccines can also be formulated as water-in-oil emulsions comprising a continuous hydrophobic phase, wherein a hydrophilic phase is dispersed within the continuous hydrophobic phase. As a non-limiting example, the emulsion can be prepared by the method described in International Publication No. WO201087791, the entire contents of which are incorporated herein by reference. Lipid formulations may comprise at least a cationic lipid, a transfection-enhancing lipid, and at least one lipid having a lipid moiety having a hydrophilic head group attached (International Publication No. WO2011076807, US Publication No. US20110200582; the entire contents of which are incorporated herein by reference). In another embodiment, a polynucleotide encoding an immunogen can be formulated in lipid vesicles, and the functionalized lipid bilayers of the lipid vesicles may have a cross-linked structure (see US Patent Publication No. US20120177724, the entire contents of which are incorporated herein by reference).

[0140] Polynucleotides can be formulated in liposomes as described in International Patent Publication No. WO2013086526, the entire contents of which are incorporated herein by reference. RNA vaccines can be encapsulated in liposomes using a reverse pH gradient and / or an optimized internal buffer composition, as described in International Patent Publication No. WO2013086526, the entire contents of which are incorporated herein by reference.

[0141] RNA vaccine drug compositions can be formulated in liposomes, including but not limited to DiLa2 liposomes (Marina Biotech, Bothell, WA), SMARTICLES® liposomes (Marina Biotech, Bothell, WA), liposomes based on neutral DOPC (1,2-dioleoyl-sn-glycerol-3-phosphocholine) (e.g. for siRNA delivery in ovarian cancer (Landene et al. Cancer Biology & Therapy 2006 5(12)1708-1713); cited in full hereto), and hyaluronic acid-coated liposomes (Quiet Therapeutics, Israel).

[0142] The cationic lipids may be low molecular weight cationic lipids, such as those described in U.S. Patent Application 20130090372, the entire contents of which are incorporated herein by reference.

[0143] RNA vaccines can be formulated in lipid vesicles, which can have cross-links between functionalized lipid bilayers.

[0144] RNA vaccines can be formulated in liposomes comprising cationic lipids. The liposomes may have a molar ratio (N:P ratio) of nitrogen atoms in the cationic lipids to phosphate groups in the RNA of 1:1 to 20:1, as described in International Patent Publication No. WO2013006825, the entire contents of which are incorporated herein by reference. In another embodiment, the liposomes may have an N:P ratio greater than 20:1 or less than 1:1.

[0145] RNA vaccines can be formulated as lipid-polycationic complexes. The formation of lipid-polycationic complexes can be achieved by methods known in the art and / or as described in U.S. Publication No. 20120178702, the entire contents of which are incorporated herein by reference. As a non-limiting example, the polycation may comprise cationic peptides or polypeptides, such as, but not limited to, polylysine, polyornithine, and / or polyarginine, and cationic peptides as described in International Publication No. WO2012013326 or U.S. Patent Publication No. US20130142818, each of which is incorporated herein by reference in its entirety. In another embodiment, the RNA vaccine can be formulated as a lipid-polycationic complex, which may also comprise non-cationic lipids, such as, but not limited to, cholesterol or dioleoylphosphatidylethanolamine (DOPE).

[0146] RNA vaccines can be formulated into amino alcohol liposomes. The amino alcohol liposomes usable in this invention can be prepared by the method described in U.S. Patent No. 8,450,298, the entire contents of which are incorporated herein by reference.

[0147] Liposome formulations can be influenced by, but are not limited to, the choice of cationic lipid components, the saturation of cationic lipids, the nature of PEGylation, the proportions of all components, and biophysical parameters such as size. In one example by Semple et al. (Semple et al. Nature Biotech. 2010 28: 172-176; cited in full hereinafter), the liposome formulation consisted of 57.1% cationic lipids, 7.1% dipalmitoylphosphatidylcholine, 34.3% cholesterol, and 1.4% PEG-c-DMA. As another example, altering the composition of cationic lipids can more effectively deliver siRNA to various antigen-presenting cells (Basha et al. Mol Ther. 2011 19:2186-2200; cited in full hereinafter). In some embodiments, the liposome formulation may comprise about 35 to about 45% cationic lipids, about 40% to about 50% cationic lipids, about 50% to about 60% cationic lipids, and / or about 55% to about 65% cationic lipids. In some embodiments, the lipid-to-mRNA ratio in the liposomes may be from about 5:1 to about 20:1, from about 10:1 to about 25:1, from about 15:1 to about 30:1, and / or at least 30:1.

[0148] In some embodiments, the proportion of PEG in the lipid nanoparticle (LNP) formulation may be increased or decreased and / or the carbon chain length of the PEG lipid may be modified from C14 to C18 to alter the pharmacokinetics and / or biodistribution of the LNP formulation. As a non-limiting example, the LNP formulation may contain about 0.5% to about 3.0%, about 1.0% to about 3.5%, about 1.5% to about 4.0%, about 2.0% to about 4.5%, about 2.5% to about 5.0% and / or about 3.0% to about 6.0% of PEG-c-DOMG (R-3-[(comethoxy-poly(ethylene glycol)2000)carbamoyl)]-1,2-dimyristyloxypropyl-3-amine) (also referred to herein as PEG-DOMG) in a lipid molar ratio compared to cationic lipids, DSPC, and cholesterol. In another embodiment, PEG-c-DOMG may be replaced by PEG lipids, such as, but not limited to, PEG-DSG (1,2-distearyl-sn-glycerol, methoxy polyethylene glycol), PEG-DMG (1,2-dimyristoyl-sn-glycerol), and / or PEG-DPG (1,2-dispalmitoyl-sn-glycerol, ...

[0149] Methoxylated polyethylene glycol). The cationic lipid may be selected from any lipid known in the art, such as, but not limited to, DLin-MC3-DMA, DLin-DMA, C12-200 and DLin-KC2-DMA.

[0150] RNA vaccines can be formulated into lipid nanoparticles, such as those described in International Publication No. WO2012170930, which is incorporated herein by reference in its entirety.

[0151] RNA vaccine formulations comprising polynucleotides may be nanoparticles, which may include at least one lipid. The lipid may be selected from, but is not limited to, DLin-DMA, DLin-K-DMA, 98N12-5, C12-200, DLin-MC3-DMA, DLin-KC2-DMA, DODMA, PLGA, PEG-DMG, PEGylated lipids, and amino alcohol lipids. Alternatively, the lipid may be a cationic lipid, such as, but not limited to, DLin-DMA, DLin-D-DMA, DLin-MC3-DMA, DLin-KC2-DMA, DODMA, and amino alcohol lipids. The amino alcohol cationic lipid may be a lipid described in and / or prepared by the method described in U.S. Patent Publication No. US20130150625, the entire contents of which are incorporated herein by reference. As non-limiting examples, the cationic lipid may be 2-amino-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-{[(9Z,2Z)-octadec-9,12-dien-1-yloxy]methyl}prop-1-ol (compound 1 in US20130150625); 2-amino-3-[(9Z)-octadec-9-en-1-yloxy]-2-{[(9Z)-octadec-9-en-1-yloxy]methyl}prop-1-ol (compound 2 in US20130150625); -amino-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-[(octoxy)methyl]prop-1-ol (compound 3 in US20130150625); and 2-(dimethylamino)-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-2-{[(9Z,12Z)-octadec-9,12-dien-1-yloxy]methyl}prop-1-ol (compound 4 in US20130150625); or any pharmaceutically acceptable salt or stereoisomer thereof.

[0152] Lipid nanoparticle formulations typically include lipids, particularly ionizable cationic lipids, such as 2,2-dilinoleo-4-dimethylaminoethyl-[1,3]-dioxacyclopentane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), or 9-((4-(dimethylamino)butyryl)oxy)heptadecanoic acid di((Z)-non-2-en-1-yl) ester (L319), and also include neutral lipids, sterols, and molecules that can reduce particle aggregation, such as PEG or PEG-modified lipids.

[0153] The lipid nanoparticle formulation may consist essentially of: (i) at least one lipid selected from the group consisting of 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319); (ii) neutral lipids selected from DSPC, DPPC, POPC, DOPE, and SM; (iii) sterols, such as cholesterol; and (iv) PEG lipids, such as PEG-DMG or PEG-cDMA, in a molar ratio of about 20-60% cationic lipids: 5-25% neutral lipids: 25-55% sterols: 0.5-15% PEG-lipids.

[0154] In one embodiment, the formulation comprises, in molar amounts, about 25% to about 75% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxacyclopentane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanoic acid di((Z)-non-2-en-1-yl) ester (L319), for example, in molar amounts, about 35% to about 65%, about 45% to about 65%, about 60%, about 57.5%, about 50%, or about 40%.

[0155] In one embodiment, the formulation comprises, by molar weight, about 0.5% to about 15% of neutral lipids, such as about 3% to about 12%, about 5% to about 10%, or about 15%, about 10%, or about 7.5% by molar weight. Exemplary neutral lipids include, but are not limited to, DSPC, POPC, DPPC, DOPE, and SM. In one embodiment, the formulation comprises, by molar weight, about 5% to about 50% of sterols, such as about 15% to about 45%, about 20% to about 40%, about 40%, about 38.5%, about 35%, or about 31% by molar weight. Exemplary sterols are cholesterol. In one embodiment, the formulation comprises, by molar weight, about 0.5% to about 20% of PEG or PEG-modified lipids, such as about 0.5% to about 10%, about 0.5% to about 5%, about 1.5%, about 0.5%, about 1.5%, about 3.5%, or about 5% by molar weight. In one embodiment, the PEG or PEG-modified lipids comprise PEG molecules with an average molecular weight of 2,000 Da. In other embodiments, PEG or PEG-modified lipids include PEG molecules with an average molecular weight of less than 2,000 Da, such as about 1,500 Da, about 1,000 Da, or about 5.00 Da. Exemplary PEG-modified lipids include, but are not limited to, PEG distearylglycerol (PEG-DMG) (also referred to herein as PEG-C14 or C14-PEG) and PEG-cDMA (described in detail in Reyes et al. J. Controlled Release, 107, 276-287 (2005), the contents of which are incorporated herein by reference in their entirety).

[0156] In one embodiment, the formulation comprises, on a molar basis, about 25% to 75% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 0.5% to 15% of a neutral lipid, 5% to 50% of a sterol, and 0.5% to 20% of PEG or PEG-modified lipids.

[0157] In one embodiment, the formulation comprises, on a molar basis, 35-65% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 3-12% of a neutral lipid, 15-45% of a sterol, and 0.5-10% of PEG or PEG-modified lipids.

[0158] In one embodiment, the formulation comprises, on a molar basis, 45-65% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), 5-0% of a neutral lipid, 25-40% of a sterol, and 0.5-10% of PEG or PEG-modified lipids.

[0159] In one embodiment, the formulation comprises, on a molar basis, about 60% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), about 7.5% of a neutral lipid, about 31% of a sterol, and about 1.5% of PEG or PEG-modified lipids.

[0160] In one embodiment, the formulation comprises, on a molar basis, about 50% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanoic acid di((Z)-non-2-en-1-yl) ester (L319), about 10% of a neutral lipid, about 38.5% of a sterol, and about 1.5% of PEG or PEG-modified lipids.

[0161] In one embodiment, the formulation comprises, on a molar basis, about 50% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), about 10% of a neutral lipid, about 35% of a sterol, about 4.5% or about 5% of a PEG or PEG-modified lipid, and about 0.5% of a targeted lipid.

[0162] In one embodiment, the formulation comprises, on a molar basis, about 40% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), about 15% of a neutral lipid, about 40% of a sterol, and about 5% of PEG or PEG-modified lipids.

[0163] In one embodiment, the formulation comprises, on a molar basis, about 57.2% of a cationic lipid selected from 2,2-dilinole-4-dimethylaminoethyl-[1,3]-dioxane (DLin-KC2-DMA), dilinoleomethyl 4-dimethylaminobutyrate (DLin-MC3-DMA), and 9-((4-(dimethylamino)butyryl)oxy)heptadecanedioic acid di((Z)-non-2-en-1-yl) ester (L319), about 7.1% of a neutral lipid, about 34.3% of a sterol, and about 1.4% of PEG or PEG-modified lipids.

[0164] In one embodiment, the formulation may contain, on a molar basis, approximately 57.5% of a PEG-cDMA cationic lipid selected from PEG lipids (PEG-cDMA is discussed in detail in Reyes et al. (J. Controlled Release, 107, 276-287 (2005), the contents of which are incorporated herein by reference in their entirety), approximately 7.5% of a neutral lipid, approximately 31.5% of a sterol, and approximately 3.5% of a PEG or PEG-modified lipid.

[0165] In a preferred embodiment, the lipid nanoparticle formulation is essentially composed of a lipid mixture, wherein the molar ratio is about 20-70% cationic lipids: 5-45% neutral lipids: 20-55% cholesterol: 0.5-15% PEG-modified lipids; more preferably, the molar ratio is about 20-60% cationic lipids: 5-25% neutral lipids: 25-55% cholesterol: 0.5-15% PEG-modified lipids.

[0166] In specific embodiments, the lipid molar ratio is approximately 50 / 10 / 38.5 / 1.5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG-modified lipids, such as PEG-DMG, PEG-DSG, or PEG-DPG), 57.2 / 7.1 / 134.3 / 1.4 (mol% cationic lipids / neutral lipids, such as DPPC / Chol / PEG-modified lipids, such as PEG-cDMA), 40 / 15 / 40 / 5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG-modified lipids, such as PEG-DMG), and 50 / 10 / 35 / 4.5 / 0.5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG-modified lipids). The lipids are 50 / 10 / 35 / 5 (cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG), 40 / 10 / 40 / 10 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA), 35 / 15 / 40 / 10 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA), or 52 / 13 / 30 / 5 (mol% cationic lipids / neutral lipids, such as DSPC / Chol / PEG modified lipids, such as PEG-DMG or PEG-cDMA).

[0167] Exemplary lipid nanoparticle compositions and their preparation methods are found, for example, in Semple et al. (2010) Nat. Biotechnol. 28: 172-176; Jayarama et al. (2012), Angew. Chem. Int. Ed., 51: 8529-8533; and Maier et al. (2013) Molecular Therapy 21, 1570-1578 (each of which is incorporated herein by reference in its entirety).

[0168] In one embodiment, the lipid nanoparticle formulation described herein may include cationic lipids, PEG lipids, and structural lipids, and optionally include non-cationic lipids. As a non-limiting example, the lipid nanoparticles may include about 40-60% cationic lipids, about 5-15% non-cationic lipids, about 1-2% PEG lipids, and about 30-50% structural lipids. As another non-limiting example, the lipid nanoparticles may include about 50% cationic lipids, about 10% non-cationic lipids, about 1.5% PEG lipids, and about 38.5% structural lipids. As yet another non-limiting example, the lipid nanoparticles may include about 55% cationic lipids, about 10% non-cationic lipids, about 2.5% PEG lipids, and about 32.5% structural lipids. In one embodiment, the cationic lipid may be any cationic lipid described herein, such as, but not limited to, DLin-KC2-DMA, DLin-MC3-DMA, and L319.

[0169] In one embodiment, the lipid nanoparticle formulation described herein may be a four-component lipid nanoparticle. The lipid nanoparticles may include cationic lipids, non-cationic lipids, PEG lipids, and structural lipids. As a non-limiting example, the lipid nanoparticles may include about 40-60% cationic lipids, about 5-15% non-cationic lipids, about 1-2% PEG lipids, and about 30-50% structural lipids. As another non-limiting example, the lipid nanoparticles may include about 50% cationic lipids, about 10% non-cationic lipids, about 1.5% PEG lipids, and about 38.5% structural lipids. As yet another non-limiting example, the lipid nanoparticles may include about 55% cationic lipids, about 10% non-cationic lipids, about 2.5% PEG lipids, and about 32.5% structural lipids. In one embodiment, the cationic lipid may be any cationic lipid described herein, such as, but not limited to, DLin-KC2-DMA, DLin-MC3-DMA, and L319.

[0170] In one embodiment, the lipid nanoparticle formulations described herein may include cationic lipids, non-cationic lipids, PEG lipids, and structured lipids. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-KC2-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG lipid PEG-DOMG, and approximately 38.5% structured lipid cholesterol. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-MC3-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG lipid PEG-DOMG, and approximately 38.5% structured lipid cholesterol. As a non-limiting example, the lipid nanoparticles comprise approximately 50% cationic lipid DLin-MC3-DMA, approximately 10% non-cationic lipid DSPC, approximately 1.5% PEG lipid PEG-DMG, and approximately 38.5% structured lipid cholesterol. As another non-limiting example, the lipid nanoparticles comprise approximately 55% cationic lipid L319, approximately 10% noncationic lipid DSPC, approximately 2.5% PEG lipid PEG-DMG, and approximately 32.5% structural lipid cholesterol.

[0171] In one embodiment, the cationic lipid may be selected from, but is not limited to, international publications WO2012040184, WO2011153120, WO2011149733, WO2011090965, WO2011043913, WO2011022460, WO2012061259, WO2012054365, WO2012044638, WO2010080724, WO2010021865, WO2008103276, and WO2013086373. The cationic lipids described herein are cited in WO2013086354, U.S. Patent Nos. 7,893,302, 7,404,969, 8,283,333, and 8,466,122, and U.S. Patent Publications US20100036115, US20120202871, US20130064894, US20130129785, US20130150625, US20130178541, and US20130225836; the contents of each of these patents are incorporated herein by reference in their entirety. In another embodiment, the cationic lipid may be selected from, but is not limited to, Formula A as described in International Publications WO2012040184, WO2011153120, WO2011149733, WO2011090965, WO2011043913, WO2011022460, WO2012061259, WO2012054365, WO2012044638, and WO2013116126 or U.S. Patent Publications US20130178541 and US20130225836, the contents of which are incorporated herein by reference in their entirety. In another embodiment, the cationic lipid may be selected from, but is not limited to, the formula CLI-CLXXIX of International Publication No. WO2008103276, the formula CLI-CLXXIX of U.S. Patent No. 7,893,302, the formula CLI-CLXXXVII of U.S. Patent No. 7,404,969, and the formulas I-VI of U.S. Patent Publication No. US20100036115 and the formula I of U.S. Patent Publication No. US20130123338; ​​the contents of each of the foregoing are incorporated herein by reference in their entirety. As a non-limiting example, the cationic lipid may be selected from (20Z,23Z)-N,N-dimethylnonadecano-20,23-diene-10-amine, (17Z,20Z)-N,N-dimethylhexadecano-17,20-diene-9-amine, (1Z,19Z)-N,N-dimethylpentadecano-16,19-diene-8-amine, (13Z,16Z)-N,N-dimethyltetradecano-13,16-diene-5-amine, (12Z,15Z)-N,N-dimethyltetradecano-12,15-diene-4-amine, (14Z,17Z)-N,N-dimethyltridecano-14,17-Dien-6-amine, (15Z,18Z)-N,N-dimethyltetracos-15,18-dien-7-amine, (18Z,21Z)-N,N-dimethylheptadec-18,21-dien-10-amine, (15Z,18Z)-N,N-dimethyltetracos-15,18-dien-5-amine, (14Z,17Z)-N,N-dimethyltridec-14,17-dien-4-amine, (19Z,22Z)-N,N-dimethyloctadec-19,22-dien-9-amine, (18Z,21Z)-N,N-dimethylheptadec-18,21-dien-8-amine, (17Z,20Z)-N,N-dimethylhexadec-17,20- Diene-7-amine, (16Z,19Z)-N,N-dimethylpentadecano-16,19-diene-6-amine, (22Z,25Z)-N,N-dimethyltridecane-22,25-diene-10-amine, (21Z,24Z)-N,N-dimethyltridecane-21,24-diene-9-amine, (18Z)-N,N-dimethylheptadecane-18-en-10-amine, (17Z)-N,N-dimethylhexadecano-17-en-9-amine, (19Z,22Z)-N,N-dimethylhexadecano-19,22-diene-7-amine, N,N-dimethylheptadecane-10-amine, (20Z,23Z)-N-ethyl-N-methylhexadecano-20,23- Dien-10-amine, 1-[(11Z,14Z)-1-nonyleicosicos-11,14-dien-1-yl]pyrrolidine, (20Z)-N,N-dimethylheptadec-20-en-10-amine, (15Z)-N,N-dimethylheptadec-15-en-10-amine, (14Z)-N,N-dimethylheptadec-14-en-10-amine, (17Z)-N,N-dimethylheptadec-17-en-10-amine, (24Z)-N,N-dimethyltriscar-24-en-10-amine, (20Z)-N,N-dimethylheptadec-20-en-10-amine, (22Z)-N,N-dimethyltriscar-22-en-10-amine, (16Z)-N N-Dimethylpentacarbon-16-en-8-amine, (12Z,15Z)-N,N-dimethyl-2-nonyltetracos-12,15-dien-1-amine, (13Z,16Z)-N,N-dimethyl-3-nonyltetracos-13,16-dien-1-amine, N,N-dimethyl-1-[(1S,2R)-2-octylcyclopropyl]heptadecane-8-amine, 1-[(1S,2R)-2-hexylcyclopropyl]-N,N-dimethylnonadecane-10-amine, N,N-dimethyl-1-[(1S,2R)-2-octylcyclopropyl]nonadecane-10-amine, N,N-dimethyl-21-[(1S,2R)-2-octylcyclopropyl]tetracos-10-amine, N,N-Dimethyl-1-[(1S,2S)-2-{[(1R,2R)-2-pentylcyclopropyl]methyl}cyclopropyl]nonacosano-10-amine, N,N-Dimethyl-1-[(1S,2R)-2-octylcyclopropyl]hexadecane-8-amine, N,N-Dimethyl-[(1R,2S)-2-undecylcyclopropyl]tetradecane-5-amine, N,N-Dimethyl-3-{7-[(1S,2R)-2-octylcyclopropyl]heptyl}dodecane-1-amine, 1-[(1R,2S)-2-heptylcyclopropyl]-N,N-dimethyloctadecane-9-amine, 1-[(1S,2R)-2-decylcyclopropyl]-N,N-dimethylpentadecane-6-amine, N,N-dimethyl-1-[( 1S,2R)-2-octylcyclopropyl]pentadecan-8-amine, RN,N-dimethyl-1-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-3-(octyloxy)prop-2-amine, SN,N-dimethyl-1-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-3-(octyloxy)prop-2-amine, 1-{2-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-1-[(octyloxy)methyl]ethyl}pyrrolidine, (2S)-N,N-dimethyl-1-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-3-[(5Z)-oct-5-en-1-yloxy] ]Propyl-2-amine, 1-{2-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]-1-[(octyloxy)methyl]ethyl}azacyclobutane, (2S)-1-(hexyloxy)-N,N-dimethyl-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]propyl-2-amine, (2S)-1-(heptyloxy)-N,N-dimethyl-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]propyl-2-amine, N,N-dimethyl-1-(nonyloxy)-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]propyl-2-amine, N,N-dimethyl-1-[(9Z)- [Octadec-9-en-1-yloxy]-3-(octyloxy)prop-2-amine, (2S)-N,N-dimethyl-1-[(6Z,9Z,12Z)-octadec-6,9,12-trien-1-yloxy]-3-(octyloxy)prop-2-amine, (2S)-1-[(11Z,14Z)-eicos-11,14-dien-1-yloxy]-N,N-dimethyl-3-(pentyloxy)prop-2-amine, (2S)-1-(hexyloxy)-3-[(11Z,14Z)-eicos-11,14-dien-1-yloxy]-N,N-dimethylprop-2-amine, 1-[(11Z,14Z)-eicos-11,14-dien-1-yloxy]-N,N-Dimethyl-3-(octyloxy)prop-2-amine, 1-[(13Z,16Z)-docosa-13,16-dien-1-yloxy]-N,N-dimethyl-3-(octyloxy)prop-2-amine, (2S)-1-[(13Z,16Z)-docosa-13,16-dien-1-yloxy]-3-(hexyloxy)-N,N-dimethylprop-2-amine, (2S)-1-[(1 3Z)-(1 ... (1-methyloctyl)oxy]-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]prop-2-amine, (2R)-1-[(3,7-dimethyloctyl)oxy]-N,N-dimethyl-3-[(9Z,12Z)-octadec-9,12-dien-1-yloxy]prop-2-amine, N,N-dimethyl-1-(octyloxy)-3-({8-[(1S ,2S)-2-{[(1R,2R)-2-pentylcyclopropyl]methyl}cyclopropyl]octyl}oxy)prop-2-amine, N,N-dimethyl-1-{[8-(2-octylcyclopropyl)octyl]oxy}-3-(octyloxy)prop-2-amine and (11E,20Z,23Z)-N,N-dimethyl-necodeca-11,20,23-trien-10-amine or their pharmaceutically acceptable salts or stereoisomers.

[0172] In one embodiment, the lipid may be a cleavable lipid, such as those described in International Publication No. WO2012170889, the entire contents of which are incorporated herein by reference. In another embodiment, the lipid may be a cationic lipid, such as, but not limited to, the cationic lipid of formula (I) described in U.S. Patent Application Publication No. US20130064894, the entire contents of which are incorporated herein by reference.

[0173] Cationic lipids can be synthesized by methods known in the art and / or by methods described in international publications such as WO2012040184, WO2011153120, WO2011149733, WO2011090965, WO2011043913, WO2011022460, WO2012061259, WO2012054365, WO2012044638, WO2010080724, WO2010021865, WO2013086373 and WO2013086354, the contents of which are incorporated herein by reference in their entirety.

[0174] The cationic lipid may be a trialkyl cationic lipid. Non-limiting examples of trialkyl cationic lipids and methods for preparing and using trialkyl cationic lipids are described in International Patent Publication No. WO2013126803, the contents of which are incorporated herein by reference in their entirety.

[0175] The LNP formulation of the RNA vaccine may contain 3% PEG-c-DOMG at a lipid molar ratio. In another embodiment, the LNP formulation of the RNA vaccine may contain 1.5% PEG-c-DOMG at a lipid molar ratio. The pharmaceutical composition of the RNA vaccine may comprise at least one PEGylated lipid described in International Publication No. WO2012099755, the entire text of which is incorporated herein by reference.

[0176] LNP formulations may contain PEG-DMG 2000 (1,2-dimyristic-sn-glycerol-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]. In one embodiment, an LNP formulation may contain PEG-DMG 2000, cationic lipids known in the art, and at least one other component. In another embodiment, an LNP formulation may contain PEG-DMG 2000, cationic lipids known in the art, DSPC, and cholesterol. As a non-limiting example, an LNP formulation may contain PEG-DMG 2000, DLin-DMA, DSPC, and cholesterol. As another non-limiting example, an LNP formulation may contain PEG-DMG 2000, DLin-DMA, DSPC, and cholesterol in a molar ratio of 2:40:10:48 (see, for example, Geall et al., Nonviral delivery of self-amplifying RNA vaccines, PNAS 2012; PMID:22908294; which is incorporated herein by reference in its entirety).

[0177] Lipid nanoparticle (LNP) formulations can be prepared by the methods described in international publications WO2011127255 or WO2008103276, the contents of which are incorporated herein by reference in their entirety. As a non-limiting example, the RNA vaccines described herein can be encapsulated in lipid nanoparticle (LNP) formulations described in WO2011127255 and / or WO2008103276, the entire contents of which are incorporated herein by reference.

[0178] The RNA vaccine described herein can be formulated into nanoparticles for administration via a parenteral route, as described in U.S. Patent Publication No. US20120207845, the contents of which are incorporated herein by reference in their entirety.

[0179] In one embodiment, the RNA vaccine may be formulated in lipid nanoparticles prepared by the methods described in U.S. Patent Publication No. US20130156845, or International Publication Nos. WO2013093648 and WO2012024526, each of which is incorporated herein by reference in its entirety. The lipid nanoparticles described herein may be prepared in a sterile environment by the systems and / or methods described in U.S. Patent Publication No. US20130164400, which is incorporated herein by reference in its entirety.

[0180] LNP formulations can be formulated in nanoparticles, such as the nucleic acid-lipid particles described in U.S. Patent 8,492,359, the entire contents of which are incorporated herein by reference. As a non-limiting example, the lipid particles may include one or more active agents or therapeutic agents; one or more cationic lipids comprising about 50 mol% to about 85 mol% of total lipids present in the particles; one or more non-cationic lipids comprising about 13 mol% to about 49.5 mol% of total lipids present in the particles; and one or more conjugated lipids that inhibit particle aggregation, comprising about 0.5 mol% to about 2 mol% of total lipids present in the particles. The nucleic acid in the nanoparticles may be a polynucleotide described herein and / or known in the art.

[0181] LNP formulations may be prepared by the methods described in International Publications WO2011127255 or WO2008103276, the contents of which are incorporated herein by reference in their entirety. As a non-limiting example, the modified RNA described herein may be encapsulated in LNP formulations as described in International Publications WO2011127255 and / or WO2008103276; the contents of which are incorporated herein by reference in their entirety. LNP formulations described herein may include polycationic compositions. As a non-limiting example, the polycationic composition may be selected from Formulas 1-60 of US Patent Publication US20050222064; the contents of which are incorporated herein by reference in their entirety. LNP formulations comprising polycationic compositions may be used for in vivo and / or in vitro delivery of the modified RNA described herein.

[0182] In one embodiment, the LNP formulation described herein may additionally include a permeability enhancer molecule. A non-limiting permeability enhancer molecule is described in U.S. Patent Publication No. US20050222064, the contents of which are incorporated herein by reference in their entirety.

[0183] RNA vaccine drug compositions can be formulated in liposomes, including but not limited to DiLa2 liposomes (Marina Biotech, Bothell, WA), SMARTICLES® liposomes (Marina Biotech, Bothell, WA), liposomes based on neutral DOPC (1,2-dioleoyl-sn-glycerol-3-phosphocholine) (e.g. for siRNA delivery in ovarian cancer (Landene et al. Cancer Biology & Therapy 2006 5(12)1708-1713); cited in full hereto), and hyaluronic acid-coated liposomes (Quiet Therapeutics, Israel).

[0184] In one embodiment, the RNA vaccine may be formulated in a lyophilized gel-phase liposome composition, as described in U.S. Publication No. US2012060293, the entire contents of which are incorporated herein by reference.

[0185] RNA vaccines can be conjugated with cationic or polycationic compounds containing protamine, nucleolin, spermine or spermidine, or other cationic peptides or proteins such as poly-L-lysine (PLL), polyarginine, basic polypeptides, cell-penetrating peptides (CPP), including HIV-binding peptides, HIV-1 Tat (HIV), Tat-derived peptides, penetrating peptides, VP22-derived or similar peptides, Erns virus, HSV, VP22 (herpes simplex virus), AP, KALA or protein transduction domain (PTD), PpT620, proline-rich peptides, arginine-rich peptides, lysine-rich peptides, MPG peptides, Pep-1, L-oligomers, calcitonin peptides, antennal foot-derived peptides (especially from Drosophila antennal foot), pAntp, plsl, FGF, lactoferrin, transport peptides, Buforin-2, Bac715-24, SynB, Syn B(1), pVEC, hCT-derived peptides, SAP, histones, cationic polysaccharides (e.g., chitosan, polygluconine), cationic polymers such as polyethyleneimine (PEI), cationic lipids such as DOTMA: [1-(2,3-diolenoyloxy)propyl]-N,N,N-trimethylammonium chloride, DMRIE, di-C14-amidine, DOTIM, SAINT, DC-Choi, BGTC, CTAP, DOPC, DODAP, DOPE: dioleoylphosphatidylethanolamine, DOSPA, DODAB, DOIC, DMEPC, DOG S: Di(octadecylamino)glycyl spermine, DIMRI: (di(myristyloxy)propyl)di(methyl)(hydroxyethyl)ammonium bromide, DOTAP: dioleoyloxy-3-(trimethylammonium)propane, DC-6-14: O,O-di(tetracosyl)-N-(α-trimethylammoniumacetyl)diethanolamine chloride, CLIP1: racemic-[(2,3-di(octadecyloxy)propyl)(2-hydroxyethyl)]dimethylammonium chloride, CLIP6: racemic-[2(2,3-di(hexadecyloxy)propoxymethoxy)ethyl]-trimethylammonium CLIP9: Racemic-[2(2,3-di(hexadecyloxy)propoxysuccinoxy)ethyl]-trimethylammonium, oligomeric transfected amines, or cationic or polycationic polymers such as modified polyamino acids like β-amino acid polymers or reverse polyamides, modified polyethylene such as PVP (poly(N-ethyl-4-vinylpyridine bromide), modified acrylates such as pDMAEMA (poly(dimethylaminoethyl methacrylate)), modified amide amines such as pAMAM (poly(amide amine)), modified polyβ-amino esters (PBAE) such as diamine-terminated diacrylate-1,Polymers such as 4-butanediol co-5-amino-1-pentanol, dendritic macromolecules such as polypropylamine dendritic macromolecules or pAMAM-based dendritic macromolecules, polyimides such as PEL (poly(ethyleneimine)) and poly(propyleneimine), polyallylamine, glycosyl backbone polymers such as cyclodextrin-based polymers, dextran-based polymers, chitosan, silane backbone polymers such as PMOXA-PDMS copolymers, and block polymers composed of one or more cationic blocks (such as those selected from the above cationic polymers) and one or more hydrophilic or hydrophobic blocks (e.g., polyethylene glycol); etc.

[0186] Alternatively, RNA vaccines do not bind to cationic or polycationic compounds.

[0187] Nanoparticle formulations may include phosphate conjugates. Phosphate conjugates can increase in vivo circulation time and / or enhance targeted delivery of nanoparticles. The phosphate conjugates used in this invention can be prepared by the methods described in International Application No. WO2013033438 or US Patent Publication No. US20130196948, the contents of which are incorporated herein by reference in their entirety. As a non-limiting example, the phosphate conjugate may comprise a compound of any of the structural formulas described in International Application No. WO2013033438.

[0188] Its full text is quoted and included in this article.

[0189] Nanoparticle formulations may include polymer conjugates. The polymer conjugates may be water-soluble conjugates. The polymer conjugates may have the structure described in U.S. Patent Application Publication No. 20130059360, the entire contents of which are incorporated herein by reference. In one aspect, the polynucleotides and polymer conjugates of the present invention...

[0190] The polymeric conjugate can be prepared using the methods and / or segmented polymeric reagents described in U.S. Patent Application 20130072709, the entire contents of which are incorporated herein by reference. Alternatively, the polymeric conjugate may have side groups including ring portions, such as, but not limited to, the polymeric conjugate described in U.S. Patent Publication No. US20130196948, the entire contents of which are incorporated herein by reference.

[0191] Nanoparticle formulations may include conjugates to enhance the delivery of the nanoparticles of the present invention to subjects. Furthermore, the conjugates may inhibit the phagocytic clearance of nanoparticles in subjects. In one aspect, the conjugate may be a “self-peptide” designed from the human membrane protein CD47 (e.g., “self-particles” described by Rodriguez et al. (Science 2013 339, 971-975), the full text of which is incorporated herein by reference). As shown by Rodriguez et al., self-peptides delay macrophage-mediated clearance of nanoparticles, enhancing nanoparticle delivery. In another aspect, the conjugate may be the membrane protein CD47 (e.g., see Rodriguez et al., Science 2013, 339, 971-975, the full text of which is incorporated herein by reference). The research by Rodriguez et al. showed that, similar to “self-peptides,” CD47 can increase the proportion of circulating particles in subjects compared to out-of-order peptides and PEG-coated nanoparticles.

[0192] RNA vaccines can be formulated into nanoparticles that include conjugates to enhance the delivery of the nanoparticles of the present invention to subjects. The conjugates may be CD47 membranes, or may be derived from CD47 membrane proteins, such as the “self-peptide” described above. Alternatively, the nanoparticles may include a conjugate of PEG and CD47 or a derivative thereof. Yet another aspect, the nanoparticles may include the “self-peptide” described above and the membrane protein CD47. The “self-peptide” and / or CD47 protein may be coupled to virus-like particles or pseudovirus particles, as described herein, for the delivery of RNA vaccines.

[0193] The formulations described herein may comprise RNA vaccine pharmaceutical compositions comprising the polynucleotides of the present invention and conjugates having degradable bonds. Non-limiting examples of conjugates include an aromatic moiety comprising an ionizable hydrogen atom, a spacer moiety, and a water-soluble polymer. As non-limiting examples, pharmaceutical compositions comprising conjugates having degradable bonds and methods of delivering such pharmaceutical compositions are described in U.S. Patent Publication No. US20130184443, the entire contents of which are incorporated herein by reference.

[0194] Nanoparticle formulations may be carbohydrate nanoparticles, including carbohydrate carriers and RNA vaccines. As a non-limiting example, the carbohydrate carrier may include, but is not limited to, anhydride-modified plant glycogen or glycogen-type materials, plant glycogen octenyl succinate, plant glycogen β-dextrin, and anhydride-modified plant glycogen β-dextrin. (See, for example, International Publication No. WO2012109121; the contents of which are incorporated herein by reference in their entirety).

[0195] Nanoparticle formulations can be coated with surfactants or polymers to improve particle delivery. In one embodiment, the nanoparticles can be coated with a hydrophilic coating, such as, but not limited to, a PEG coating and / or a coating having a neutral surface charge. Hydrophilic coatings can facilitate the delivery of nanoparticles with larger payloads within the central nervous system, such as, but not limited to, RNA vaccines. As a non-limiting example, nanoparticles including hydrophilic coatings and methods for preparing such nanoparticles are described in U.S. Patent Publication No. US20130183244, the entire contents of which are incorporated herein by reference.

[0196] In one embodiment, the lipid nanoparticles of the present invention may be hydrophilic polymer particles. Non-limiting examples of hydrophilic polymer particles and methods for preparing hydrophilic polymer particles are described in U.S. Patent Publication No. US20130210991, the entire contents of which are incorporated herein by reference.

[0197] In another embodiment, the lipid nanoparticles of the present invention may be hydrophobic polymer particles.

[0198] Lipid nanoparticle formulations can be improved by replacing cationic lipids with biodegradable cationic lipids (referred to as rapidly eliminating lipid nanoparticles (reLNPs)). Ionizable cationic lipids, such as, but not limited to, DLinDMA, DLin-KC2-DMA, and DLin-MC3-DMA, have been shown to accumulate in plasma and tissues over time and may be a potential source of toxicity. The rapid metabolism of rapidly eliminating lipids has improved the tolerability and therapeutic index of lipid nanoparticles in rats at doses ranging from 1 mg / kg to 10 mg / kg. Including enzymatically degradable ester bonds can improve the degradation and metabolic properties of the cationic component while maintaining the activity of the reLNP formulation. The ester bond may be located inside the lipid chain or at the end of the lipid chain. The lactone bond may replace any carbon in the lipid chain. In one embodiment, the lactone bond may be located on either side of the saturated carbon.

[0199] In one embodiment, an immune response can be initiated by delivery of lipid nanoparticles, which may comprise nanospecies, polymers, and immunogens. (US Publication No. 20120189700 and International Publication No. WO2012099805; each incorporated herein by reference in its entirety). The polymer may encapsulate or partially encapsulate the nanomaterials. The immunogen may be a recombinant protein, modified RNA, and / or polynucleotide as described herein. In one embodiment, the lipid nanoparticles may be formulated for use in vaccines, such as, but not limited to, vaccines against pathogens. The lipid nanoparticles may be engineered to alter the surface properties of the particles, enabling them to penetrate mucosal barriers. Mucus is located on mucosal tissues, such as, but not limited to, the oral cavity (e.g., buccal and esophageal membranes and tonsil tissues), eyes, gastrointestinal tract (e.g., stomach, small intestine, large intestine, colon, rectum), nose, respiratory tract (e.g., nasal, pharyngeal, tracheal, and bronchial membranes), and genitals (e.g., vaginal, cervical, and urethral membranes). For higher drug encapsulation efficiency and the ability to provide sustained delivery of a wide range of drugs, nanoparticles larger than 10–200 nm are preferred, as they are considered too large to diffuse rapidly across the mucosal barrier. Mucus is continuously secreted, effluxed, discarded, or digested and recycled, so most trapped particles can be removed from mucosal tissue within seconds or hours. Large polymer nanoparticles (200–500 nm in diameter), when densely coated with low molecular weight polyethylene glycol (PEG), diffuse at a rate only 4–6 times lower in mucus than in water (Lai et al., PNAS 2007, 104 (5): 1482–1487; Lai et al., Adv Drug Deliv Rev. 2009, 61(2): 158–171; each cited in full hereto). Nanoparticle transport can be determined using permeation rate and / or fluorescence microscopy techniques, including but not limited to fluorescence recovery after photobleaching (FRAP) and high-resolution multi-particle tracking (MPT). As a non-limiting example, compositions capable of penetrating mucosal barriers can be prepared according to the methods described in U.S. Patent No. 8,241,670 or International Patent Publication No. WO2013110028, the contents of which are incorporated herein by reference in their entirety.

[0200] Lipid nanoparticles designed to permeate mucus may include polymeric materials (i.e., polymeric cores) and / or polymer-vitamin conjugates and / or triblock copolymers. Polymeric materials may include, but are not limited to, polyamines, polyethers, polyamides, polyesters, polyurethanes, polyureas, polycarbonates, poly(styrene), polyimides, polysulfones, polyurethanes, polyacetylene, polyethylene, polyethyleneimine, polyisocyanates, polyacrylates, polymethacrylates, polyacrylonitrile, and polyarylates. Polymeric materials may be biodegradable and / or biocompatible. Non-limiting examples of biocompatible polymers are described in International Patent Publication No. WO2013116804, the entire contents of which are incorporated herein by reference. Polymeric materials may be additionally irradiated. As a non-limiting example, polymeric materials may be irradiated with gamma rays (see, for example, International Application No. WO201282165, the entire contents of which are incorporated herein by reference).Non-limiting examples of specific polymers include polycaprolactone (PCL), ethylene vinyl acetate polymer (EVA), poly(lactic acid) (PLA), poly(L-lactic acid) (PLLA), poly(glycolic acid) (PGA), poly(lactic acid coglycolic acid) (PLGA), poly(L-lactic acid coglycolic acid) (PLLGA), poly(D,L-lactide) (PDLA), poly(L-lactide) (PLLA), poly(D,L-lactide cocaprolactone), poly(D,L-lactide cocaprolactone coglycolide), poly(D,L-lactide coPEO co- D,L-lactide), poly(D,L-lactide co-PPO co-D,L-lactide), polyalkyl cyanoacrylate, polyurethane, poly-L-lysine (PLL), hydroxypropyl methacrylate (HPMA), polyethylene glycol, poly-L-glutamic acid, poly(hydroxy acid), polyanhydride, polyorthoester, poly(esteramide), polyamide, poly(ester ether), polycarbonate, polyolefins such as polyethylene and polypropylene, polyalkylene glycols (such as polyethylene glycol (PEG)), polyalkylene oxide (PEO), poly(terephthalate) such as polyethylene terephthalate, polyethylene glycol, poly(ethylene terephthalate), ... Enols (PVA), polyvinyl ethers, polyvinyl esters such as poly(vinyl acetate), polyhalogenated vinyls such as poly(vinyl chloride) (PVC), polyvinylpyrrolidone, polysiloxanes, polystyrene (PS), polyurethanes, cellulose derivatives such as alkyl cellulose, hydroxyalkyl cellulose, cellulose ethers, cellulose esters, nitrocellulose, hydroxypropyl cellulose, carboxymethyl cellulose, acrylic polymers such as poly((meth)acrylate) (PMMA), poly(((meth)acrylate) ethyl acrylate), poly((((meth)acrylate) butyl acrylate), poly((((meth)acrylate) isobutyl acrylate), poly(((meth)acrylate)... Hexyl acrylate, poly(isodecyl methacrylate), poly(laurate methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), poly(octadecyl acrylate) and their copolymers and mixtures, polydioxane and its copolymers, polyhydroxyalkanoates, propylene fumarate, polyoxymethylene, poloxamer, poly(ortho)esters, poly(butyric acid), poly(valeric acid), poly(lactide cocaprolactone), PEG-PLGA-PEG and trimethylene carbonate, polyvinylpyrrolidone. Lipid nanoparticles may be coated with or bound to copolymers, such as, but not limited to, block copolymers (e.g., branched polyether-polyamide block copolymers described in International Publication No. WO2013012476, which are incorporated herein by reference in their entirety), and (poly(ethylene glycol))-(poly(propylene oxide))-(poly(ethylene glycol)) triblock copolymers (see, for example, U.S. Publication Nos. 20120121718, 20100003337 and U.S. Patent No. 8,263,665, which are incorporated herein by reference in their entirety).The copolymer can be a generally considered safe polymer (GRAS), and the formation of lipid nanoparticles can be done in a manner that does not create new chemical entities. For example, lipid nanoparticles can include poloxamer coated on the surface of polylactic-glycolic acid copolymer (PLGA) nanoparticles without forming new chemical entities that can still rapidly penetrate human mucus (Yang et al. Angew. Chem. Int. Ed. 2011 50:2597-2600; the contents of which are incorporated herein by reference in their entirety).

[0201] Xu et al. describe a non-limiting, scalable method for generating nanoparticles that can penetrate human mucus (see, for example, J Control Release 2013, 170(2): 279-86; the contents of which are incorporated herein by reference in their entirety).

[0202] The vitamin in the polymer-vitamin conjugate may be vitamin E. The vitamin portion in the conjugate may be replaced with other suitable components, such as, but not limited to, vitamin A, vitamin E, other vitamins, cholesterol, hydrophobic portions, or hydrophobic components of other surfactants (e.g., sterol chains, fatty acids, hydrocarbon chains, and epoxide alkane chains).

[0203] Lipid nanoparticles designed to penetrate mucus may contain surface modifiers, such as, but not limited to, polynucleotides, anionic proteins (e.g., bovine serum albumin), surfactants (e.g., cationic surfactants, such as dimethyl di(octadecyl)ammonium bromide), sugars or sugar derivatives (e.g., cyclodextrin), nucleic acids, polymers (e.g., heparin, polyethylene glycol, and poloxamer), mucus dissolving agents (e.g., N-acetylcysteine, Artemisia argyi, bromelain, papain, Indigofera tinctoria, acetylcysteine, bromhexine, carboxycysteine, ipramone, mesna, ambroxol, sobrorilol, domoxol, letostan, tepronin, Gilesin, thymosin β4, alfa-chain enzyme, netticine, erdosteine), and various deoxyribonucleases, including recombinant human deoxyribonuclease. Surface modifiers may be embedded or interwoven into the particle surface, or attached to the lipid nanoparticle surface through, for example, coating, adsorption, covalent linkage, or other means. (See, for example, U.S. Publication Nos. 20100215580, 20080166414, and 20130164343; the contents of each are quoted in full and incorporated herein by reference.)

[0204] Mucus-permeable lipid nanoparticles may include at least one polynucleotide as described herein. The polynucleotide may be encapsulated within the lipid nanoparticles and / or disposed on the particle surface. The polynucleotide may be covalently coupled to the lipid nanoparticles. Formulations of mucus-permeable lipid nanoparticles may include a variety of nanoparticles. Furthermore, the formulation may contain particles that can interact with mucus and alter the structure and / or adhesive properties of surrounding mucus to reduce mucosal adhesion, thereby increasing the delivery of mucus-permeable lipid nanoparticles to mucosal tissues.

[0205] Mucus-permeable lipid nanoparticles may be hypotonic formulations comprising a mucosal permeability-enhancing coating. The formulation may be hypotonic to the epithelium to which it is delivered. Non-limiting examples of hypotonic formulations can be found in International Patent Publication No. WO2013110028, the contents of which are incorporated herein by reference in their entirety. To enhance delivery across the mucosal barrier, RNA vaccine formulations may include or be hypotonic solutions. Studies have found that hypotonic solutions can accelerate the arrival of mucus-inert particles, such as, but not limited to, mucus-permeable particles, at the vaginal epithelial surface (see, for example, Ensign et al. Biomaterials 2013 34(28):6922-9; the contents of which are incorporated herein by reference in their entirety).

[0206] In one embodiment, the RNA vaccine is formulated as a lipid complex, such as, but not limited to, the ATUPLEXTM system, the DACC system, the DBTC system, and other siRNA-lipid complex technologies from Silence Therapeutics (London, UK), STEMFECT™ from STEMGENT® (Cambridge, Massachusetts), and targeted and non-targeted nucleic acid delivery systems based on polyethyleneimine (PEI) or protamine (Aleku et al. Cancer Res. 2008 68:9788-9798; Strumberg et al. Int J Clin Pharmacol Ther 2012 50:76-78; Santel et al., GeneTher 2006 13: 1222-1234; Santel et al., Gene Ther 2006 13: 1360-1370; Gutbieret et al., Pulm Pharmacol.Ther. 2010 23:334-344; Kaufmann et al. al. Microvasc Res 201080:286-293; Weide et al. J Immunother. 2009 32:498-507; Weide et al. J Immunother. 2008 31: 180-188; Pascolo Expert Opin. Biol. Ther. 4: 1285-1294; Fotin-Mleczek et al., 2011 J. Immunother. 34: 1-15; Song et al., Nature Biotechnol. 2005, 23:709-717; Peer et al., Proc Natl Acad Sci US A. 2007 6;104:4095-4100; de Fougerolles Hum Gene Ther. 2008 19: 125-132; all of these are cited in full and incorporated herein by reference.

[0207] Such formulations can also be constructed or modified to passively or actively target different cell types in vivo, including but not limited to hepatocytes, immune cells, tumor cells, endothelial cells, antigen-presenting cells, and leukocytes (Akinc et al. Mol Ther. 2010 18: 1357-1364; Song et al., Nat Biotechnol. 2005 23: 709-717; Judge et al., J Clin Invest. 2009 119: 661-673; Kaufmann et al., Microvasc Res 2010 80: 286-293; Santel et al., Gene Ther 2006 13: 1222-1234; Santel et al., Gene Ther 2006 13: 1360-1370; Gutbier et al., PulmPharmacol. Ther. 2010). 23:334-344; Basha et al., Mol.Ther.2011 19:2186-2200; Fenske and Cullis, Expert Opin Drug Deliv.2008 5:25-44; Peer et al., Science.2008 319:627-630; Peer and Lieberman, Gene Ther.2011 18: 1127-1133; all of which are cited in full and are incorporated herein by reference. An example of passively targeted hepatocyte formulations includes lipid nanoparticle formulations based on DLin-DMA, DLin-KC2-DMA, and DLin-MC3-DMA, which have been shown to bind apolipoprotein E and promote the binding and uptake of these formulations by hepatocytes in vivo (Akinc et al. Mol Ther.2010 18: 1357-1364; all of which are cited in full and are incorporated herein by reference).The formulation can also achieve selective targeting by expressing different ligands on its surface, such as, but not limited to, folic acid, transferrin, N-acetylgalactosamine (GalNAc), and antibody targeting strategies (Kolhatkar et al., Curr DrugDiscov Technol. 2011 8: 197-206; Musacchio and Torchilin, Front Biosci. 2011 16:1388-1412; Yu et al., Mol Membr Biol. 2010 27:286-298; Patil et al., Crit RevTher Drug Carrier Syst. 2008 25: 1-61; Benoit et al., Biomacromolecules. 2011 12:2708-2714; Zhao et al., Expert Opin Drug Deliv. 2008 5:309-319; Akinc et al., Mol Ther. 2010). 18: 1357-1364; Srinivasan et al., Methods Mol Biol.2012 820:105-116; Ben-Arie et al., Methods Mol Biol.2012 757:497-507; Peer 2010 JControl Release.20:63-68; Peer et al., Proc Natl Acad Sci US A.2007 104:4095-4100; Kim et al., Methods Mol Biol.2011 721:339-353; Subramanya et al., MolTher.2010 18:2028-2037; Song et al., Nat Biotechnol.2005 23:709-717; Peer etal., Science.2008 319:627-630; Peer and Lieberman, Gene Ther. 2011 18: 1127-1133; all of which are cited in full and incorporated herein by reference.

[0208] RNA vaccines can be formulated as solid lipid nanoparticles. Solid lipid nanoparticles (SLNs) can be spherical with an average diameter of 10 to 1000 nm. SLNs have a solid lipid core matrix that can dissolve lipophilic molecules and can be stabilized with surfactants and / or emulsifiers. In another embodiment, the lipid nanoparticles can be self-assembled lipid-polymer nanoparticles (see Zhang et al., ACS Nano, 2008, 2 (8), pp 1696-1702; the entire contents of which are incorporated herein by reference). As a non-limiting example, SLNs can be those described in International Patent Publication No. WO2013105101, the entire contents of which are incorporated herein by reference. As another non-limiting example, SLNs can be prepared by the methods or processes described in International Patent Publication No. WO2013105101, the entire contents of which are incorporated herein by reference.

[0209] Liposomes, lipid complexes, or lipid nanoparticles can be used to enhance the efficacy of polynucleotide-guided protein production because these formulations may be able to increase cell transfection of RNA vaccines and / or increase the translation of encoded proteins. One example involves the use of lipid encapsulation technology to achieve efficient systemic delivery of polynucleotide-mediated DNA (Heyes et al., Mol Ther. 2007 15:713-720; cited in full hereto). Liposomes, lipid complexes, or lipid nanoparticles can also be used to increase the stability of polynucleotides.

[0210] The RNA vaccine of the present invention can also be formulated for controlled release and / or targeted delivery. As used herein, “controlled release” refers to a release profile of a pharmaceutical composition or compound that conforms to a specific release pattern to achieve a therapeutic outcome. In one embodiment, the rRNA vaccine may be encapsulated in a delivery agent known herein and / or in the art for controlled release and / or targeted delivery. As used herein, the term “encapsulation” means to close, surround, or enclose. When referring to formulations of compounds of the present invention, encapsulation may be substantially, completely, or partially. The term “substantially encapsulated” means that at least 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, 99.9, or more than 99.999% of the pharmaceutical composition or compound of the present invention may be encapsulated, surrounded, or wrapped within the delivery agent. “Partially encapsulated” means that less than 10, 20, 30, 40, 50, or fewer of the pharmaceutical composition or compound of the present invention may be encapsulated, surrounded, or wrapped within the delivery agent.

[0211] Advantageously, encapsulation can be determined by measuring the escape or activity of the pharmaceutical composition or compound of the present invention using fluorescence and / or electron microscopy. For example, at least 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, 99.9, 99.99%, or greater than 99.99% of the pharmaceutical composition or compound of the present invention is encapsulated in a delivery agent. Controlled-release formulations may contain, but are not limited to, triblock copolymers. As a non-limiting example, formulations may contain two different types of triblock copolymers (International Publications WO2012131104 and WO2012131106; the contents of which are incorporated herein by reference in their entirety).

[0212] RNA vaccines can be encapsulated in lipid nanoparticles or rapidly eliminating lipid nanoparticles, which can then be encapsulated in polymers, hydrogels, and / or surgical sealants described herein and / or known in the art. As non-limiting examples, polymers, hydrogels, or surgical sealants may be PLGA, ethylene vinyl acetate (EVAc), poloxamer, GELSITE® (Nanotherapeutics, Alachua, Florida), HYLENEX® (Halozyme Therapeutics, San Diego, California), surgical sealants such as fibrinogen polymers (Ethicon Inc., Cornelia, Georgia), TISSELL® (Baxter International, Inc., Deerfield, Illinois), polyethylene glycol-based sealants, and COSEAL® (Baxter International, Inc., Deerfield, Illinois).

[0213] Lipid nanoparticles can be encapsulated in any polymer known in the art, which can form a gel when injected into a subject. As another non-limiting example, lipid nanoparticles can be encapsulated in a biodegradable polymer matrix.

[0214] RNA vaccine formulations for controlled release and / or targeted delivery may also contain at least one controlled release coating. Controlled release coatings include, but are not limited to: OPADRY®, polyvinylpyrrolidone / vinyl acetate copolymer, polyvinylpyrrolidone, hydroxypropyl methylcellulose, hydroxypropyl cellulose, hydroxyethyl cellulose, EUDRAGIT RL®, EUDRAGIT RS®, and cellulose derivatives such as ethyl cellulose aqueous dispersions (AQUACOAT® and SURELEASE®).

[0215] In one embodiment, an RNA vaccine controlled-release and / or targeted delivery formulation may include at least one degradable polyester containing polycationic side chains. The degradable polyester includes, but is not limited to, poly(serine ester), poly(L-lactide co-L-lysine), poly(4-hydroxy-L-proline ester), and combinations thereof. In another embodiment, the degradable polyester may contain PEG conjugations to form a PEGylated polymer. An RNA vaccine controlled-release and / or targeted delivery formulation comprising at least one polynucleotide may include at least one PEG and / or PEG-related polymer derivatives, as described in U.S. Patent No. 8,404,222, the entire contents of which are incorporated herein by reference.

[0216] A controlled-release delivery formulation of an RNA vaccine comprising at least one polynucleotide may be a controlled-release polymer system described in US20130130348, the entire contents of which are incorporated herein by reference. The RNA vaccine of the present invention may be encapsulated in therapeutic nanoparticles, referred to herein as a "therapeutic nanoparticle RNA vaccine". Therapeutic nanoparticles may be formulated using methods described herein and known in the art, such as, but not limited to, international publications WO2010005740, WO2010030763, WO2010005721, WO2010005723, WO2012054923, and US publications US20110262491, US20100104645, and US20100087. US20100068285, US20110274759, US20100068286, US20120288541, US20130123351, and US20130230567, and US Patent Nos. 8,206,747, 8,293,276, 8,318,208, and 8,318,211, the contents of which are incorporated herein by reference in their entirety. In another embodiment, the therapeutic polymer nanoparticles can be identified by the method described in US Publication No. US20120140790, the entire contents of which are incorporated herein by reference.

[0217] Therapeutic nanoparticle RNA vaccines can be formulated for sustained release. As used herein, “sustained release” means a pharmaceutical composition or compound that meets a release rate over a specific time period. The time period may include, but is not limited to, hours, days, weeks, months, and years. As a non-limiting example, sustained-release nanoparticles may include polymers and therapeutic agents, such as, but not limited to, the polynucleotides of the present invention (see International Publication No. 2010075072 and U.S. Publications US20100216804, US20110217377, and US20120201859, each of which is incorporated herein by reference in its entirety). In another non-limiting example, sustained-release formulations may include agents that allow for sustained bioavailability, such as, but not limited to, crystals, macromolecular gels, and / or particulate suspensions (see U.S. Patent Publication US20130150295, which is incorporated herein by reference in its entirety).

[0218] In one embodiment, the therapeutic nanoparticle RNA vaccine may be formulated to be target-specific. As a non-limiting example, the therapeutic nanoparticles may contain corticosteroids (see International Publication No. WO2011084518; the contents of which are incorporated herein by reference in their entirety). As a non-limiting example, the therapeutic nanoparticles may be formulated as the nanoparticles described in International Publications WO2008121949, WO2010005726, WO2010005725, WO2011084521 and U.S. Publications US20100069426, US20120004293, and US20100104655, each of which is incorporated herein by reference in its entirety.

[0219] The nanoparticles of the present invention may include a polymer matrix. As a non-limiting example, the nanoparticles may include two or more polymers, such as, but not limited to, polyethylene, polycarbonate, polyanhydride, polyhydroxy acid, polypropylene fumarate, polycaprolactone, polyamide, polyacetal, polyether, polyester, poly(orthoester), polycyanoacrylate, polyvinyl alcohol, polyurethane, polyphosphazene, polyacrylate, polymethacrylate, polyurea, polystyrene, polyamine, polylysine, poly(ethyleneimine), poly(serine ester), poly(L-lactide co-L-lysine), poly(4-hydroxy-L-proline ester), or combinations thereof.

[0220] In one embodiment, the therapeutic nanoparticles comprise a diblock copolymer. In another embodiment, the diblock copolymer may comprise a combination of PEG and a polymer.

[0221] Polymers include, but are not limited to, polyethylene, polycarbonate, polyanhydride, polyhydroxy acid, polypropylene fumarate, polycaprolactone, polyamide, polyacetal, polyether, polyester, poly(orthoester), polycyanoacrylate, polyvinyl alcohol, polyurethane, polyphosphazene, polyacrylate, polymethacrylate, polyurea, polystyrene, polyamine, polylysine, poly(ethyleneimine), poly(serine ester), poly(L-lactide co-L-lysine), poly(4-hydroxy-L-proline ester), or combinations thereof. In another embodiment, the diblock copolymer may include the diblock copolymers described in the European Patent Publication, the entire contents of which are incorporated herein by reference. In yet another embodiment, the diblock copolymer may be a high-X diblock copolymer, such as those described in International Patent Publication No. WO2013120052, the entire contents of which are incorporated herein by reference.

[0222] As a non-limiting example, therapeutic nanoparticles include PLGA-PEG block copolymers (see U.S. Publication No. US20120004293 and U.S. Patent No. 8,236,330, each of which is incorporated herein by reference in its entirety). In another non-limiting example, the therapeutic nanoparticles are stealth nanoparticles comprising diblock copolymers of PEG and PLA or PEG and PLGA (see U.S. Patent No. 8,246,968 and International Publication No. WO2012166923, each of which is incorporated herein by reference in its entirety). In yet another non-limiting example, the therapeutic nanoparticles are stealth nanoparticles or target-specific stealth nanoparticles, as described in U.S. Patent Publication No. US20130172406, the entire contents of which are incorporated herein by reference.

[0223] Therapeutic nanoparticles may include multiblock copolymers (see, for example, U.S. Patent Nos. 8,263,665, 8,287,910 and U.S. Patent Publication No. US20130195987; the contents of which are incorporated herein by reference in their entirety). In another non-limiting example, lipid nanoparticles include block copolymers PEG-PLGA-PEG (see, for example, the thermosensitive hydrogel (PEG-PLGA-PEG) used as a TGF-β1 gene delivery vector in Lee et al. Thermosensitive Hydrogel as a TGF-β1 Gene Delivery Vehicle Enhances Diabetic Wound Healing. Pharmaceutical Research, 2003 20(12): 1995-200; used as a controlled gene delivery system in Li et al. Controlled Gene Delivery System Based on Thermosensitive Biodegradable Hydrogel. Pharmaceutical Research 2003 20(6):884-888; and Chang et al., Non-ionic amphiphilicbiodegradable PEG-PLGA-PEG copolymer enhances gene delivery efficiency in ratskeletal muscle. J Controlled Release. 2007 118:245-253; each of which is incorporated herein by reference in its entirety).

[0224] The RNA vaccine of the present invention can be formulated into lipid nanoparticles comprising PEG-PLGA-PEG block copolymers. Therapeutic nanoparticles may comprise multiblock copolymers (see, for example, U.S. Patent Nos. 8,263,665, 8,287,910 and U.S. Patent Publication No. US20130195987; the contents of which are incorporated herein by reference in their entirety). The block copolymers described herein may be contained in polyionic complexes comprising nonpolymerized micelles and block copolymers (see, for example, U.S. Publication No. 20120076836; the entire contents of which are incorporated herein by reference).

[0225] Therapeutic nanoparticles may include at least one acrylic polymer. Acrylic polymers include, but are not limited to: acrylic acid, methacrylic acid, copolymers of acrylic acid and methacrylic acid, methyl methacrylate copolymers, ethoxyethyl methacrylate, cyanoethyl methacrylate, aminoalkyl methacrylate copolymers, poly(acrylic acid), poly(methacrylic acid), polycyanoacrylate, and combinations thereof.

[0226] Therapeutic nanoparticles may include at least one poly(vinyl ester) polymer. The poly(vinyl ester) polymer may be a copolymer, such as a random copolymer. As a non-limiting example, a random copolymer may have structures, for example, those described in International Application No. WO2013032829 or U.S. Patent Publication No. US20130121954, the contents of which are incorporated herein by reference in their entirety. In one aspect, the poly(vinyl ester) polymer may be conjugated to the polynucleotides described herein. In another aspect, the poly(vinyl ester) polymer used in the present invention may be one of the polymers described herein, the entire contents of which are incorporated herein by reference.

[0227] Therapeutic nanoparticles may include at least one diblock copolymer. The diblock copolymer may be, but is not limited to, a poly(lactic acid)-poly(ethylene) glycol copolymer (see, for example, International Patent Publication No. WO2013044219; the entire contents of which are incorporated herein by reference). As a non-limiting example, therapeutic nanoparticles may be used to treat cancer (see International Patent Publication No. WO2013044219; the entire contents of which are incorporated herein by reference).

[0228] In one embodiment, the therapeutic nanoparticles may include at least one cationic polymer described herein and / or known in the art.

[0229] Therapeutic nanoparticles may include at least one amine-containing polymer, such as, but not limited to, polylysine, polyethyleneimine, poly(amidoamine) dendritic polymers, poly(β-amino esters) (see, for example, U.S. Patent No. 8,287,849; the entire contents of which are incorporated herein by reference) and combinations thereof.

[0230] In another embodiment, the nanoparticles described herein may include amine cationic lipids, such as those described in International Patent Application No. WO2013059496 (the entire contents of which are incorporated herein by reference). In one aspect, the cationic lipids may have an amino-amine or amino-amide moiety.

[0231] Therapeutic nanoparticles may include at least one biodegradable polyester, which may have polycationic side chains. Biodegradable polyesters include, but are not limited to, poly(serine ester), poly(L-lactide co-L-lysine), poly(4-hydroxy-L-proline ester), and combinations thereof. In another embodiment, the biodegradable polyester may include PEG conjugations to form a PEGylated polymer.

[0232] Therapeutic nanoparticles may contain conjugations of at least one targeting ligand. The targeting ligand may be any ligand known in the art, such as, but not limited to, monoclonal antibodies (Kirpotin et al, Cancer Res. 2006 66:6732-6740; the full text of which is incorporated herein by reference).

[0233] Therapeutic nanoparticles can be formulated into aqueous solutions and can be used to target cancer (see International Publication No. WO2011084513 and US Publication No. US20110294717, each of which is cited in full and incorporated herein by reference).

[0234] Therapeutic nanoparticle RNA vaccines (e.g., therapeutic nanoparticles comprising at least one RNA vaccine) can be formulated using the method described by Podobinski et al. in U.S. Patent No. 8,404,799, the contents of which are incorporated herein by reference in their entirety.

[0235] RNA vaccines can be encapsulated, linked, and / or associated with synthetic nanocarriers. Synthetic nanocarriers include, but are not limited to, those described in international publications WO2010005740, WO2010030763, WO201213501, WO2012149252, WO2012149255, WO2012149259, WO2012149265, WO2012149268, WO2012149282, and WO201214. References to US Publications 9301, WO2012149393, WO2012149405, WO2012149411, WO2012149454 and WO2013019669, and US Publications US20110262491, US20100104645, US20100087337 and US20120244222, each of which is incorporated herein by reference in its entirety. The synthetic nanocarriers can be formulated using methods known in the art and / or those described herein. As a non-limiting example, synthetic nanocarriers can be formulated using the methods described in International Publications WO2010005740, WO2010030763, and WO201213501 and U.S. Publications US20110262491, US20100104645, US20100087337, and US2012024422, the entire contents of which are incorporated herein by reference. In another embodiment, synthetic nanocarrier formulations can be lyophilized using the methods described in International Publication WO2011072218 and U.S. Patent 8,211,473; the entire contents of which are incorporated herein by reference. In yet another embodiment, formulations of the present invention, including but not limited to synthetic nanocarriers, can be lyophilized or reconstituted using the methods described in U.S. Patent Publication US20130230568, the entire contents of which are incorporated herein by reference.

[0236] In one embodiment, the synthetic nanocarrier may contain reactive groups to release the polynucleotides described herein (see International Publication No. WO20120952552 and US Publication No. US20120171229, each of which is incorporated herein by reference in its entirety).

[0237] Synthetic nanocarriers may contain immunostimulants to enhance the immune response following delivery from the synthetic nanocarriers. As a non-limiting example, the synthetic nanocarriers may include Th1 immunostimulants that enhance Th1-based immune responses (see International Publication No. WO2010123569 and US Publication No. US20110223201, each incorporated herein by reference in its entirety). The synthetic nanocarriers may be formulated for targeted release. In one embodiment, the synthetic nanocarriers are formulated to release polynucleotides at a specified pH and / or after a desired time interval. As a non-limiting example, synthetic nanoparticles may be formulated to release an RNA vaccine after 24 hours and / or at pH 4.5 (see International Publications WO2010138193, WO2010138194 and US Publications US20110020388, US20110027217, each incorporated herein by reference in its entirety).

[0238] Synthetic nanocarriers can be formulated for controlled and / or sustained release of the polynucleotides described herein. As a non-limiting example, synthetic nanocarriers for sustained release can be formulated by methods known in the art, as described herein and / or as described in International Publication No. WO2010138192 and U.S. Publication No. 20100303850, each of which is incorporated herein by reference in its entirety.

[0239] In one embodiment, the RNA vaccine can be formulated for controlled and / or sustained release, wherein the formulation includes at least one polymer that is a crystalline side-chain (CYSC) polymer. CYSC polymers are described in U.S. Patent No. 8,399,007, the entire contents of which are incorporated herein by reference.

[0240] Synthetic nanocarriers can be formulated for use as vaccines. In one embodiment, the synthetic nanocarrier may encapsulate at least one polynucleotide encoding at least one antigen. As a non-limiting example, the synthetic nanocarrier may comprise at least one antigen and excipient for a vaccine formulation (see International Publication No. WO2011150264 and US Publication No. US20110293723, each of which is incorporated herein by reference in its entirety). As another non-limiting example, the vaccine formulation may comprise at least two synthetic nanocarriers and excipients having the same or different antigens (see International Publication No. WO2011150249 and US Publication No. US20110293701, each of which is incorporated herein by reference in its entirety). The vaccine formulation may be selected by methods described herein, known in the art, and / or described in International Publication No. WO2011150258 and US Publication No. US20120027806 (each of which is incorporated herein by reference in its entirety).

[0241] Synthetic nanocarriers may include at least one polynucleotide encoding at least one adjuvant. As a non-limiting example, the adjuvant may include dimethyl di(octadecyl)ammonium bromide, dimethyl di(octadecyl)ammonium chloride, dimethyl di(octadecyl)ammonium phosphate, or dimethyl di(octadecyl)ammonium acetate (DDA) and a nonpolar component or a portion of said nonpolar component from a total lipid extract of mycobacteria (see, for example, U.S. Patent No. 8,241,610, the entire contents of which are incorporated herein by reference). In another embodiment, the synthetic nanocarrier may include at least one polynucleotide and an adjuvant. As a non-limiting example, the synthetic nanocarrier and adjuvant may be formulated by methods described in International Publication No. WO2011150240 and U.S. Publication No. US20110293700, each of which is incorporated herein by reference in its entirety. The synthetic nanocarrier may encapsulate at least one polynucleotide encoding a peptide, fragment, or region derived from a virus. As a non-limiting example, the synthetic nanocarriers may include, but are not limited to, those described in International Publications WO2012024621, WO201202629, WO2012024632 and U.S. Publications US20120064110, US20120058153 and US20120058154, each of which is incorporated herein by reference in its entirety.

[0242] T-synthetic nanocarriers may be coupled with polynucleotides that may trigger humoral and / or cytotoxic T lymphocyte (CTL) responses (see, for example, International Publication No. WO2013019669, the full text of which is incorporated herein by reference).

[0243] In one embodiment, the RNA vaccine may be encapsulated, linked, and / or associated with zwitterionic lipids. Non-limiting examples of zwitterionic lipids and methods using zwitterionic lipids are described in U.S. Patent Publication No. US20130216607, the entire contents of which are incorporated herein by reference. In one aspect, zwitterionic lipids can be used in the liposomes and lipid nanoparticles described herein.

[0244] In one embodiment, the RNA vaccine may be formulated in a colloidal nanocarrier, as described in U.S. Patent Publication No. US20130197100, the contents of which are incorporated herein by reference in their entirety.

[0245] Nanoparticles can be optimized for oral administration. The nanoparticles may include at least one cationic biopolymer, such as, but not limited to, chitosan or derivatives thereof. As a non-limiting example, the nanoparticles may be formulated using the methods described in U.S. Patent Publication No. US20120282343, the entire contents of which are incorporated herein by reference. In some embodiments, lipid nanoparticles (LNPs) include the lipid KL52 (an aminolipid disclosed in U.S. Patent Application Publication No. 2012 / 0295832, the entire contents of which are explicitly incorporated herein by reference). Incorporation of these lipids can improve the activity and / or safety of LNP administration (as determined by detecting one or more of ALT / AST, white blood cell count, and cytokine induction). LNPs including KL52 can be administered intravenously and / or at one or more doses. In some embodiments, administration of LNPs including KL52 results in equivalent or improved mRNA and / or protein expression compared to LNPs including MC3.

[0246] In some implementations, smaller LNPs can be used to deliver RNA vaccines. These particles can have diameters ranging from less than 0.1 µm to 100 nm, for example, but not limited to, less than 0.1 µm, less than 1.0 µm, less than 5 µm, less than 10 µm, less than 15 µm, less than 20 µm, less than 25 µm, less than 30 µm, less than 35 µm, less than 40 µm, less than 50 µm, less than 55 µm, less than 60 µm, less than 65 µm, less than 70 µm, less than 75 µm, less than 80 µm, less than 85 µm, less than 90 µm, less than 95 µm, less than 100 µm, less than 125 µm, less than 150 µm, less than 175 µm, less than 200 µm, less than 225 µm, less than 250 µm, less than 275 µm, less than 300 µm, less than 325 µm, less than 350 µm, less than 375 µm, less than 400 µm, less than 425 µm, less than 450 µm. <475 µm, <500 µm, <525 µm, <550 µm, <575 µm, <600 µm, <575 µm, <650 µm, <675 µm, <700 µm, <725 µm, <775 µm, <800 µm, <825 µm, <850 µm, <875 µm, <900 µm, <925 µm, <950 µm, <975 µm.

[0247] RNA vaccines can be delivered using smaller LNPs, which may include diameters of approximately 1 nm to 100 nm, approximately 1 nm to 10 nm, approximately 1 nm to 20 nm, approximately 1 nm to 30 nm, approximately 1 nm to 40 nm, approximately 1 nm to 50 nm, approximately 1 nm to 60 nm, approximately 1 nm to 70 nm, approximately 1 nm to 80 nm, approximately 1 nm to 90 nm, approximately 5 nm to 100 nm, approximately 5 nm to 10 nm, approximately 5 nm to 20 nm, approximately 5 nm to 30 nm, approximately 5 nm to 40 nm, approximately 5 nm to 50 nm, approximately 5 nm to 60 nm, approximately 5 nm to 70 nm, approximately 5 nm to 80 nm, approximately 5 nm to 90 nm, approximately 10 nm to 50 nm, approximately 20 nm to 50 nm, approximately 30 nm to 50 nm, approximately 40 nm to 50 nm, approximately 20 nm to 60 nm, approximately 60 nm to 70 nm, approximately 70 nm to 20 nm, and approximately 70 nm to 20 nm. nm, about 40 to about 70 nm, about 50 to about 70 nm, about 60 to about 70 nm, about 20 to about 80 nm, about 30 to about 80 nm, about 40 to about 80 nm, about 50 to about 80 nm, about 60 to about 80 nm, about 20 to about 90 nm, about 30 to about 90 nm, about 40 to about 90 nm, about 50 to about 90 nm, about 60 to about 90 nm and / or about 70 to about 90 nm.

[0248] This LNP can be synthesized using methods that include microfluidic mixers. Exemplary microfluidic mixers may include, but are not limited to, slit-interlaced micromixers, including, but not limited to, products manufactured by Microinnova (Allerheiligen beiWildon, Austria) and / or slit-interlaced herringbone micromixers (SHM) (Zhigaltsev, IV et al., Bottom-up design and synthesis of limit size lipid nanoparticle systems with aqueous and triglyceride cores using millisecond microfluidic mixing, Langmuir. 2012. 28:3633-40; Belliveau, NM et al., Microfluidic synthesis of highly potent limit-size lipid nanoparticles for in vivo delivery of siRNA, Molecular Therapy-Nucleic Acids. 2012. 1:e37; Chen, D. et al., Rapid discovery of potent siRNA-containing lipid nanoparticles enabled by controlled microfluidic formulation, J Am Chem Soc. 2012.) 134(16):6948-51; each of which is incorporated herein by reference in its entirety. In some embodiments, the method for preparing LNPs using SHM further includes mixing at least two feed streams, wherein mixing is achieved through microstructure-induced chaotic convection (MICA). According to this method, the fluid stream flows through a herringbone-patterned channel, thereby generating a rotating flow and causing the fluids to intertwine and entangle. This method may also include a surface for fluid mixing that changes orientation during fluid circulation. The method for preparing LNPs using SHM includes the disclosures of U.S. Patent Application Publications 2004 / 0262223 and 2012 / 0276209, each of which is incorporated herein by reference in its entirety.

[0249] The RNA vaccine of the present invention can be formulated into lipid nanoparticles using micromixers such as, but not limited to, the Slit Interdigital Microstructured Mixer (SIMM-V2), Standard Slit Interdigital Micro Mixer (SSIMM), Caterpillar (CPMM), or Impinging-jet (IJMM) from Institute Fiir Mikrotechnik Mainz GmbH, Mainz, Germany. The RNA vaccine of the present invention can be formulated as lipid nanoparticles using microfluidic technology (see Whitesides, George M. The Origins and the Future of Microfluidics. Nature, 2006 442: 368-373; Abraham et al. ChaoticMixer for Microchannels. Science, 2002 295: 647-651; each cited in full herein). As a non-limiting example, controllable microfluidic formulation technology includes a passive method of mixing constant-pressure driven fluid flows in microchannels at low Reynolds numbers (see, for example, Abraham et al. Chaotic Mixer for Microchannels. Science, 2002 295: 647-651; the entire text of which is incorporated herein by reference). The RNA vaccine of the present invention can be formulated into lipid nanoparticles produced using a micromixer chip, for example, but not limited to those from Harvard Apparatus (Holliston, Massachusetts) or Dolomite Microfluidics (Royston, UK). The micromixer chip can be used to rapidly mix two or more fluid flows using a splitting and recombination mechanism.

[0250] The RNA vaccine of the present invention can be formulated into a preparation for delivery using drug-encapsulated microspheres as described in International Patent Publication No. WO2013063468 or US Patent No. 8,440,614, the entire contents of which are incorporated herein by reference. The microspheres may include compounds of formulas (I), (II), (III), (IV), (V), or (VI) as described in International Patent Publication No. WO2013063468, the entire contents of which are incorporated herein by reference. Alternatively, amino acids, peptides, polypeptides, and lipids (APPL) may be used to deliver the RNA vaccine of the present invention into cells (see International Patent Publication No. WO2013063468, the entire contents of which are incorporated herein by reference).

[0251] The RNA vaccine of the present invention can be formulated into lipid nanoparticles with a diameter of about 10 to about 200 nm, such as, but not limited to, about 10 to about 20 nm, about 10 to about 30 nm, about 10 to about 40 nm, about 10 to about 50 nm, about 10 to about 60 nm, about 10 to about 70 nm, about 10 to about 80 nm, about 10 to about 90 nm, about 20 to about 30 nm, about 20 to about 40 nm, about 20 to about 50 nm, about 20 to about 60 nm, about 20 to about 70 nm, about 20 to about 80 nm, about 20 to about 90 nm, about 20 to about 100 nm, about 30 to about 40 nm, about 30 to about 50 nm, about 40 to about 60 nm, about 40 to about 70 nm, about 40 to about 80 nm, about 40 to about 80 nm, about 40 to about 80 nm, about 30 to about 80 nm, about 30 to about 70 nm, about 30 to about 80 nm, about 30 to about 100 nm, about 40 to about 50 nm, about 40 to about 60 nm, about 40 to about 70 nm, about 40 to about 80 nm, about 40 to about 80 nm, about 30 to about 80 nm, about 30 to about 70 nm, about 30 to about 80 nm, about 30 to about 80 nm, about 30 to about 70 nm, about 30 to about 80 nm, about 30 to about 70 nm, about 30 to about 80 nm, about 30 to about 70 nm, about 30 to about 80 nm, about 30 to about nm, about 40 to about 90 nm, about 40 to about 100 nm, about 50 to about 60 nm, about 50 to about 70 nm, about 50 to about 80 nm, about 50 to about 90 nm, about 50 to about 100 nm, about 50 to about 150 nm, about 50 to about 200 nm, about 60 to about 70 nm, about 60 to about 80 nm, about 60 to about 90 nm, about 60 to about 150 nm, about 70 nm, about 90 to about 70 nm, about 90 nm, about 70 to about 100 nm, about 70 to about 150 nm, about 70 to about 200 nm, about 80 to about 90 nm, about 80 to about 100 nm, about 80 to about 150 nm, about 80 to about 200 nm, about 90 to about 100 nm, about 90 to about 150 nm, and / or about 90 to about 200 nm.

[0252] Lipid nanoparticles can have diameters ranging from approximately 10 to 500 nm.

[0253] In one embodiment, the lipid nanoparticles may have a diameter greater than 100 nm, greater than 150 nm, greater than 200 nm, greater than 250 nm, greater than 300 nm, greater than 350 nm, greater than 400 nm, greater than 450 nm, greater than 500 nm, greater than 550 nm, greater than 600 nm, greater than 650 nm, greater than 700 nm, greater than 750 nm, greater than 800 nm, greater than 850 nm, greater than 900 nm, greater than 950 nm, or greater than 1000 nm.

[0254] The lipid nanoparticles may be the size-restricted lipid nanoparticles described in International Patent Publication No. WO2013059922, the entire contents of which are incorporated herein by reference. Size-restricted lipid nanoparticles may include a lipid bilayer surrounding an aqueous or hydrophobic core; wherein the lipid bilayer may include phospholipids, such as, but not limited to, diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramides, sphingomyelin, dihydrosphingomyelin, cephalin, cerebrosides, C8-C20 fatty acid diacylphosphatidylcholine, and 1-palmitoyl-2-oleoylphosphatidylcholine (POPC). Alternatively, size-restricted lipid nanoparticles may include polyethylene glycol-lipids, such as, but not limited to, DLPE-PEG, DMPE-PEG, DPPC-PEG, and DSPE-PEG.

[0255] RNA vaccines can be delivered, positioned, and / or concentrated at specific locations using the delivery method described in International Patent Publication No. WO2013063530, the entire contents of which are incorporated herein by reference. As a non-limiting example, empty polymer particles can be administered to a subject before, simultaneously with, or after the delivery of an RNA vaccine. Upon contact with the subject, the empty polymer particles undergo a volume change and become contained, embedded, fixed, or captured at specific locations within the subject.

[0256] RNA vaccines can be formulated in active substance release systems (see, for example, U.S. Patent Publication No. US20130102545, the entire contents of which are incorporated herein by reference). An active substance release system may include 1) at least one nanoparticle bound to an oligonucleotide inhibitory chain hybridized to a catalytically active nucleic acid and 2) a compound bound to at least one substrate molecule linked to a therapeutically active substance (e.g., a polynucleotide described herein), wherein the therapeutically active substance is released by cleavage of the substrate molecule by the catalytically active nucleic acid.

[0257] RNA vaccines can be formulated into nanoparticles comprising a core containing non-cellular material and an outer surface containing a cell membrane. The cell membrane can be derived from a cell or a viral membrane. As a non-limiting example, the nanoparticles can be prepared by the method described in International Patent Publication No. WO2013052167, the entire contents of which are incorporated herein by reference. As another non-limiting example, the nanoparticles described in International Patent Publication No. WO2013052167 can be used to deliver the RNA vaccine described herein, the entire contents of which are incorporated herein by reference.

[0258] RNA vaccines can be formulated in a lipid bilayer (protocells) supported by porous nanoparticles. The protocells are described in International Patent Publication No. WO2013056132, the contents of which are incorporated herein by reference in their entirety.

[0259] The RNA vaccines described herein can be formulated into polymer nanoparticles, as described or prepared by methods described in U.S. Patents 8,420,123 and 8,518,963 and European Patent EP2073848B1, the contents of which are incorporated herein by reference in their entirety. As a non-limiting example, the polymer nanoparticles may have a high glass transition temperature, such as the nanoparticles described in U.S. Patent 8,518,963 or nanoparticles prepared by methods thereof, the contents of which are incorporated herein by reference in their entirety. As another non-limiting example, polymer nanoparticles for oral and parenteral formulations can be prepared by methods described in European Patent EP2073848B1, the contents of which are incorporated herein by reference in their entirety.

[0260] The RNA vaccines described herein can be formulated into nanoparticles for imaging. The nanoparticles may be liposome nanoparticles, such as those described in U.S. Patent Publication No. US20130129636, the entire contents of which are incorporated herein by reference. As a non-limiting example, liposomes may comprise 2-{4,7-bis-carboxymethyl-10-[(N,N-distearivamidomethyl-N'-amidomethyl]-1,4,7,10-tetraazacyclododecane-1-yl}-gadolinium(III) and a neutral, fully saturated phospholipid component (see, for example, U.S. Patent Publication No. US20130129636, the entire contents of which are incorporated herein by reference).

[0261] The nanoparticles used in this invention can be formed by the method described in U.S. Patent Application No. US20130130348, the entire contents of which are incorporated herein by reference. The nanoparticles of this invention may also contain nutrients, such as, but not limited to, those deficiencies that can lead to health hazards ranging from anemia to neural tube defects (see, for example, the nanoparticles described in International Patent Publication No. WO2013072929, the entire contents of which are incorporated herein by reference). As a non-limiting example, the nutrients may be ferrous iron, ferric salts, or elemental iron, iodine, folic acid, vitamins, or micronutrients.

[0262] The RNA vaccine of the present invention can be formulated into swellable nanoparticles. The swellable nanoparticles may be, but are not limited to, those described in U.S. Patent No. 8,440,231, the entire contents of which are incorporated herein by reference. As a non-limiting embodiment, the swellable nanoparticles can be used to deliver the RNA vaccine of the present invention to the pulmonary system (see, for example, U.S. Patent No. 8,440,231, the entire contents of which are incorporated herein by reference).

[0263] The RNA vaccine of the present invention can be formulated into polyanhydride nanoparticles, such as, but not limited to, those described in U.S. Patent No. 8,449,916, the entire contents of which are incorporated herein by reference.

[0264] The nanoparticles and microparticles of the present invention can be geometrically engineered to modulate macrophage and / or immune responses. In one aspect, the geometrically engineered particles can have different shapes, sizes, and / or surface charges to encapsulate the polynucleotides of the present invention and achieve targeted delivery, for example, but not limited to, lung delivery (see, for example, International Publication No. WO2013082111, the entire contents of which are incorporated herein by reference). Other physical characteristics that geometrically engineered particles may possess include, but are not limited to, windowing, angled arms, asymmetry and surface roughness, and charges that can alter interactions with cells and tissues. As a non-limiting example, the nanoparticles of the present invention can be prepared by the method described in International Publication No. WO2013082111, the entire contents of which are incorporated herein by reference.

[0265] The nanoparticles of this invention can be water-soluble nanoparticles, such as, but not limited to, those described in International Publication No. WO2013090601, the entire contents of which are incorporated herein by reference. The nanoparticles can be inorganic nanoparticles with tightly packed zwitterionic ligands to exhibit good water solubility. The nanoparticles can also have small hydrodynamic diameter (HD), stability relative to time, pH, and salinity, and low levels of nonspecific protein binding. In one embodiment, the nanoparticles of this invention can be developed by the method described in U.S. Patent Publication No. US20130172406, the entire contents of which are incorporated herein by reference.

[0266] The nanoparticles of this invention may be stealth nanoparticles or target-specific stealth nanoparticles, such as, but not limited to, those described in U.S. Patent Publication No. US20130172406, the entire contents of which are incorporated herein by reference. The nanoparticles of this invention may be prepared by the method described in U.S. Patent Publication No. US20130172406, the entire contents of which are incorporated herein by reference.

[0267] Stealthy or target-specific stealth nanoparticles may comprise a polymer matrix. The polymer matrix may comprise two or more polymers, such as, but not limited to, polyethylene, polycarbonate, polyanhydride, polyhydroxy acid, polypropylene fumarate, polycaprolactone, polyamide, polyacetal, polyether, polyester, poly(orthoester), polycyanoacrylate, polyvinyl alcohol, polyurethane, polyphosphazene, polyacrylate, polymethacrylate, polycyanoacrylate, polyurea, polystyrene, polyamine, polyester, polyanhydride, polyether, polyurethane, polymethacrylate, polyacrylate, polycyanoacrylate, or combinations thereof.

[0268] Nanoparticles may be nanoparticle-nucleic acid hybrid structures with a high-density nucleic acid layer. As a non-limiting example, nanoparticle-nucleic acid hybrid structures can be prepared by the method described in U.S. Patent Publication No. US20130171646, the entire contents of which are incorporated herein by reference. Nanoparticles may include nucleic acids, such as, but not limited to, those described herein and / or polynucleotides known in the art.

[0269] Nanoparticles can be embedded in the core of a nanostructure or coated with a low-density porous 3D structure or coating, and can carry or associate at least one effective load within or on the surface of the nanostructure. Non-limiting examples of nanostructures including at least one nanoparticle are described in International Patent Publication No. WO2013123523, the contents of which are incorporated herein by reference in their entirety.

[0270] Other formulations include those described in US20170136121A1, US9221891B2, EP2971033B1 and US20160331828A1, the full text of which is incorporated herein by reference.

[0271] A method for generating mRNA encoding at least one immunogenic peptide fragment is also provided, the method comprising: (a) A first polynucleotide comprising an open reading frame encoding an immunogenic peptide fragment and a second polynucleotide comprising a 5'-UTR are conjugated to a solid support; (b) under suitable conditions, the 3' end of the second polynucleotide is ligated to the 5' end of the first polynucleotide, wherein the suitable conditions include a DNA ligase, thereby producing a first ligation product; (c) under suitable conditions, ligating the 5' end of a third polynucleotide including a 3'-UTR to the 3' end of a first ligation product, wherein said suitable conditions include RNA ligase, thereby producing a second ligation product; and (d) Release the second bonding product from the solid support.

[0272] This results in the production of mRNA encoding immunogenic peptide fragments.

[0273] A kit is also provided for preparing mRNA cancer vaccines. The kit may have one or more containers containing one or more polynucleotides including a 5'-ORF, one or more polynucleotides including a 3'-ORF, one or more polynucleotides including a poly(A) tail, a ligase, and instructions for ligating one or more polynucleotides including an ORF encoding a patient-specific epitope to one or more polynucleotides including a 5'-ORF, a 3'-ORF, and a poly(A) tail.

[0274] An exemplary preferred composition according to the present invention comprises, but is not limited to, the following:

[0275] • According to the invention, the composition comprises two or more different polypeptides, and more preferably, the composition comprises 2 to about 20, about 30, about 40, or preferably about 50 different polypeptides, and optionally, the different polypeptides are included in a continuous polypeptide sequence.

[0276] The polynucleotide according to the invention is preferably mRNA, more preferably the mRNA encodes 2 to about 20, about 30, about 40 or preferably about 50 different polypeptides, and optionally the polynucleotide is a single mRNA molecule encoding 2 to about 20, about 30, about 40 or preferably about 50 different polypeptides.

[0277] • A variety of polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, and preferably wherein the polypeptides are 8-11 polymers (e.g., a variety of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0278] • A polypeptide comprising preferably 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein each polypeptide of the present invention is an 8-11 polymer (e.g., for example, multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0279] • An mRNA molecule comprising sequences encoding a plurality of polypeptides of the present invention, preferably wherein the mRNA molecule encodes 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally wherein the mRNA molecule encodes a plurality of polypeptides within a frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0280] • Multiple mRNA molecules encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, and preferably wherein the polypeptides are 8-11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0281] • A DNA molecule comprising sequences encoding a plurality of polypeptides of the present invention, preferably wherein the DNA molecule encodes 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, and preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally wherein the DNA molecule encodes a plurality of polypeptides within a frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0282] • Multiple DNA molecules encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0283] A viral vector comprising sequences encoding multiple polypeptides of the present invention, preferably wherein the viral vector encodes 2 to 20, 30, 40, or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8-11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally wherein multiple polypeptides are encoded within the viral vector frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0284] • Multiple viral vectors encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8-11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0285] • A variety of polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a variety of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptide is an 8 to 100 polymer, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0286] • An mRNA molecule comprising sequences encoding multiple polypeptides of the present invention, preferably wherein the DNA molecule encodes 2 to 20, 30, 40, or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptides are 8 to 100 polymers, and optionally wherein multiple polypeptides are encoded within the DNA molecule frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0287] • Multiple mRNA molecules encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptides are 8 to 100 polymers, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0288] • A DNA molecule comprising sequences encoding a plurality of polypeptides of the present invention, preferably wherein the DNA molecule encodes 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptides are 8 to 100 polymers, and optionally wherein the DNA molecule encodes a plurality of polypeptides within a frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0289] • Multiple DNA molecules encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptides are 8 to 100 polymers, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0290] A viral vector comprising sequences encoding multiple polypeptides of the present invention, preferably wherein the viral vector encodes 2 to 20, 30, 40, or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptides are 8 to 100 polymers, and optionally wherein multiple polypeptides are encoded within the viral vector frame to form a continuous polypeptide, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0291] • Multiple viral vectors encoding multiple polypeptides of the present invention, preferably comprising 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the polypeptides are 8 to 100 polymers, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0292] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a variety of polypeptides of the present invention, preferably wherein the variety of polypeptides comprises 2 to 20, 30, 40, or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8-11 polymers (e.g., a variety of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), wherein the syngeneic DC is adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or an excipient.

[0293] • A syngeneic (patient-derived) dendritic cell (DC) maturation in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein maturation is performed by transfection with mRNA carrying the coding sequences of the plurality of polypeptides, wherein the syngeneic DC is adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0294] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein maturation is performed by transfection with a plurality of mRNA molecules, wherein each mRNA molecule carries a coding sequence for one of the plurality of polypeptides, wherein the syngeneic DC is adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0295] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the polypeptides are 8 to 100 polymers, preferably wherein maturation is achieved by transfection with mRNA carrying the coding sequences of the plurality of polypeptides, wherein the syngeneic DC is adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0296] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the polypeptides are 8 to 100 polymers, preferably wherein maturation is performed by transfection with a plurality of mRNA molecules, wherein each mRNA molecule carries a coding sequence for one of the plurality of polypeptides, wherein the syngeneic DC is adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0297] • A syngeneic (patient-derived) dendritic cell (DC) maturation in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein maturation is performed by infection with a viral vector carrying the coding sequences of the plurality of polypeptides, wherein the syngeneic DCs are adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0298] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention, preferably wherein the polypeptides are 8 to 11 polymers (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein maturation is achieved by infection with a plurality of viral vectors, wherein each viral vector molecule carries a coding sequence of one of the plurality of polypeptides, wherein the syngeneic DCs are adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0299] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the polypeptides are 8 to 100 polymers, preferably wherein maturation is performed by infection with a viral vector carrying the coding sequences of the plurality of polypeptides, wherein the syngeneic DCs are adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0300] • A syngeneic (patient-derived) dendritic cell (DC) maturated in vitro by incubation with a plurality of polypeptides of the present invention, preferably wherein the plurality of polypeptides comprises 2 to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., a plurality of camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the polypeptides are 8 to 100 polymers, preferably wherein maturation is achieved by infection with a plurality of viral vectors, wherein each viral vector molecule carries a coding sequence of one of the plurality of polypeptides, wherein the syngeneic DCs are adapted for reintroduction into a patient, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0301] • A CAR-T cell carrying a receptor for one or more peptides of the present invention, preferably up to 20, 30, 40 or preferably 50 different peptides, preferably wherein the peptides are 8-11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0302] • A CAR-T cell carrying a receptor for one or more peptides of the present invention, preferably up to 20, 30, 40 or preferably 50 different peptides (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), preferably wherein the peptides are 8-100 polymers, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0303] • Multiple antibodies, which are generated against one or more polypeptides of the present invention, preferably up to 20, 30, 40 or preferably 50 different polypeptides of the present invention, and preferably wherein the polypeptides are 8-11 polymers (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or an excipient.

[0304] • Multiple antibodies generated against one or more polypeptides of the present invention, preferably up to 20, 30, 40 or preferably 50 different polypeptides of the present invention (e.g., multiple camyo epitopes as defined herein according to SEQ ID NO: 98 to 611), and preferably wherein the polypeptide is an 8-100 polymer, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative and / or excipient.

[0305] • Any of the described vaccine compositions, combined with other tumor antigens, may be used as a combination vaccine, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or excipient.

[0306] • Any of the vaccine compositions described herein, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or excipient, preferably wherein the composition is suitable for any route of administration (e.g., intravenous, intramuscular, intrathecal).

[0307] • Any of the vaccine compositions described herein, and optionally at least one adjuvant, a pharmaceutically acceptable carrier, a preservative, and / or excipient, in combination with any kind of other modality of treatment.

[0308] Treatment methods, diagnostic methods, and other uses

[0309] The polypeptides, polynucleotides, carriers, cells, or compositions of the present invention can be used in methods for treating or preventing diseases or conditions in subjects. The polypeptides, polynucleotides, carriers, cells, or compositions of the present invention can be used in the preparation of medicaments for treating or preventing diseases or conditions in subjects.

[0310] The terms “treatment,” “curing,” or “improvement” refer to therapeutic or preventative / preventive treatment. Treatment is therapeutic if it improves symptoms of at least one disease in an individual, or if it delays the progression of the disease or prevents the onset of other related diseases.

[0311] The terms "prevention," "protection," and "preventatively" refer to the administration of a compound before the onset of a disease (e.g., before the onset of certain symptoms of the disease). Disease prevention may include reducing the likelihood of disease occurrence, delaying the onset of disease, improving long-term symptoms, or delaying the eventual progression of disease.

[0312] The method includes administering the polypeptide, the polynucleotide, the carrier, the cell, or the composition to the subject. A therapeutically effective or prophylactically effective amount of the polypeptide, the polynucleotide, the carrier, the cell, or the composition may be administered to the subject in need. Administration may be via any suitable route, such as intranasal, intravenous (IV), intradermal, intramuscular (IM), intrathecal (IT), or intraperitoneal. In some embodiments, administration is a single dose. IV, IM, and IT are preferred. In some embodiments, the polypeptide, polynucleotide, carrier, cell, or composition may be administered to the subject more than once.

[0313] In the method of the present invention, the cells of the present invention are applied to a subject, preferably the cells being genetically homologous to the subject.

[0314] The disease or condition may be colorectal cancer, preferably microsatellite stable colorectal cancer (MSS-CRC). Treatment or prevention may involve inducing an immune response against colorectal cancer in an individual. Subjects may have colorectal cancer at any stage.

[0315] Subjects requiring treatment may have either an active or a weakened immune system. Technicians understand the characteristics of a weakened immune system. For example, a weakened immune system may be characterized by a reduced ability of effector T cells to secrete cytokines compared to an individual with a healthy immune system.

[0316] The method may include simultaneous or sequential administration with other cancer therapies. These other cancer therapies may be selected from cytokine therapy, T-cell therapy, NK therapy, immune system checkpoint inhibitors, chemotherapy, radiation therapy, immunostimulants, gene therapy, or antibodies. Preferably, any known colorectal cancer therapy may be preferred.

[0317] Immune system checkpoint inhibitors are preferred as an additional cancer therapy. Examples of immune system checkpoints include: a) The interaction between indoleamine 2,3-dioxygenase (IDO1) and its substrate; b) The interaction between PD1 and PDL1 and / or PD1 and PDL2; c) Interactions between CTLA4 and CD86 and / or CTLA4 and CD80; d) Interactions between B7-H3 and / or B7-H4 and their respective ligands; e) The interaction between HVEM and BTLA; f) The interaction between GAL9 and TIM3; g) Interactions between type I or type II MHCs and LAG3; and h) Interactions between Class I or Class II MHCs and KIRs.

[0318] Checkpoint inhibitors can be any immunomodulator (e.g., an antibody) that blocks or inhibits checkpoints of the immune system, or can be an immunotherapeutic composition that includes components of the immune system checkpoints or immunogenic fragments of said components, which stimulate the immune system to target the checkpoints.

[0319] Another cancer treatment option is antibodies.

[0320] The antibodies may include abavoxib, abcixib, accumulumab, adalimumab, adetoxib, afemoxib, afutuzumab, acetumumab, pegoxib, ALD518, alenzab, allizumab, artumumab, pentrozine, amatoxib, anatoxib, malatadine, anruginzab, apolizumab, acetoxib, acetoxib, and acetoxib. Atenumab, Atolizumab (=Tocilizumab), Atolizumab, Bavizumab, Baliximab, Bavituscitumab, Bectomumab, Belimumab, Benalizumab, Betilizumab, Betilizumab, Besoxumab, Bevacizumab, Belotuscitumab, Bisirolimus, Bimarumab, Bivartuscitumab (Metansin), Bonatumab, Eloxumab Bentoximab, Vitin, Brigitte, Brodatumab, Canatumab, Cantuzumab, Metaseline, Cantuzumab, Lavaltansin, Caprizumab, Captotumumab, Pendimethalin, Carolumab, Captoxomab, CC49, Siddilimumab, Cetrusumab, Pegox, Cetuximab, Ch.14.18, Sitadecumumab, Pogato, Cetuximab, Krazazumab, Crenliximab, Klevatocumab, Tetrahexose, Conamucin, Conxicumab, Knifedilimumab, CR6261, Dacituzumab, Dalizumab, Dalotuzumab, Dalotuzumab, Decizumab, Denosumab, Dolimomab, Alito, Zozartuzumab, Duligoruzumab, Dupilumab, Ducigituzumab Antibiotics, Eclomexicox, Iculizumab, Edobamoxicillin, Ezocurumab, Efalizumab, Ifencoumarab, Elotuzumab, Elotuzumab, Ecilizumab, Enatuzumab, Enlimomab, Pego, Enochizumab, Enochetizumab, Encetoxicox, Epimetuzumab, Cetrastane, Ipatizumab, Erizumab, Erlizumab, Ertomac, Etatram. Anti-, Etroribizumab, Ivocurumab, Ekovirumab, Fanosomumab, Falalimumab, Falatozumab, Fasinumab, FBTA05, Flavizumab, Fizajinumab, Flavoxetumab, Fragatozumab, Fravoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Flavoxetumab, Galixetumab, Gantenalimumab, Gavilimoumab, Gejutuzumab, Ozomicin, Gvogizumab, Gelentozumab, Glebetozumab, Vitin, Golimumab, Gomiliximab, GS6624, Ibarizumab, Tiimozumab, Ikrugumab, Igvovumab, Insirozumab, Ingatozumab, Inclazatumab, Indazotumab Lavalitancieneca, Infliximab, Intitutumab, Enoximozumab, Ozomicin, Ipilimumab, Iratocilizumab, Itocilizumab, Ixizumab, Keliximab, Labetizumab, Lanparibizumab, Lelicilizumab, Lemasoxumab, Ledlicilizumab, Lexatrazumab, Libivirumab, LigiricilizumabLintozumab, Lilirumab, Lodexizumab, Lovotozumab, Metansine, Lucatumumab, Lumiliximab, Mapatumumab, Maslimumab, Mavriliximab, Matozumab, Mepalizumab, Meteliximab, Milatumab, Minrutozumab, Mitozumab, Mogliximab, Moroliximab, Motazumab, Mosetumab, Parsidodactone, Moromona-CD3, Nacomomab, Tafenalo, Namirumab, Naptozumab, Etafenalo, Nanatozumab, Natazumab, Nebakumab, Nexiximab, Neraliximab, Nesvacuumab, Nitozumab, Nivolumab, Nofetozumab, Mebentan, Obintozumab, Oka Latozumab, Orizumab, Odulimomab, Ofamumab, Olanzab, Olokizumab, Omarzab, Onatuzumab, Optozumab, Ogovomumab, Otecurumab, Oteliximab, Oxylurumab, Ozolamumab, Ozolamumab, Perzibaci, Pallizumab, Panibakumab, Persatuzumab, Pascolizumab, Pateklizumab, Pertuzumab, Pembrolizumab, Pentozumab, Peracuzumab, Pertuzumab, Pexiximab, Pidtilimab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab, Pentozumab 140. Quinolizumab, Lacotomumab, Laretomumab, Lafifevirumab, Ramucirumab, Ranibizumab, Racibaciximab, Regavirumab, Relizumab, Rilotumab, Rituximab, Robacirumab, Romossuzumab, Romossuzumab, Runterolizumab, Rovirolizumab, Rupulolizumab, Samarolizumab, Sariluzumab Satomumab, pendimethalin, secukinumab, seribanumab, cetoxaximab, sevirumab, sibutruzumab, cifalimumab, cilizumab, cetuzumab, ciprizumab, cilukumab, sorapuzumab, soritumab, soneprezumab, sotozumab, tamulumab, sulesomumab, sevirumab, tabarumab, tacalutumab Tadocemumab tetraxose, Tadocemumab, Talizumab, Tanezumab, Taprizumab, Paptoto, Tefilbaximab, Telizumab, Alitoto, Tenatozumab, Teneriximab, Teprizumab, Teprizumab, TGN1412, Teximumab (= Trimelimumab), Tedezumab, Tegalzumab, TNX-650, Tocilizumab (= Atolizumab, tolaolizumab, tosimozumab, tralacinumab, trastuzumab, TRBS07, trogazumab, trimelimumab, tococurumab, selmorukin, tuverumab, ulituximab, urerumab, ultosac, uterotumab, vapaliximab, valtizumab, vedozumab, vertuzumab, virtuzumab, virtuzumab, virpalimozumabVesincuumab, Vesizumab, Voloxizumab, Vorsutozumab, Mafudin, Vorsutozumab, Zalutuzumab, Zanolimub, Zalutuzumab, Zalutuzumab, Zolalimumab, or Zorimumab (Alato).

[0321] Preferred antibodies include natezumab, vedolizumab, belimumab, acecilip, alexandrazepam, oteliximab, teplezumab, rituximab, oflavumab, ozoglucomab, iprazizumab, alenzab, abatacept, iculizumab, omalizumab, canatumab, mepolizumab, rellizumab, tocilizumab, uterotium, brevizizumab, etanercept, infliximab, adalimumab, cetozumab, golimumab, trastuzumab, gemtuzumab, ozomicin, teimozumab, teimozumab, tosimob, cetuximab, bevacizumab, panitumumab, deshutumab, ipilimumab, bentoximab, and vetin.

[0322] Anti-PD1 antibodies such as nivolumab and pembrolizumab are also preferred.

[0323] Other cancer treatment options include a combination of free thalidomide, azacitidine, azathioprine, bleomycin, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, deoxyfluorouridine, doxorubicin, epirubicin, etoposide, fludarabine, fluorouracil, gemcitabine, hydroxyurea, idarubicin, irinotecan, lenalidomide, leucovorin, nitrogen mustard, melphalan, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, lenalidomide, temozolomide, teniposide, thioguanine, pentorubicin, vincristine, vinblastine, vinorelbine, vindesine, and vinorelbine.

[0324] The present invention also provides a method for diagnosing a disease or condition in a subject. The method includes analyzing the presence of one or more camyoRNA, camyo peptide, or camyo epitope sequences disclosed herein in a sample taken from the individual, wherein the presence of said sequences, optionally at an elevated level relative to corresponding levels in a sample taken from a healthy subject, indicates that the individual has colorectal cancer or is at increased risk for it. The sample can be any suitable sample, such as a tumor biopsy or other tissue or fluid sample. The sequences in the sample can be detected by any suitable method, including those described herein. For example, the method may include measuring an immune response evoked in response to the sample.

[0325] The invention is further illustrated by the following embodiments; however, these embodiments should not be construed as limiting the scope of protection. The features disclosed in the foregoing description and the following embodiments may be, individually or in any combination thereof, in different forms, constitute the material for implementing the invention.

[0326] Table 3

[0327] CamyoRNA Expression coverage Baseline Mean <![CDATA[log2 multiple change]]> Normal mean TPM Mean tumor mass (TPM) SEQ ID NO camyoRNA number lnc-TRPC5-3:1 97.5 318.5721773 6.008808492 0.103389388 5.163076308 1 1 lnc-HOXB8-1:5 77.92 557.1827017 6.245253412 0.071819909 4.408348056 2 11 lnc-SLC39A10-2:1 75.83 116.3258911 7.160784732 0.046219876 5.080354424 3 2 lnc-TH-1:1 72.92 1882.813689 8.274754045 0.057297395 14.15389676 4 8 lnc-SLC39A10-7:1 71.25 155.4054043 7.363136044 0.021145659 2.798184874 5 6 CYP1B1-AS1:12 62.92 60.54029527 7.48002405 0.125151118 18.04120882 6 17 lnc-LRRTM4-3:3 59.17 45.85682261 7.478925532 0.011667005 1.35285096 7 18 LINC02418:9 55.42 183.5313217 11.18174359 0.000600914 1.354811113 8 4 LINC02563:3 50 5.785799437 7.718261333 0.010117382 1.635045411 9 14 lnc-OR52J3-1:1 45.83 48.42286448 6.44292717 0.061776652 4.465071022 10 16 lnc-FANCM-10:1 43.33 60.0286497 7.382898449 0.06247368 8.570731129 11 7 lnc-HSF5-2:1 42.08 30.58961936 7.43878821 0.014749631 2.58211221 12 5 lnc-TACR3-1:1 25 30.6932299 7.315185116 0.030091188 3.825574581 13 12 lnc-CAMK1D-2:1 12.92 20.38474189 5.370875612 0.078014653 3.159821959 14 9 lnc-PLA2G1B-2:3 8.33 378.3920214 5.184820977 0.133099558 2.976924064 15 3 lnc-CTR9-1:2 7.92 37.56762553 6.313637203 0.358941273 14.36570473 16 10 LINC01715:13 7.5 17.40558898 6.27086754 0.014818106 1.078654387 17 3 lnc-CHM-1:1 6.25 1.278129006 7.766517095 0.010291955 2.432198743 18 15

[0328] Table 4

[0329] Camyo peptides SEQ IDNO peptide sequence Translation coverage (MS) Camyo RNA Encoding probability peptide length Maximum value of sample BMSt Sample BMSt median lncTRPC53116031801 19 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASNYAALS* 81.05 lnc-TRPC5-3:1 0.92672619 66 0.000420875 0 lncTRPC531701830 20 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* 47.37 lnc-TRPC5-3:1 0.94672619 43 0 0 lncTRPC531668830 21 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* 47.37 lnc-TRPC5-3:1 0.948571429 54 0 0 lncTRPC5318691010 22 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* 45.26 lnc-TRPC5-3:1 0.983690476 47 0 0 lncTRPC531722830 23 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* 44.21 lnc-TRPC5-3:1 0.960059524 36 0 0 lncTRPC531734830 24 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* 44.21 lnc-TRPC5-3:1 0.960654762 32 0 0 lncTRPC531755830 25 MDMVAGIAMMTKAAETMIEAMIPG* 42.11 lnc-TRPC5-3:1 0.935416667 25 0 0 lncTRPC531761830 26 MVAGIAMMTKAAETMIEAMIPG* 40 lnc-TRPC5-3:1 0.972738095 23 0 0 lncTRPC5318721010 27 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* 33.68 lnc-TRPC5-3:1 0.99077381 46 0 0 lncTRPC5318991010 28 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* 27.37 lnc-TRPC5-3:1 0.992440476 37 0 0 lncSLC39A1021699888 29 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* 20 lnc-SLC39A10-2:1 0.981845238 63 0 0 lncTRPC5319111010 30 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* 18.95 lnc-TRPC5-3:1 0.993869048 33 0 0 lncTRPC5319231010 31 MIGRGAPEMITLGMIIGVMIDVPPKDPN* 17.89 lnc-TRPC5-3:1 0.985238095 29 0 0 lncTRPC5319471010 32 MITLGMIIGVMIDVPPKDPN* 16.84 lnc-TRPC5-3:1 0.925119048 21 0 0 lncPLA2G1B231094711151 33 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* 16.84 lnc-PLA2G1B-2:3 0.900595238 68 0.000408497 0 LINC02418923092465 34 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* 14.74 LINC02418:9 0.986428571 52 0.000267094 0 lncTRPC531160328 35 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* 12.63 lnc-TRPC5-3:1 0.842083333 56 0 0 lncTRPC53128328 36 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* 12.63 lnc-TRPC5-3:1 0.994166667 100 0 0 LINC02418923602465 37 MPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* 12.63 LINC02418 : 9 0.95797619 35 0 0 lncHSF521481574 38 MLVSKDGAGKPSTTDCKHLNFRRPFSDYYF* 12.63 lnc-HSF5-2:1 0.971130952 31 0 0 lncSLC39A1021811913 39 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* 11.58 lnc-SLC39A10-2:1 0.992797619 34 0 0 lncPLA2G1B231098611151 40 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* 11.58 lnc-PLA2G1B-2:3 0.866011905 55 0 0 lncPLA2G1B231099211151 41 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* 11.58 lnc-PLA2G1B-2:3 0.770119048 53 0 0 lncTRPC531779830 42 MMTKAAETMIEAMIPG* 10.53 lnc-TRPC5-3:1 0.948392857 17 0 0 LINC02418923782465 43 MHVRDRVEKDCARLHHTTQNGTQFRTYK* 10.53 LINC02418 : 9 0.96172619 29 0 0 lncTRPC531782830 44 MTKAAETMIEAMIPG* 9.47 lnc-TRPC5-3:1 0.929821429 16 0 0 LINC02418931663253 45 SCRRASKPKTHRE* 9.47 LINC02418 : 9 0.737678571 29 0 0 lncSLC39A107115561769 46 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* 9.47 lnc-SLC39A10-7:1 0.834047619 71 0 0 lncSLC39A107115411769 47 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* 9.47 lnc-SLC39A10-7:1 0.960238095 76 0.000365497 0 lncTRPC5319621010 48 MIIGVMIDVPPKDPN* 8.42 lnc-TRPC5-3:1 0.747321429 16 0 0 lncFANCM10125163 49 MARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* 8.42 lnc-FANCM-10:1 0.736071429 46 0 0 lncFANCM10122163 50 MMARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* 8.42 lnc-FANCM-10:1 0.707261905 47 0.000295508 0 lncPLA2G1B2383028395 51 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* 7.37 lnc-PLA2G1B-2:3 0.828869048 31 0 0 lncCAMK1D2113431439 52 MILSLNVEIRGRGKENPMELVAGEALVSLRQ* 6.32 lnc-CAMK1D-2:1 0.868630952 32 0.000434028 0 lncTH1135283804 53 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* 5.26 lnc-TH-1:1 0.806904762 92 0 0 lncTH1135223804 54 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* 5.26 lnc-TH-1:1 0.844285714 94 0 0 lncCTR912215350 55 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHSKKEKEV* 5.26 lnc-CTR9-1:2 0.979464286 45 0 0 lncHOXB81519402135 56 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* 5.26 lnc-HOXB8-1:5 0.893869048 65 0.000106838 0 lncPLA2G1B2392559342 57 MGTESQFPPLGMKDKVLEVSSDDGYTTM* 3.16 lnc-PLA2G1B-2:3 0.926011905 29 0 0 LINC02418933743500 58 MGPGGSAWDQEDQHGTRKQQASECELHSQQGDDVGLGNLQI* 3.16 LINC02418:9 0.952738095 42 0 0 LINC02418929103054 59 MTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* 3.16 LINC02418:9 0.770654762 48 0 0 LINC02418928443054 60 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* 3.16 LINC02418:9 0.882321429 70 0 0 lncTACR311255462 61 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* 3.16 lnc-TACR3-1:1 0.838690476 69 0 0 LINC017151320532128 62 MRSEGQDQPGQYGETLSLLKIQKI* 3.16 LINC01715:13 0.712261905 25 0 0 lncPLA2G1B2330093069 63 MPGLLISTWQHRFMKPLTL* 2.11 lnc-PLA2G1B-2:3 0.818630952 20 0 0 lncPLA2G1B2365746625 64 MSFLTILANTVKPHLY* 2.11 lnc-PLA2G1B-2:3 0.816071429 17 0 0 lncPLA2G1B2397619845 65 MSRGRNKLALRSGSIVANEVYPRRDYC* 2.11 lnc-PLA2G1B-2:3 0.824345238 28 0 0 LINC02418925582597 66 MSATLMPSRPEE* 2.11 LINC02418:9 0.884880952 13 0 0 lncHSF521497638 67 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* 2.11 lnc-HSF5-2:1 0.886666667 47 0 0 lncTH1133223427 68 MVWTRRCGASPTSYNWGRLTTTVEGTPWNSQTTS* 2.11 lnc-TH-1:1 0.763154762 35 0 0 lncHOXB81514691532 69 MQILEYECWPEIRYFLPSSC* 2.11 lnc-HOXB8-1:5 0.742857143 21 0 0 lncHOXB81511121196 70 MYAKHMGVQVHHPKAMASSVFPKSLRL* 2.11 lnc-HOXB8-1:5 0.813333333 28 0 0 LINC025633122206 71 MQWKLSVLCPAVPSSIQESTPVDERRN* 2.11 LINC02563:3 0.980059524 28 0 0 lncTRPC53198164 72 MGVLVEEAPMFPNQSAGLMKR* 1.05 lnc-TRPC5-3:1 0.941011905 22 0 0 lncSLC39A1021686782 73 MGLGHVPTCSSLYSDWTWKGRREARASILIL* 1.05 lnc-SLC39A10-2:1 0.923333333 32 0 0 lncSLC39A1021271373 74 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* 1.05 lnc-SLC39A10-2:1 0.858571429 34 0 0 lncSLC39A1021250373 75 MTARFKRMKSVEVRPLDALAWKSHILLAKANHKATTNSRR* 1.05 lnc-SLC39A10-2:1 0.87922619 41 0 0 lncPLA2G1B2361366280 76 MIKVKESKFTTLLVFSFYPGCELNKKSAAVAHACNPSPWGGRGGRIT* 1.05 lnc-PLA2G1B-2:3 0.815595238 48 0 0 lncPLA2G1B2314041488 77 MLARLVSNSRPQVIRQPRPPKMLGLQA* 1.05 lnc-PLA2G1B-2:3 0.822738095 28 0 0 lncPLA2G1B2392889342 78 MKDKVLEVSSDDGYTTM* 1.05 lnc-PLA2G1B-2:3 0.840595238 18 0 0 LINC024189857923 79 MKARAVAKGTSPSGEASSAQL* 1.05 LINC02418:9 0.811785714 22 0 0 LINC024189745778 80 MDGFLEEEAR* 1.05 LINC02418:9 0.919166667 11 0 0 LINC024189706778 81 MREHRGEAPTLGFMDGFLEEEAR* 1.05 LINC02418:9 0.935 24 0 0 LINC02418942034404 82 MSLLIRECLSSLYLNFSKRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* 1.05 LINC02418:9 0.827380952 67 0 0 LINC02418938063863 83 MMKPRYTAYLAFRQGKPA* 1.05 LINC02418:9 0.850595238 19 0 0 lncSLC39A107116011769 84 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* 1.05 lnc-SLC39A10-7:1 0.889464286 56 0 0 lncTH1121342221 85 MPDQDWAQPPALQVDRLRSAASEAAWDG* 1.05 lnc-TH-1:1 0.843988095 29 0 0 lncTH1139804010 86 MMRKEMRPA* 1.05 lnc-TH-1:1 0.781190476 10 0 0 lncCAMK1D2113941439 87 MELVAGEALVSLRQ* 1.05 lnc-CAMK1D-2:1 0.761190476 15 0 0 lncCAMK1D2114651522 88 MEKRSQAKTAVGQSFGET* 1.05 lnc-CAMK1D-2:1 0.767857143 19 0 0 lncHOXB81512971396 89 MGNNTLEWSGNCWPLSPAVLPEGNPNRRSDSQ* 1.05 lnc-HOXB8-1:5 0.889047619 33 0 0 lncHOXB81537173807 90 MEKGQRKRHEKGRGREAQLWELNQETQIE* 1.05 lnc-HOXB8-1:5 0.831785714 30 0 0 lncHOXB81528042888 91 MQKMEATGRGWESLGFRKEAPGSPVLL* 1.05 lnc-HOXB8-1:5 0.796785714 28 0 0 lncTACR311275302 92 MSFWRETE* 1.05 lnc-TACR3-1:1 0.856488095 9 0 0 LINC0171513855891 93 MRKLFGNCVTV* 1.05 LINC01715:13 0.709761905 12 0 0 lncCHM11111138 94 MAPSAGNP* 1.05 lnc-CHM-1:1 0.718392857 9 0 0 lncOR52J31128127 95 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* 1.05 lnc-OR52J3-1:1 0.962797619 33 0 0 CYP1B1AS11257141 96 MGAVCEALRQYSPGGFQGSRAASVFSR* 1.05 CYP1B1-AS1:12 0.944047619 28 0 0 lncLRRTM433474639 97 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* 1.05 lnc-LRRTM4-3:3 0.905952381 55 0 0

[0330] Table 5

[0331] Camyo epitope SEQ ID NO Camyo epitope size Camyo peptide ID Camyo peptide sequence Camyo RNA neoIM score neoMS presented HLA quantity neoMS presented HLA MYQHVHHYTVI 98 11 lncSLC39A1021699888 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* lnc-SLC39A10-2:1 0.77835 1 ['A*24:02'] KLFGNCVTV 99 9 LINC0171513855891 MRKLFGNCVTV* LINC01715:13 0.7602 5 ['A*03:01', 'A*24:02', 'B*07:02', 'B*08:01', 'B*44:02'] LNFRRPFSDYY 100 11 lncHSF521481574 MLVSKDGAGKPSTTDCKHLNFRRPFSDYYF* lnc-HSF5-2:1 0.74035 1 ['A*01:01'] SFLTILANTVK 101 11 lncPLA2G1B2365746625 MSFLTILANTVKPHLY* lnc-PLA2G1B-2:3 0.73795 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] LISEDPFLITI 102 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.73625 1 ['A*02:01'] YTAYLAFRQGK 103 11 LINC02418938063863 MMKPRYTAYLAFRQGKPA* LINC02418:9 0.736 3 ['A*01:01', 'A*03:01', 'A*11:01'] LISTWQHRFMK 104 11 lncPLA2G1B2330093069 MPGLLISTWQHRFMKPLTL* lnc-PLA2G1B-2:3 0.7339 2 ['A*03:01', 'A*11:01'] QILEYECWPEI 105 11 lncHOXB81514691532 MQILEYECWPEIRYFLPSSC* lnc-HOXB8-1:5 0.72685 1 ['A*02:01'] MAHAGIWMDMV 106 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.72285 1 ['C*06:02'] MAHAGIWMDMV 107 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.72285 1 ['C*06:02'] MAHAGIWMDMV 108 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.72285 1 ['C*06:02'] MAHAGIWMDMV 109 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.72285 1 ['C*06:02'] ILISEDPFL 110 9 lncHSF521497638 MVQENQVQLIFE SILENCEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.7204 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] STWQHRFMKPL 111 11 lncPLA2G1B2330093069 MPGLLISTWQHRFMKPLTL* lnc-PLA2G1B-2:3 0.72015 1 ['A*03:01'] STYVSKPVSWA 112 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.717 6 ['A*02:01', 'A*03:01', 'A*11:01', 'B*07:02', 'B*08:01', 'C*07:0 KTVRSSCLDRK 113 11 lncFANCM10125163 MARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.71275 2 ['A*03:01', 'A*11:01'] KTVRSSCLDRK 114 11 lncFANCM10122163 MMARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.71275 2 ['A*03:01', 'A*11:01'] IIGVMIDVPPK 115 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 116 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 117 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 118 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 119 11 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 120 11 lncTRPC5319471010 MITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IIGVMIDVPPK 121 11 lncTRPC5319621010 MIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7119 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] SIHPMTGALCL 122 11 LINC02418928443054 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418:9 0.71105 2 ['A*02:01', 'C*03:04'] MIIGVMIDV 123 9 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 124 9 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 125 9 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 126 9 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 127 9 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 128 9 lncTRPC5319471010 MITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MIIGVMIDV 129 9 lncTRPC5319621010 MIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.7108 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] APTLGFMDGFL 130 11 LINC024189706778 MREHRGEAPTLGFMDGFLEEEAR* LINC02418:9 0.70625 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] GQALTLNVMVV 131 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.70575 1 ['A*02:01'] GQALTLNVMVV 132 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.70575 1 ['A*02:01'] GQALTLNVMVV 133 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.70575 1 ['A*02:01'] SYNWGRLTTTV 134 11 lncTH1133223427 MVWTRRCGASPTSYNWGRLTTTVEGTPWNSQTTS* lnc-TH-1:1 0.7051 3 ['A*24:02', 'C*05:01', 'C*04:01'] ITISKDVHIVL 135 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.69995 8 ['A*02:01', 'A*03:01', 'A*11:01', 'B*08:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] MVQENQVQLIV 136 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6994 1 ['A*02:01'] GFHQVLFFQKK 137 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.69875 2 ['A*03:01', 'A*11:01'] FLTILANTV 138 9 lncPLA2G1B2365746625 MSFLTILANTVKPHLY* lnc-PLA2G1B-2:3 0.6943 13 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] RRWFHDFLAVV 139 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6941 1 ['C*06:02'] RRWFHDFLAVV 140 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6941 1 ['C*06:02'] TSYTRTHGQAL 141 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6937 3 ['B*08:01', 'C*07:01', 'C*03:04'] TSYTRTHGQAL 142 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6937 3 ['B*08:01', 'C*07:01', 'C*03:04'] TSYTRTHGQAL 143 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6937 3 ['B*08:01', 'C*07:01', 'C*03:04'] WMDMVAGIAMM 144 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6927 3 ['A*01:01', 'C*05:01', 'C*04:01'] WMDMVAGIAMM 145 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6927 3 ['A*01:01', 'C*05:01', 'C*04:01'] WMDMVAGIAMM 146 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6927 3 ['A*01:01', 'C*05:01', 'C*04:01'] WMDMVAGIAMM 147 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6927 3 ['A*01:01', 'C*05:01', 'C*04:01'] IYKPTRIAWNK 148 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.69235 2 ['A*03:01', 'A*11:01'] IYKPTRIAWNK 149 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.69235 2 ['A*03:01', 'A*11:01'] IYKPTRIAWNK 150 11 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.69235 2 ['A*03:01', 'A*11:01'] KFTTLLVFSFY 151 11 lncPLA2G1B2361366280 MIKVKESKFTTLLVFSFYPGCELNKKSAAVAHACNPSPWGGRGGRIT* lnc-PLA2G1B-2:3 0.6914 2 ['A*01:01', 'A*24:02'] CLYEKYRKYPA 152 11 lncPLA2G1B2383028395 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* lnc-PLA2G1B-2:3 0.68965 1 ['A*02:01'] ALTLNVMVV 153 9 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.68945 4 ['A*03:01', 'A*11:01', 'B*08:01', 'C*07:01'] ALTLNVMVV 154 9 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.68945 4 ['A*03:01', 'A*11:01', 'B*08:01', 'C*07:01'] ALTLNVMVV 155 9 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.68945 4 ['A*03:01', 'A*11:01', 'B*08:01', 'C*07:01'] FSFYPGCELNK 156 11 lncPLA2G1B2361366280 MIKVKESKFTTLLVFSFYPGCELNKKSAAVAHACNPSPWGGRGGRIT* lnc-PLA2G1B-2:3 0.68445 1 ['A*11:01'] AVVTAVGQLWV 157 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.68175 1 ['A*02:01'] AVVTAVGQLWV 158 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.68175 1 ['A*02:01'] AMMTKAAETMI 159 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] AMMTKAAETMI 160 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] AMMTKAAETMI 161 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] AMMTKAAETMI 162 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] AMMTKAAETMI 163 11 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] AMMTKAAETMI 164 11 lncTRPC531761830 MVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.68125 1 ['A*02:01'] DPFLITISKDV 165 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.68005 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] ETLSLLKIQKI 166 11 LINC017151320532128 MRSEGQDQPGQYGETLSLLKIQKI* LINC01715:13 0.6795 1 ['B*44:02'] NFTDFRRLAL 167 10 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.6789 1 ['B*44:02'] FTDFRRLALIS 168 11 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.6789 1 ['A*01:01'] KLAIYKPTRIA 169 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6768 1 ['A*02:01'] KLAIYKPTRIA 170 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6768 1 ['A*02:01'] KLAIYKPTRIA 171 11 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6768 1 ['A*02:01'] VMIQTGIGM 172 9 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6766 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LISEDPFLI 173 9 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6766 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] NFTDFRRLALI 174 11 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.67485 1 ['A*24:02'] ALETSIGIVMI 175 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.67305 3 ['A*02:01', 'A*01:01', 'C*05:01'] SYTRTHGQAL 176 10 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6727 2 ['B*44:02', 'B*44:03'] SYTRTHGQAL 177 10 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6727 2 ['B*44:02', 'B*44:03'] SYTRTHGQAL 178 10 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6727 2 ['B*44:02', 'B*44:03'] LTLNVMVVIIR 179 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6724 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] LTLNVMVVIIR 180 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6724 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] LTLNVMVVIIR 181 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6724 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] KFSSASNYAAL 182 11 lncTRPC53116031801 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASNYAALS* lnc-TRPC5-3:1 0.672 5 ['A*24:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01'] VNMPGKGIMHV 183 11 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418 : 9 0.6717 3 ['A*02:01', 'C*07:01', 'C*06:0 RILTALTMPRK 184 11 lncFANCM10125163 MARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.671 2 ['A*03:01', 'A*11:0 RILTALTMPRK 185 11 lncFANCM10122163 MMARLKTVRSSCLDRKATGCSPGSSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.671 2 ['A*03:01', 'A*11:0 TFIAPVMKKRM 186 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.6709 1 ['A*24:02'] ANEVYPRRDYC 187 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.6706 1 ['A*01:01'] VMIQTGIGMGI 188 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.66965 1 ['A*02:01'] EMFRQLGTVTM 189 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.66965 5 ['A*02:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:0 EMFRQLGTVTM 190 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.66965 5 ['A*02:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:0 GIMHVRDRVEK 191 11 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.6692 2 ['A*03:01', 'A*11:01'] IMHVRDRVEK 192 11 LINC02418923602465 MPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.6692 2 ['A*03:01', 'A*11:01'] VHHYTVIGLGK 193 11 lncSLC39A1021699888 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* lnc-SLC39A10-2:1 0.6687 3 ['A*03:01', 'A*11:01', 'C*03:04'] TTVEGTPWNSQ 194 11 lncTH1133223427 MVWTRRCGASPTSYNWGRLTTTVEGTPWNSQTTS* lnc-TH-1:1 0.66825 1 ['A*01:01'] APATRPASKDA 195 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.66705 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] APATRPASKDA 196 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.66705 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] KYGWWSGNTSY 197 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6649 4 ['A*01:01', 'A*24:02', 'B*44:03', 'C*07:01'] KYGWWSGNTSY 198 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6649 4 ['A*01:01', 'A*24:02', 'B*44:03', 'C*07:0 KYGWWSGNTSY 199 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.6649 4 ['A*01:01', 'A*24:02', 'B*44:03', 'C*07:0 TYSQLPKLKMF 200 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.66325 2 ['A*01:01', 'A*24:0 GLLGNPISTGA 201 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.66255 1 ['A*02:01'] GLLGNPISTGA 202 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.66255 1 ['A*02:01'] QLWELNQETQI 203 11 lncHOXB81537173807 MEKGQRKRHEKGRGREAQLWELNQETQIE* lnc-HOXB8-1:5 0.66075 1 ['A*02:01'] GFRAGTFIAPV 204 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.66 1 ['A*24:02'] TQNGTQFRTYK 205 11 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418 : 9 0.65855 5 ['A*01:01', 'A*03:01', 'A*11:01', 'C*06:02', 'C*03:0 TQNGTQFRTYK 206 11 LINC02418923602465 MPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418 : 9 0.65855 5 ['A*01:01', 'A*03:01', 'A*11:01', 'C*06:02', 'C*03:0 TQNGTQFRTYK 207 11 LINC02418923782465 MHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418 : 9 0.65855 5 ['A*01:01', 'A*03:01', 'A*11:01', 'C*06:02', 'C*03:0 LTILANTVKPH 208 11 lncPLA2G1B2365746625 MSFLTILANTVKPHLY* lnc-PLA2G1B-2:3 0.6585 1 ['A*03:01'] AVFPNRHPTLL 209 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.65805 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*06:02', 'C*03:04'] AVFPNRHPTLL 210 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.65805 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*06:02', 'C*03:04'] SASNYAAL 211 8 lncTRPC53116031801 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEKKKPEENPASKFSSASNYALS* lnc-TRPC5-3:1 0.65785 1 ['A*02:01'] KPTRIAWNKFF 212 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.65725 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] KPTRIAWNKFF 213 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.65725 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] KPTRIAWNKFF 214 11 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.65725 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] ASSVFPKSLRL 215 11 lncHOXB81511121196 MYAKHMGVQVHHPKAMASSVFPKSLRL* lnc-HOXB8-1:5 0.6566 2 ['A*03:01', 'C*03:04'] MTTEEAGTAMK 216 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPKDPN* lnc-TRPC5-3:1 0.65645 15 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MTTEEAGTAMK 217 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPKDPN* lnc-TRPC5-3:1 0.65645 15 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] FHDFLAVV 218 8 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.65565 3 ['B*44:02', 'B*44:03', 'B*51:01'] FHDFLAVV 219 8 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.65565 3 ['B*44:02', 'B*44:03', 'B*51:01'] MIALETSIGIV 220 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6551 1 ['A*02:01'] NFRRPFSDYYF 221 11 lncHSF521481574 MLVSKDGAGKPSTTDCKHLNFRRPFSDYYF* lnc-HSF5-2:1 0.65255 1 ['A*24:02'] EMITLGMIIGV 222 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6517 1 ['A*02:01'] EMITLGMIIGV 223 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6517 1 ['A*02:01'] EMITLGMIIGV 224 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6517 1 ['A*02:01'] EMITLGMIIGV 225 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6517 1 ['A*02:01'] EMITLGMIIGV 226 11 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6517 1 ['A*02:01'] FRQLGTVTMTM 227 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.65125 2 ['C*07:02', 'C*06:02'] FRQLGTVTMTM 228 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.65125 2 ['C*07:02', 'C*06:0 GAPEMITLGMI 229 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.651 2 ['A*24:02', 'C*06:0 GAPEMITLGMI 230 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.651 2 ['A*24:02', 'C*06:0 GAPEMITLGMI 231 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.651 2 ['A*24:02', 'C*06:0 GAPEMITLGMI 232 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.651 2 ['A*24:02', 'C*06:0 GAPEMITLGMI 233 11 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.651 2 ['A*24:02', 'C*06:0 FSFVLVRRPSR 234 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.6509 1 ['A*03:01'] EIETILANTVK 235 11 lncSLC39A1021811913 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* lnc-SLC39A10-2:1 0.65 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] FIAPVMKKRMK 236 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.64945 2 ['A*03:01', 'A*11:01'] SQFPPLGMKDK 237 11 lncPLA2G1B2392559342 MGTESQFPPLGMKDKVLEVSSDDGYTTM* lnc-PLA2G1B-2:3 0.64935 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] FGFHQVLFFQK 238 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.64935 6 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*06:02', 'C*03:04'] MSYNIYMHIER 239 11 LINC02418931663253 MSYNIYMHIERGCEYSCRRASKPKTHRE* LINC02418:9 0.6493 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] ISKDVHIVLRL 240 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6491 6 ['A*03:01', 'B*08:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] EYECWPEIRYF 241 11 lncHOXB81514691532 MQILEYECWPEIRYFLPSSC* lnc-HOXB8-1:5 0.649 1 ['A*24:02'] ISTTRAGVRQD 242 11 LINC02418928443054 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418:9 0.64875 6 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*06:02'] GTDLPSTVRIT 243 11 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.64865 3 ['A*01:01', 'A*03:01', 'A*11:01'] TAVGQLWVTLK 244 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6483 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] TAVGQLWVTLK 245 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6483 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] GMAHAGIWMDM 246 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64715 1 ['A*02:01'] GMAHAGIWMDM 247 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64715 1 ['A*02:01'] GMAHAGIWMDM 248 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64715 1 ['A*02:01'] GTFIAPVMKKR 249 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.6464 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] IWMDMVAGIAM 250 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64635 2 ['A*24:02', 'C*05:01'] IWMDMVAGIAM 251 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64635 2 ['A*24:02', 'C*05:01'] IWMDMVAGIAM 252 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64635 2 ['A*24:02', 'C*05:01'] IWMDMVAGIAM 253 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.64635 2 ['A*24:02', 'C*05:01'] YEKYRKYPAEV 254 11 lncPLA2G1B2383028395 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* lnc-PLA2G1B-2:3 0.64595 1 ['B*44:02'] LISEDPFL 255 8 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.64575 9 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] KLALRSGSIVA 256 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.6454 1 ['A*02:01'] APEMITLGMII 257 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6428 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] APEMITLGMII 258 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6428 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] APEMITLGMII 259 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6428 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] APEMITLGMII 260 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6428 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] APEMITLGMII 261 11 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6428 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] FLAVVTAV 262 8 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.64205 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] FLAVVTAV 263 8 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.64205 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] AMKTDMTDGMI 264 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.64 1 ['A*02:01'] AMKTDMTDGMI 265 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.64 1 ['A*02:01'] PMFPNQSAGLM 266 11 lncTRPC53198164 MGVLVEEAPMFPNQSAGLMKR* lnc-TRPC5-3:1 0.63975 3 ['B*07:02', 'B*35:01', 'B*51:01'] GVISAHFNLRL 267 11 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.63965 3 ['A*02:01', 'A*03:01', 'A*11:01'] KHMGVQVHHPK 268 11 lncHOXB81511121196 MYAKHMGVQVHHPKAMASSVFPKSLRL* lnc-HOXB8-1:5 0.6391 1 ['A*03:01'] DMVAGIAMMTK 269 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.639 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMMTK 270 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.639 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMMTK 271 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.639 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMMTK 272 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.639 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMMTK 273 11 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.639 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*08:01', 'B*44:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] SSASNYAAL 274 9 lncTRPC53116031801 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEKKKPEENPASKFSSASNYALS* lnc-TRPC5-3:1 0.6388 2 ['A*03:01', 'A*11:0 TTQNGTQFRTY 275 11 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.63875 7 ['A*01:01', 'A*03:01', 'A*11:01', 'B*35:01', 'C*07:01', 'C*07:02', 'C*06:02'] TTQNGTQFRTY 276 11 LINC02418923602465 MPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.63875 7 ['A*01:01', 'A*03:01', 'A*11:01', 'B*35:01', 'C*07:01', 'C*07:02', 'C*06:02'] TTQNGTQFRTY 277 11 LINC02418923782465 MHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.63875 7 ['A*01:01', 'A*03:01', 'A*11:01', 'B*35:01', 'C*07:01', 'C*07:02', 'C*06:02'] GQTKDNFTDFR 278 11 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.63865 3 ['A*03:01', 'A*11:01', 'C*03:04'] ASPTSYNWGRL 279 11 lncTH1133223427 MVWTRRCGASPTSYNWGRLTTTVEGTPWNSQTTS* lnc-TH-1:1 0.6386 4 ['A*02:01', 'A*01:01', 'A*24:02', 'C*06:02'] AQSIHPMTGAL 280 11 LINC02418928443054 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418:9 0.6372 1 ['C*03:04'] DFLAVVTAV 281 9 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.63705 16 ['A*02:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DFLAVVTAV 282 9 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.63705 16 ['A*02:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] VPSFPLLHGLL 283 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.63465 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 VPSFPLLHGLL 284 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.63465 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 VDVLMKRRNLK 285 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6335 2 ['A*03:01', 'A*11:0 VISAHFNL 286 8 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.63315 15 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] PQVIRQPRPPK 287 11 lncPLA2G1B2314041488 MLARLVSNSRPQVIRQPRPPKMLGLQA* lnc-PLA2G1B-2:3 0.6331 1 ['A*11:01'] PPMQMGLKYGW 288 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.63295 1 ['B*51:01'] LLIRECLSSLY 289 11 LINC02418942034404 MSLLIRECLSSLYLNFSKRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418:9 0.63265 1 ['A*01:01'] ISEDPFLI 290 8 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6303 2 ['B*07:02', 'B*35:01'] LWVTLKGHSDK 291 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.62915 2 ['A*03:01', 'A*11:01'] LWVTLKGHSDK 292 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.62915 2 ['A*03:01', 'A*11:01'] GTESQFPPLGM 293 11 lncPLA2G1B2392559342 MGTESQFPPLGMKDKVLEVSSDDGYTTM* lnc-PLA2G1B-2:3 0.6287 1 ['A*01:01'] MPVILALWEAK 294 11 lncSLC39A1021811913 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* lnc-SLC39A10-2:1 0.6286 2 ['A*03:01', 'A*11:01'] SHPEGHLTRPL 295 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.6282 6 ['C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LRSGSIVANEV 296 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.628 1 ['C*06:02'] VPSSIQESTPV 297 11 LINC025633122206 MQWKLSVLCPAVPSSIQESTPVDERRN* LINC02563:3 0.62795 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] MFVAGSGTSGF 298 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.62765 7 ['A*01:01', 'A*24:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01', 'C*04:01'] YMHIERGCEY 299 10 LINC02418931663253 MSYNIYMHIERGCEYSCRRASKPKTHRE* LINC02418:9 0.6276 6 ['A*02:01', 'A*01:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03'] QYGETLSLLKI 300 11 LINC017151320532128 MRSEGQDQPGQYGETLSLLKIQKI* LINC01715:13 0.62745 2 ['A*01:01', 'A*24:02'] AMASSVFPKSL 301 11 lncHOXB81511121196 MYAKHMGVQVHHPKAMASSVFPKSLRL* lnc-HOXB8-1:5 0.6274 3 ['A*02:01', 'A*03:01', 'C*03:0 PISTGAVFPNR 302 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.62715 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] PISTGAVFPNR 303 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.62715 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] STLGGQSGRIT 304 11 lncSLC39A1021699888 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* lnc-SLC39A10-2:1 0.62575 2 ['A*03:01', 'A*11:0 KVLEVSSDDGY 305 11 lncPLA2G1B2392559342 MGTESQFPPLGMKDKVLEVSSDDGYTTM* lnc-PLA2G1B-2:3 0.6255 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] KVLEVSSDDGY 306 11 lncPLA2G1B2392889342 MKDKVLEVSSDDGYT™* lnc-PLA2G1B-2:3 0.6255 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'B*44:03', 'B*35:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] KAAETMIEAMI 307 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 308 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 309 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 310 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 311 11 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 312 11 lncTRPC531761830 MVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 313 11 lncTRPC531779830 MMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 KAAETMIEAMI 314 11 lncTRPC531782830 MTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6252 6 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] RWFHDFLAVVT 315 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6245 1 ['A*24:02'] RWFHDFLAVVT 316 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6245 1 ['A*24:02'] QSGRITRSGDR 317 11 lncSLC39A1021699888 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* lnc-SLC39A10-2:1 0.62325 1 ['A*03:01'] MFPNQSAGLM 318 10 lncTRPC53198164 MGVLVEEAPMFPNQSAGLMKR* lnc-TRPC5-3:1 0.62285 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] AMWRHREKLAI 319 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.62285 1 ['A*02:01'] AMWRHREKLAI 320 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.62285 1 ['A*02:01'] ALAWKSHILLA 321 11 lncSLC39A1021271373 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.622 1 ['A*02:01'] ALAWKSHILLA 322 11 lncSLC39A1021250373 MTARFKRMKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.622 1 ['A*02:01'] FLITISKDVHI 323 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.62195 1 ['A*02:01'] SHILLAKANHK 324 11 lncSLC39A1021271373 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.62175 2 ['A*03:01', 'A*11:01'] SHILLAKANHK 325 11 lncSLC39A1021250373 MTARFKRMKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.62175 2 ['A*03:01', 'A*11:01'] SHIPPINGTIAAPVM 326 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.62125 3 ['C*07:01', 'C*07:02', 'C*06:02'] LYSDWTWKGRR 327 11 lncSLC39A1021686782 MGLGHVPTCSSLYSDWTWKGRREARASILIL* lnc-SLC39A10-2:1 0.6207 2 ['A*03:01', 'A*11:01'] SIVANEVYPRR 328 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.62005 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] EEGNVEWVASI 329 11 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.61965 2 ['B*44:02', 'B*44:03'] GTGGGSTYVSK 330 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.61865 10 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 NVEWVASILIC 331 11 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.61815 8 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:0 GSIVANEVYPR 332 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.6179 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] VSWADETMTWK 333 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.617 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*04:01', 'C*06:02', 'C*03:04'] QNLSSFAQWQY 334 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61675 1 ['A*01:01'] QNLSSFAQWQY 335 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61675 1 ['A*01:01'] QNLSSFAQWQY 336 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61675 1 ['A*01:01'] EEGNVEWV 337 8 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.61565 2 ['A*03:01', 'A*11:0 RTSNSDGSRVF 338 11 LINC02418942034404 MSLLIRECLSSLYLNFSCRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418 : 9 0.6156 5 ['A*01:01', 'A*03:01', 'A*24:02', 'B*44:03', 'C*07:0 GHLTRPLEQTK 339 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.6156 2 ['A*03:01', 'A*11:0 SWADETMTWK 340 10 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.61555 12 ['A*02:01', 'A*01:01', 'A*24:02', 'B*44:02', 'B*44:03', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] IALETSIGIVM 341 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.61525 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] STTDCKHLNFR 342 11 lncHSF521481574 MLVSKDGAGKPSTTDCKHLNFRRPFSDYYF* lnc-HSF5-2:1 0.6152 1 ['A*03:01'] RLVSNSRPQVI 343 11 lncPLA2G1B2314041488 MLARLVSNSRPQVIRQPRPPKMLGLQA* lnc-PLA2G1B-2:3 0.6149 1 ['A*02:01'] KPVSWADETMT 344 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.6142 1 ['B*07:02'] GVISAHFNL 345 9 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.614 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] RTHGQALTLNV 346 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61395 1 ['A*03:01'] RTHGQALTLNV 347 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61395 1 ['A*03:01'] RTHGQALTLNV 348 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.61395 1 ['A*03:01'] TAMKTDMTDGM 349 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6127 3 ['B*08:01', 'B*35:01', 'B*51:0 TAMKTDMTDGM 350 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.6127 3 ['B*08:01', 'B*35:01', 'B*51:0 SEDPFLITIS 351 10 lncHSF521497638 MVQENQVQLIFE SILENCEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.61205 1 ['B*51:01'] LLGNPIST 352 8 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.61075 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LLGNPIST 353 8 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.61075 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] QENQVQLIVSI 354 11 lncHSF521497638 MVQENQVQLIFE SILENCEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6104 2 ['B*44:02', 'B*44:0 NSDGSRVFLAA 355 11 LINC02418942034404 MSLLIRECLSSLYLNFSCRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418 : 9 0.6098 1 ['A*01:01'] TSNSDGSRVFL 356 11 LINC02418942034404 MSLLIRECLSSLYLNFSKRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418:9 0.60965 3 ['C*07:02', 'C*06:02', 'C*03:04'] AIYKPTRI 357 8 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6096 13 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] AIYKPTRI 358 8 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6096 13 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] AIYKPTRI 359 8 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6096 13 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] SFYPGCELNKK 360 11 lncPLA2G1B2361366280 MIKVKESKFTTLLVFSFYPGCELNKKSAAVAHACNPSPWGGRGGRIT* lnc-PLA2G1B-2:3 0.6095 1 ['A*11:01'] FLAVVTAVGQL 361 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6086 1 ['A*02:01'] FLAVVTAVGQL 362 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.6086 1 ['A*02:01'] EMITLGMII 363 9 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60725 3 ['A*03:01', 'A*24:02', 'A*11:01'] EMITLGMII 364 9 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60725 3 ['A*03:01', 'A*24:02', 'A*11:01'] EMITLGMII 365 9 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60725 3 ['A*03:01', 'A*24:02', 'A*11:01'] EMITLGMII 366 9 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60725 3 ['A*03:01', 'A*24:02', 'A*11:01'] EMITLGMII 367 9 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60725 3 ['A*03:01', 'A*24:02', 'A*11:01'] VLVEEAPMF 368 9 lncTRPC53198164 MGVLVEEAPMFPNQSAGLMKR* lnc-TRPC5-3:1 0.60695 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LTALTMPRKGR 369 11 lncFANCM10125163 MARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.60695 1 ['A*03:01'] LTALTMPRKGR 370 11 lncFANCM10122163 MMARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.60695 1 ['A*03:01'] LTAPPLQSCSL 371 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.60685 1 ['C*03:04'] LTAPPLQSCSL 372 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.60685 1 ['C*03:04'] LTAPPLQSCSL 373 11 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.60685 1 ['C*03:04'] GSLEAWKQRLK 374 11 lncPLA2G1B2383028395 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* lnc-PLA2G1B-2:3 0.60655 2 ['A*03:01', 'A*11:01'] REFGFHQVLFF 375 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.60655 3 ['B*44:02', 'B*44:03', 'C*07:02'] ALAWKSHI 376 8 lncSLC39A1021271373 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.60625 1 ['A*24:02'] ALAWKSHI 377 8 lncSLC39A1021250373 MTARFKRMKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.60625 1 ['A*24:02'] MMTTEEAGTAM 378 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.606 1 ['A*02:01'] GMIGRGAPEMI 379 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60595 1 ['A*02:01'] GMIGRGAPEMI 380 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60595 1 ['A*02:01'] GMIGRGAPEMI 381 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60595 1 ['A*02:01'] GMIGRGAPEMI 382 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60595 1 ['A*02:01'] IWMDMVAGI 383 9 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6059 12 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01'] IWMDMVAGI 384 9 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6059 12 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01'] IWMDMVAGI 385 9 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6059 12 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01'] IWMDMVAGI 386 9 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.6059 12 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01'] FLITISKDV 387 9 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.6058 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] QTKDNFTDFRR 388 11 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.6058 3 ['A*01:01', 'A*03:01', 'A*11:01'] SLNVEIRGRGK 389 11 lncCAMK1D2113431439 MILSLNVEIRGRGKENPMELVAGEALVSLRQ* lnc-CAMK1D-2:1 0.60575 3 ['A*01:01', 'A*03:01', 'A*11:01'] DALAWKSHILL 390 11 lncSLC39A1021271373 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.60555 3 ['B*08:01', 'B*35:01', 'B*51:01'] DALAWKSHILL 391 11 lncSLC39A1021250373 MTARFKRMKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.60555 3 ['B*08:01', 'B*35:01', 'B*51:01'] SSDSPASASRV 392 11 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.60545 3 ['A*01:01', 'C*05:01', 'C*04:01'] MVAGIAMMTKA 393 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MVAGIAMMTKA 394 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MVAGIAMMTKA 395 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MVAGIAMMTKA 396 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MVAGIAMMTKA 397 11 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MVAGIAMMTKA 398 11 lncTRPC531761830 MVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.60505 2 ['A*02:01', 'A*03:01'] MPDQDWAQPPA 399 11 lncTH1121342221 MPDQDWAQPPALQVDRLRSAASEAAWDG* lnc-TH-1:1 0.6039 3 ['B*07:02', 'B*08:01', 'B*35:01'] GGFQGSRAASV 400 11 CYP1B1AS11257141 MGAVCEALRQYSPGGFQGSRAASVFSR* CYP1B1-AS1:12 0.6022 1 ['A*02:01'] LAIYKPTRIAW 401 11 lncSLC39A107115561769 MKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6018 3 ['B*08:01', 'B*44:03', 'B*51:01'] LAIYKPTRIAW 402 11 lncSLC39A107115411769 MVDVLMKRRNLKTDTPKENAMWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6018 3 ['B*08:01', 'B*44:03', 'B*51:01'] LAIYKPTRIAW 403 11 lncSLC39A107116011769 MWRHREKLAIYKPTRIAWNKFFHHTPQKESTLTAPPLQSCSLQNCETIHFCCLRR* lnc-SLC39A10-7:1 0.6018 3 ['B*08:01', 'B*44:03', 'B*51:01'] MTDGMIGRGAP 404 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60155 1 ['A*01:01'] MTDGMIGRGAP 405 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60155 1 ['A*01:01'] MTDGMIGRGAP 406 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60155 1 ['A*01:01'] MTDGMIGRGAP 407 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.60155 1 ['A*01:01'] HVHHYTVI 408 8 lncSLC39A1021699888 MYQHVHHYTVIGLGKAEEKQEPASSSYKQKSCLGVVAHACNPSTLGGQSGRITRSGDRDHPG* lnc-SLC39A10-2:1 0.60075 3 ['A*01:01', 'A*03:01', 'A*11:01'] GLLGNPIST 409 9 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5998 8 ['B*07:02', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] GLLGNPIST 410 9 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5998 8 ['B*07:02', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] MYAKHMGV 411 8 lncHOXB81511121196 MYAKHMGVQVHHPKAMASSVFPKSLRL* lnc-HOXB8-1:5 0.5994 3 ['A*01:01', 'A*24:02', 'B*51:0 RAGTFIAPVMK 412 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.59935 3 ['A*03:01', 'A*11:01', 'C*03:0 TKDNFTDF 413 8 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHCAKEKEV* lnc-CTR9-1:2 0.59875 5 ['B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:0 LSSLYLNFSKR 414 11 LINC02418942034404 MSLLIRECLSSLYLNFSCRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418 : 9 0.59855 3 ['A*03:01', 'C*06:02', 'C*03:0 PSREFGFHQVL 415 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.59845 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01'] GASPTSYNWGR 416 11 lncTH1133223427 MVWTRRCGASPTSYNWGRLTTTVEGTPWNSQTTS* lnc-TH-1:1 0.59795 8 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] DVHIVLRLLLL 417 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.5976 1 ['B*08:01'] ENGFSFVLVRR 418 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.59595 6 ['A*01:01', 'A*03:01', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] AQEENGFSFVL 419 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.59565 4 ['A*02:01', 'A*01:01', 'C*05:01', 'C*04:01'] KTDMTDGMIGR 420 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.59555 3 ['A*01:01', 'A*03:01', 'A*11:01'] KTDMTDGMIGR 421 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.59555 3 ['A*01:01', 'A*03:01', 'A*11:01'] KTDMTDGMIGR 422 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.59555 3 ['A*01:01', 'A*03:01', 'A*11:01'] EVSSDDGYTTM 423 11 lncPLA2G1B2392559342 MGTESQFPPLGMKDKVLEVSSDDGYTTM* lnc-PLA2G1B-2:3 0.59545 1 ['B*51:01'] EVSSDDGYTTM 424 11 lncPLA2G1B2392889342 MKDKVLEVSSDDGYT™* lnc-PLA2G1B-2:3 0.59545 1 ['B*51:01'] MVAGIAMM 425 8 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 MVAGIAMM 426 8 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 MVAGIAMM 427 8 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 MVAGIAMM 428 8 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 MVAGIAMM 429 8 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 MVAGIAMM 430 8 lncTRPC531761830 MVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5951 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*11:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:0 ALQVDRLRSAA 431 11 lncTH1121342221 MPDQDWAQPPALQVDRLRSASEAAAWDG* lnc-TH-1:1 0.5949 1 ['A*02:01'] LGNPISTGAVF 432 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5945 6 ['A*01:01', 'A*24:02', 'B*51:01', 'C*07:01', 'C*07:02', 'C*03:0 LGNPISTGAVF 433 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5945 6 ['A*01:01', 'A*24:02', 'B*51:01', 'C*07:01', 'C*07:02', 'C*03:0 AGTFIAPVMKK 434 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.5944 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:0 GMKDKVLEV 435 9 lncPLA2G1B2392559342 MGTESQFPPLGMKDKVLEVSSDDGYT™* lnc-PLA2G1B-2:3 0.59395 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] GFQGSRAASV 436 10 CYP1B1AS11257141 MGAVCEALRQYSPGGFQGSRAASVFSR* CYP1B1-AS1:12 0.59395 2 ['B*44:02', 'B*44:03'] SSRGPGDGGNK 437 11 lncTRPC53116031801 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASNYAALS* lnc-TRPC5-3:1 0.59375 2 ['A*03:01', 'A*11:01'] RGAPEMITLGM 438 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5933 2 ['C*07:01', 'C*07:02'] RGAPEMITLGM 439 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5933 2 ['C*07:01', 'C*07:02'] RGAPEMITLGM 440 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5933 2 ['C*07:01', 'C*07:02'] RGAPEMITLGM 441 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5933 2 ['C*07:01', 'C*07:02'] RGAPEMITLGM 442 11 lncTRPC5319231010 MIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5933 2 ['C*07:01', 'C*07:02'] GWWSGNTSYTR 443 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.59255 8 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] GWWSGNTSYTR 444 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.59255 8 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] GWWSGNTSYTR 445 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.59255 8 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:04'] EAQEENGFSFV 446 11 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.592 1 ['B*51:01'] VEWVASILI 447 9 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.5919 13 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01', 'C*03:04'] DGMIGRGAPEM 448 11 lncTRPC5318691010 MMTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5911 1 ['B*08:01'] DGMIGRGAPEM 449 11 lncTRPC5318721010 MTTEEAGTAMKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5911 1 ['B*08:01'] DGMIGRGAPEM 450 11 lncTRPC5318991010 MKTDMTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5911 1 ['B*08:01'] DGMIGRGAPEM 451 11 lncTRPC5319111010 MTDGMIGRGAPEMITLGMIIGVMIDVPPKDPN* lnc-TRPC5-3:1 0.5911 1 ['B*08:01'] VHIVLRLLLLK 452 11 lncHSF521497638 MVQENQVQLIVSILISEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.59105 2 ['A*03:01', 'A*11:01'] DMVAGIAMM 453 9 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.59095 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMM 454 9 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.59095 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMM 455 9 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.59095 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMM 456 9 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.59095 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] DMVAGIAMM 457 9 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.59095 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] APMFPNQSAGL 458 11 lncTRPC53198164 MGVLVEEAPMFPNQSAGLMKR* lnc-TRPC5-3:1 0.5905 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 GSRDQEIETIL 459 11 lncSLC39A1021811913 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* lnc-SLC39A10-2:1 0.59005 2 ['C*07:01', 'C*06:0 RSGSIVANEVY 460 11 lncPLA2G1B2397619845 MSRGRNKLALRSGSIVANEVYPRRDYC* lnc-PLA2G1B-2:3 0.58895 5 ['A*01:01', 'A*03:01', 'B*44:03', 'C*07:01', 'C*07:0 TISKDVIVLR 461 11 lncHSF521497638 MVQENQVQLIFE SILENCEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.58875 6 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*06:02', 'C*03:0 LTDFLAEDGGT 462 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58865 1 ['A*01:01'] RPSREFGFHQV 463 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.5886 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 LSETYSQLPKL 464 11 lncLRRTM433474639 MDSAPEEENLETLRLSETYSQLPKLKMFVAGSGTSGFRAGTFIAPVMKKRMKCG* lnc-LRRTM4-3:3 0.58845 2 ['A*01:01', 'C*05:0 ASAKKKNKKKGK 465 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58785 2 ['A*03:01', 'A*11:0 TQAGVEGSGVI 466 11 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.58735 1 ['A*02:01'] MGIGMAHAGIW 467 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5869 1 ['B*44:03'] MGIGMAHAGIW 468 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5869 1 ['B*44:03'] MGIGMAHAGIW 469 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.5869 1 ['B*44:03'] GFMDGFLEEE 470 10 LINC024189706778 MREHRGEAPTLGFMDGFLEEEAR* LINC02418 : 9 0.5869 16 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] NPISTGAVF 471 9 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5866 9 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'C*06:02'] NPISTGAVF 472 9 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5866 9 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*44:02', 'B*44:03', 'C*06:02'] SLYSDWTWKGR 473 11 lncSLC39A1021686782 MGLGHVPTCSSLYSDWTWKGRREARASILIL* lnc-SLC39A10-2:1 0.5861 8 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*04:01', 'C*06:02', 'C*03:0 SGVISAHFNLR 474 11 lncTACR311255462 MKRAWPPCHSGERQSKTKKTESCSATQAGVEGSGVISAHFNLRLLGSSDSPASASRVAGTTAASLQVS* lnc-TACR3-1:1 0.58585 10 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*04:01', 'C*06:02', 'C*03:0 KVKESKFTTLL 475 11 lncPLA2G1B2361366280 MIKVKESKFTTLLVFSFYPGCELNKKSAAVAHACNPSPWGGRGGRIT* lnc-PLA2G1B-2:3 0.58545 5 ['A*02:01', 'A*03:01', 'C*07:01', 'C*07:02', 'C*06:0 GSTYVSKPVSW 476 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.585 1 ['B*44:03'] NMPGKGIMHVR 477 11 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418 : 9 0.585 3 ['A*03:01', 'A*11:01', 'C*03:0 LTVPSFPL 478 8 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58495 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LTVPSFPL 479 8 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58495 17 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] EQGTRLPRGSW 480 11 LINC02418929103054 MTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418 : 9 0.58445 2 ['B*44:02', 'B*44:0 EQGTRLPRGSW 481 11 LINC02418928443054 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418 : 9 0.58445 2 ['B*44:02', 'B*44:0 ILSLNVEIRGR 482 11 lncCAMK1D2113431439 MILSLNVEIRGRGKENPMELVAGEALVSLRQ* lnc-CAMK1D-2:1 0.5843 7 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:02', 'C*06:02', 'C*03:0 HLNFRRPFSDY 483 11 lncHSF521481574 MLVSKDGAGKPSTTDCKHLNFRRPFSDYYF* lnc-HSF5-2:1 0.5842 1 ['A*01:01'] KYPAEVGGGSL 484 11 lncPLA2G1B2383028395 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* lnc-PLA2G1B-2:3 0.5837 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'B*07:02', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] FMDGFLEEEA 485 10 LINC024189706778 MREHRGEAPTLGFMDGFLEEEAR* LINC02418:9 0.5832 4 ['B*44:02', 'B*44:03', 'B*35:01', 'B*51:01'] NLSSFAQWQYR 486 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.5819 2 ['A*03:01', 'A*11:01'] NLSSFAQWQYR 487 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.5819 2 ['A*03:01', 'A*11:01'] NLSSFAQWQYR 488 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.5819 2 ['A*03:01', 'A*11:01'] YTRTHGQALTL 489 11 lncPLA2G1B231094711151 MFDTGCSNNKKPPMQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.58145 2 ['B*08:01', 'C*07:01'] YTRTHGQALTL 490 11 lncPLA2G1B231098611151 MQMGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.58145 2 ['B*08:01', 'C*07:01'] YTRTHGQALTL 491 11 lncPLA2G1B231099211151 MGLKYGWWSGNTSYTRTHGQALTLNVMVVIIRGGAGREQNLSSFAQWQYRSQ* lnc-PLA2G1B-2:3 0.58145 2 ['B*08:01', 'C*07:01'] QTKDNFTDF 492 9 lncCTR912215350 MRPLETHWRAGQTKDNFTDFRRLALISHNLRSQDAGHSKKEKEV* lnc-CTR9-1:2 0.58095 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'A*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*04:01', 'C*06:0 EENGFSFVLVR 493 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.5808 11 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] LLGNPISTGAV 494 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58025 1 ['A*02:01'] LLGNPISTGAV 495 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58025 1 ['A*02:01'] RIISTTRAGVR 496 11 LINC02418928443054 MELRIISTTRAGVRQDAQSIHPMTGALCLRSAKPRSEVLTRLHQEQGTRLPRGSWSTEGRDAHKHTMSK* LINC02418 : 9 0.58025 2 ['A*03:01', 'A*11:0 NPISTGAVFPN 497 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58005 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 NPISTGAVFPN 498 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.58005 4 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:0 SECTION PVDER 499 11 LINC025633122206 MQWKLSVLCPAVPSSIQESTPVDERRN* LINC02563 : 3 0.5791 15 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] TVPSFPLLHGL 500 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5787 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] TVPSFPLLHGL 501 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5787 14 ['A*02:01', 'A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*07:02', 'B*08:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] IAMMTKAAETM 502 11 lncTRPC531701830 MIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] IAMMTKAAETM 503 11 lncTRPC531668830 MIALETSIGIVMIQTGIGMGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] IAMMTKAAETM 504 11 lncTRPC531722830 MGIGMAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] IAMMTKAAETM 505 11 lncTRPC531734830 MAHAGIWMDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] IAMMTKAAETM 506 11 lncTRPC531755830 MDMVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] IAMMTKAAETM 507 11 lncTRPC531761830 MVAGIAMMTKAAETMIEAMIPG* lnc-TRPC5-3:1 0.57865 8 ['B*07:02', 'B*08:01', 'B*35:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] VEWVASILIKK 508 11 lncOR52J31128127 MSDRREEEGNVEWVASILIKKGTDLPSTVRIT* lnc-OR52J3-1:1 0.5782 8 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'C*07:01', 'C*07:02', 'C*06:02', 'C*03:04'] FLNEDSPGGS 509 10 LINC02418942034404 MSLLIRECLSSLYLNFSKRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418:9 0.57745 4 ['A*24:02', 'B*44:02', 'B*44:03', 'B*51:01'] SPGSCVRILTA 510 11 lncFANCM10125163 MARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.5773 3 ['B*07:02', 'B*08:01', 'B*35:01'] SPGSCVRILTA 511 11 lncFANCM10122163 MMARLKTVRSSCLDRKATGCSPGSCVRILTALTMPRKGRSCCFIRD* lnc-FANCM-10:1 0.5773 3 ['B*07:02', 'B*08:01', 'B*35:01'] GFQGSRAASVF 512 11 CYP1B1AS11257141 MGAVCEALRQYSPGGFQGSRAASVFSR* CYP1B1-AS1:12 0.5768 3 ['A*24:02', 'B*51:01', 'C*05:01'] EALRQYSPGGF 513 11 CYP1B1AS11257141 MGAVCEALRQYSPGGFQGSRAASVFSR* CYP1B1-AS1:12 0.57655 2 ['B*35:01', 'B*51:01'] GPGDGGNKDHW 514 11 lncTRPC53116031801 MNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASNYAALS* lnc-TRPC5-3:1 0.5762 1 ['B*51:01'] AQEENGFSF 515 9 lncHOXB81519402135 MENLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.57595 5 ['B*07:02', 'B*51:01', 'C*07:01', 'C*05:01', 'C*03:04'] ETILANTVKPR 516 11 lncSLC39A1021811913 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* lnc-SLC39A10-2:1 0.57555 11 ['A*01:01', 'A*03:01', 'A*24:02', 'A*11:01', 'B*51:01', 'C*07:01', 'C*07:02', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] AFRTSNSDGSR 517 11 LINC02418942034404 MSLLIRECLSSLYLNFSKRENAFRTSNSDGSRVFLAALFLNEDSPGGSLCCRDTQISPCSCSFQSF* LINC02418:9 0.575 2 ['A*03:01', 'A*11:01'] TTQNGTQF 518 8 LINC02418923092465 MAAEPLVGAECRVCSVNMPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.5748 13 ['A*02:01', 'A*03:01', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] TTQNGTQF 519 8 LINC02418923602465 MPGKGIMHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.5748 13 ['A*02:01', 'A*03:01', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] TTQNGTQF 520 8 LINC02418923782465 MHVRDRVEKDCARLHHTTQNGTQFRTYK* LINC02418:9 0.5748 13 ['A*02:01', 'A*03:01', 'A*11:01', 'B*07:02', 'B*08:01', 'B*44:02', 'B*44:03', 'B*35:01', 'B*51:01', 'C*05:01', 'C*04:01', 'C*06:02', 'C*03:04'] LVAGEALV 521 8 lncCAMK1D2113431439 MILSLNVEIRGRGKENPMELVAGEALVSLRQ* lnc-CAMK1D-2:1 0.5745 5 ['A*01:01', 'B*07:02', 'B*44:02', 'B*44:03', 'B*35:0 LVAGEALV 522 8 lncCAMK1D2113941439 MELVAGEALVSLRQ* lnc-CAMK1D-2:1 0.5745 5 ['A*01:01', 'B*07:02', 'B*44:02', 'B*44:03', 'B*35:0 QEIETILANTV 523 11 lncSLC39A1021811913 MPVILALWEAKAGGSRDQEIETILANTVKPRLY* lnc-SLC39A10-2:1 0.5741 2 ['B*44:02', 'B*44:0 FPNRHPTLL 524 9 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5735 4 ['A*02:01', 'A*03:01', 'A*24:02', 'A*11:0 FPNRHPTLL 525 9 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.5735 4 ['A*02:01', 'A*03:01', 'A*24:02', 'A*11:0 KNOWN FLIGHT 526 11 lncHSF521497638 MVQENQVQLIFE SILENCEDPFLITISKDVHIVLRLLLLKQCRLGHRF* lnc-HSF5-2:1 0.5733 1 ['A*02:01'] GAVFPNRHPTL 527 11 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.57155 4 ['B*08:01', 'C*07:01', 'C*07:02', 'C*03:0 GAVFPNRHPTL 528 11 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.57155 4 ['B*08:01', 'C*07:01', 'C*07:02', 'C*03:0 SREFGFHQVLF 529 11 lncHOXB81519402135 BUTLLLSHPEGHLTRPLEQTKGAGSQSLRSQFSEAQEENGFSFVLVRRPSREFGFHQVLFFQKK* lnc-HOXB8-1:5 0.57155 3 ['C*07:02', 'C*04:01', 'C*06:0 AVFPNRHPTL 530 10 lncTRPC531160328 MTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.57105 1 ['B*51:01'] AVFPNRHPTL 531 10 lncTRPC53128328 MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETMTWKEMFRQLGTVTMTMCIGCLQLTVPSFPLLHGLLGNPISTGAVFPNRHPTLLF* lnc-TRPC5-3:1 0.57105 1 ['B*51:01'] EAPTLGFMDGF 532 11 LINC024189706778 MREHRGEAPTLGFMDGFLEEEAR* LINC02418 : 9 0.57045 4 ['A*01:01', 'A*24:02', 'B*35:01', 'B*51:0 KTRQLQNCERR 533 11 lncTH1135283804 MCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.57035 1 ['A*03:01'] KTRQLQNCERR 534 11 lncTH1135223804 MQMCSQWPWQNLTKSAPATRPASKDALSRRPLQLSSDCPRDTLSEHCPAKTRQLQNCERRWFHDFLAVVTAVGQLWVTLKGHSDKGHLPACVT* lnc-TH-1:1 0.57035 1 ['A*03:01'] YRKYPAEV 535 8 lncPLA2G1B2383028395 MVRSCLYEKYRKYPAEVGGGSLEAWKQRLK* lnc-PLA2G1B-2:3 0.57 3 ['A*01:01', 'A*03:01', 'A*11:01'] LAWKSHILLAK 536 11 lncSLC39A1021271373 MKSVEVRPLDALAWKSHILLAKANHKATTNSRR* lnc-SLC39A10-2:1 0.569 2 ['A*03:01', 'A...

Claims

1. A polypeptide encoded by an open reading frame in a long non-coding RNA gene (lncRNA), wherein the lncRNA is overexpressed in colorectal cancer cells relative to healthy cells, preferably wherein the lncRNA is defined according to any one of SEQ ID NO: 1 to 18.

2. A polypeptide comprising a 6-amino acid sequence, a 7-amino acid sequence, or preferably an 8-amino acid sequence, or a variant thereof, included in any polypeptide sequence as defined in SEQ ID NO: 19 to 97.

3. The polypeptide of claim 2, wherein the variant has at least 70%, at least 80%, or at least 90% sequence identity with an 8-amino acid sequence included in any polypeptide sequence as defined in SEQ ID NO: 19 to 97.

4. The polypeptide according to any of the preceding claims, wherein the polypeptide comprises any polypeptide sequence defined according to SEQ ID NO: 98 to 611.

5. The polypeptide according to any of the preceding claims, wherein the polypeptide comprises a sequence of about 6 to 32 amino acids, preferably about 7 to 30 amino acids, and most preferably about 8 to 11 or about 12 to 28 amino acids.

6. A polynucleotide encoding one or more polypeptides according to any of the preceding claims, preferably wherein the polynucleotide is a DNA or mRNA molecule.

7. A vector comprising the polynucleotide according to claim 6.

8. A cell in which: (i) The cell is a T cell expressing a receptor specific to a polypeptide as defined in any one of claims 1 to 5 and / or a polypeptide encoded by a polynucleotide as described in claim 6 and / or a polypeptide encoded by a vector as described in claim 7, optionally wherein the T cell is engineered to express the receptor (e.g., it is a CAR-T) or wherein the T cell generates the polypeptide; or (ii) The cells are dendritic cells (DCs) matured in vitro using a variety of polypeptides as defined in any one of claims 1 to 5, optionally wherein: a. The plurality of polypeptides includes 2 to 20 different polypeptides; and / or b. The one or more polypeptides are 8-11 polymers; and / or c. Each of the aforementioned polypeptides is defined according to any 2 to 20 of SEQ ID NO: 98 to 611. Preferably, maturity is achieved through: i. Transfection with multiple mRNA molecules, each carrying a coding sequence for one of the multiple polypeptides; or ii. Infection with multiple viral vectors, wherein each viral vector molecule carries a coding sequence for one of the multiple polypeptides; and / or (iii) The cell comprises the polynucleotide according to claim 6 and / or the carrier according to claim 7.

9. A composition comprising a polypeptide according to any one of claims 1 to 5, a polynucleotide according to claim 6, a carrier according to claim 7, or a cell according to claim 8, and a pharmaceutically acceptable carrier.

10. The composition of claim 9, wherein the composition comprises a plurality of polypeptides according to any one of claims 1 to 5, optionally wherein: i. The plurality includes 2 to 20 different polypeptides; and / or ii. The one or more polypeptides are 8-11 polymers; and / or iii. Each of the said polypeptides is defined according to any 2 to 20 of SEQ ID NO: 98 to 611.

11. The composition of claim 9, wherein the composition comprises the polynucleotide of claim 6 and the polynucleotide is mRNA, optionally wherein: i. The mRNA encodes multiple polypeptides according to any one of claims 1 to 5, preferably wherein the mRNA molecule encodes 2 to 20 different polypeptides; and / or ii. The one or more polypeptides are 8-11 polymers; and / or iii. Each of the said polypeptides is defined according to any 2 to 20 of SEQ ID NO: 98 to 611; and / or iv. The mRNA molecular frame encodes multiple polypeptides according to any one of claims 1 to 5 to form a continuous polypeptide.

12. The composition of claim 9, wherein the composition comprises the carrier of claim 7, and optionally wherein: i. The vector is a viral vector; and / or ii. The vector encodes a polypeptide according to any one of claims 1 to 5, preferably wherein the vector encodes 2 to 20 different polypeptides; and / or iii. The one or more polypeptides are 8-11 polymers; and / or iv. Each of the said polypeptides is defined according to any 2 to 20 of SEQ ID NO: 98 to 611; and / or v. The vector molecular frame encodes multiple polypeptides according to any one of claims 1 to 5 to form a continuous polypeptide.

13. A method for treating or preventing colorectal cancer in an individual, the method comprising administering to the individual a polypeptide according to any one of claims 1 to 5, a polynucleotide according to claim 6, a carrier according to claim 7, a cell according to claim 8, or a composition according to any one of claims 9 to 12.

14. A method for inducing an immune response against colorectal cancer in an individual, the method comprising administering to the individual a polypeptide according to any one of claims 1 to 5, a polynucleotide according to claim 6, a carrier according to claim 7, a cell according to claim 8, or a composition according to any one of claims 9 to 12.

15. A method for diagnosing colorectal cancer in an individual, the method comprising analyzing a sample taken from the individual for any one of the following lncRNAs: SEQ ID NO: 1 to 18; a polypeptide: any one of SEQ ID NO: 19 to 97; or a polypeptide: any one of SEQ ID NO: 98 to 611.

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