The present disclosure provides shared neoantigenic peptides derived from the expression of tumor-specific transposable element, as well as nucleic acids, vaccines, antibodies and immune cells that can be used in cancer therapy.

The present invention relates to an endogenous tumor-derived circular ribonucleic acid (circ RNA) as well as one or more proteins expressed from said tumor-derived circ RNA. The invention further relates said tumor-derived circ RNA and the protein(s) expressed thereof for use vaccines in the prophylaxis and/or treatment of cancer.

Disclosed are compositions and methods for identifying neoantigens and using neoantigens in the use of treating cancer, as well as autoimmune diseases, where antigens causing tissue destruction.

This invention provides a method for maximizing the immune response to mutated tumor specific proteins, either by means of stimulation of dendritic cells or T cells in vitro followed by administration of these cells to a patient, or by means of administration of a neoantigen vaccine in which de novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's MHC alleles. This invention further provides for modulating the immune response in an immunopathology other than cancer.

The present invention relates to polypeptides comprising a fragment of a teleost invariant chain optionally fused to one or more antigens or a teleost invariant chain fused to one or more antigens or antigenic fragments thereof, a polynucleotide encoding such polypeptides, vectors comprising such polynucleotides, collection of vectors comprising such polynucleotides and use of such polypeptides, polynucleotides, vectors for treating or preventing diseases, in particular tumor diseases. The teleost invariant chain polypeptides or fragments thereof act as T cell enhancer converting non-immunogenic antigenic sequences into immunogenic T cell antigens.

The disclosure relates to methods of manufacturing individualized vaccines that comprise nucleic acid molecules that encode one or more neoantigens specific for antigens that are expressed by a tumor in a subject. Compositions comprising coding regions encoding neoantigens organized in a pattern of nucleic acid sequences are also disclosed as well as methods of immunizing a subject using the same.

Methods and compositions for use in generating or promoting an immune response to cancer or an infection, comprising promoting differentiation of neutrophils into dendritic cells using a combination of GMCSF and (i) an immune complex comprising an antigen and an antibody comprising an Fc region that binds to FcRIIA or FcRIIIB, (ii) a conjugate comprising an antigen and an anti-FcRIIIB antibody, or (iii) an anti-FcRIIIB antibody.

Systems and methods for predicting MHC presentation of a neoepitope of a tumor or for predicting an immune response against an MHC presented neoepitope of a tumor are disclosed. The methods use sequence information of the neoepitope.

The present disclosure relates to a method for selecting a tumor neoantigenic peptide wherein said method comprises: a step of identifying, among mRNA sequences from cancer cells of a subject, a fusion transcript sequence comprising a transposable element (TE) sequence and an exonic sequence, and including an open reading frame (ORF), anda step of selecting a tumor neoantigenic peptide of at least 8 amino acids, encoded by a part of said ORF of the fusion transcript sequence, wherein said ORF overlaps the junction between the TE and the exonic sequence, is pure TE and/or is non-canonical, and wherein said tumor neoantigenic peptide binds to at least one Major Histocompatibility Complex (MHC) molecule of said subject. The present disclosure also relates to tumor neoantigenic peptide obtained according to the present method, vaccine or immunogenic composition, antibodies and immune cells derived thereof and their use in therapy of cancer.