The present disclosure provides materials and methods for cell-free expression of epitopes for immunotherapy applications. In particular, the present disclosure provides materials and methods for expressing concatenated epitopes using a cell-free protein synthesis platform for high throughput, large scale, and unbiased epitope screening and the generation of multi-epitope vaccines.

A method for identifying neoantigens that are likely to be presented on a surface of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequence of each of the neoantigens is associated with one or more k-mer blocks of a plurality of k-mer blocks of the nucleotide sequencing data of the subject; The peptide sequences and the associated k-mer blocks are input into a machine-learned presentation model to generate presentation likelihoods for the tumor neoantigens, each presentation likelihood representing the likelihood that a neoantigen is presented by an MHC allele on the surfaces of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods.

The present disclosure is directed to epitope-tagged antibodies, as well as methods of employing the epitope-tagged antibodies for detecting one or more targets in a biological sample, e.g. a tissue sample.

Isolated monoclonal antibodies and antigen binding fragments thereof that specifically bind neuraminidase (NA) of an N1 subtype influenza virus are disclosed herein. These antibodies and antigen binding fragments can be used for the detection of an N1 subtype influenza virus and for determining the immunogenicity of vaccines. The antibodies and antigen binding fragments also can be used for the treatment of a subject to prevent or ameliorate an influenza infection.

The present invention refers to an antibody able to recognize and bind to an epitope comprised in a sequence of human Migration Stimulating Factor (MSF), and that doesn't recognize and bind human Fibronectin 1 (hFn1) and to uses in diagnostic methods and therapy.

The invention relates to a method for quantitatively identifying relevant HLA-bound peptide antigens from primary tissue specimens on a large scale without labeling approaches. This method can not only be used for the development of peptide vaccines, but is also highly valuable for a molecularly defined immunomonitoring and the identification of new antigens for any immunotherapeutic strategy in which HLA-restricted antigenic determinants function as targets, such as a variety of subunit vaccines or adoptive T-cell transfer approaches in cancer, or infectious and autoimmune diseases.

This invention provides an anti-idiotype antibody that binds to the antigen-binding region of an antibody encoded by antibody genes selected from the group consisting of Set I, Set II, Set III, Set IV, Set V, Set VIa, Set VIb, Set VIc, Set VId, Set VIe, Set VII, and Set VIII, hybridomas and methods of treatments using such.

The present invention relates to a method for detecting a spatial proximity of a first and a second epitope (11, 21) of a protein or of a first and a second protein (10, 20) of a protein complex (1) in a sample of a subject. The method comprises binding a first binding member (30) having a first oligonucleotide (31) conjugated thereto to the first epitope (11), binding a second binding member (40) having a second oligonucleotide (41) conjugated thereto to the second epitope (21), and determining whether a Fluorescence Resonance Energy Transfer (FRET) effect is present between a donor fluorophore (32) and an acceptor fluorophore (42), which are associated with the first oligonucleotide (31) and the second oligonucleotide (41), wherein the presence of the FRET effect indicates a spatial proximity of the first and the second oligonucleotide (31, 41) and, thus, the spatial proximity of the first and the second epitope (11, 21).

Described herein are methods of identifying immunologically protective neo-epitopes from the cancer tissue DNA of cancer patients using biophysical principles as well as bioinformatics techniques. The identification of immunologically protective neo-epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a method of using the conformational stability of an epitope in an MHC protein-binding groove to predict immunogenicity of peptides in a putative neo-peptide set from a tumor from a cancer patient. Pharmaceutical compositions and methods of administration are also included.

Provided is a monoclonal antibody specifically reactive with a C-terminal neo-epitope of PIIINP comprised in a C-terminal amino acid sequence CPTGXQNYSP-COOH (SEQ ID NO: 4) in which X is Gly or Pro, and where the monoclonal antibody does not recognize or bind an elongated version of the C-terminal amino acid sequence CPTGXQNYSPQZ-COOH (SEQ ID NO: 5), in which Z is absent or is one or more amino acids of the sequence of collagen type III. Also provided is a method of immunoassay for detecting in a biological sample the C-terminal neo-epitope of PIIINP generated by N-protease cleavage of intact type III procollagen, by contacting the sample with the monoclonal antibody, and determining the amount of binding of the antibody.