Identification of cell surface antigens which induce t-cell responses and their uses
AssigneeVerdi Solutions GmbH
InventorsJulianna Lisziewicz, Robert Gergely Lisziewicz
Life of this patent
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Abstract
Disclosed is a computer-implemented method for identifying, for a subject, at least one antigen which is expected to induce a T-cell response to attack unhealthy cells in the subject. The invention further relates to using said antigens for designing personalized vaccines and to the use of such personalized vaccine and personalized vaccine compositions in kits and methods for the treatment of disease.
Claims21
A computer-implemented method for identifying in a subject at least one antigen, which is expected to induce a T-cell response to attack unhealthy cells in the subject, the method comprising:
- receiving subject data identifying multiple major histocompatibility complex (MHC) molecules for the subject;
- receiving sequence data for a plurality of epitopes within a protein which that is expressed in the unhealthy cells, wherein each epitope of the plurality of epitopes is an amino acid sequence within the protein;
- obtaining, for each epitope of the plurality of epitopes, a potency score indicative of a likelihood that each of the identified multiple MHC molecules displays an epitope on their surface;
- generating a ranked list of epitopes based on the determined potency scores;
- identifying at least one antigen by selecting at least one epitope that is a highly ranked in the ranked list;
- and
- outputting at least one of the ranked list and sequence data for the identified at least one antigen.
A method of designing a personalized vaccine to induce a T-cell response to attack unhealthy cells in a subject, the method comprising
- receiving subject data identifying multiple major histocompatibility complex (MHC) molecules for the subject, wherein the subject data identifies at least one of a set of HLA class I molecules and a set of HLA class II molecules;
- receiving sequence data for a plurality of epitopes within a protein expressed in the unhealthy cells, wherein each epitope is an amino acid sequence within the protein;
- obtaining, for each epitope of the plurality of epitopes, a first potency score that is indicative of a likelihood that each of the identified set of HLA class I molecules displays an epitope on their surface;
- generating a first ranked list of epitopes based on the first potency score for each epitope of the plurality of epitopes;
- selecting multiple epitopes that are highly ranked in the first ranked list;
- identifying subitopes of each of the selected multiple epitopes using a directed graph network;
- identifying each subitope that is common to more than one of the selected multiple epitopes;
- identifying at least one first antigen by selecting at least one subitope that is itself a highly ranked epitope in the first ranked list;
- and
- outputting the identified at least one first antigen for the personalized vaccine.
14-22. (canceled)
A method of treating a patient with cancer or infectious disease with a personalized vaccine that induces immune responses against unhealthy cells, the method comprising:
- a) obtaining at least one sample from a subject, the sample containing the unhealthy cells;
- b) analyzing the at least one sample to identify an expression of major histocompatibility complex (MHC) class I and MHC class II molecules in the subject and at least one protein expressed in the unhealthy cells;
- c) generating a ranked list of epitopes from the at least one protein based on an ability of the epitopes to be displayed by the MHC molecules of the subject and to induce CD4 and CD8 T-cell responses;
- d) selecting multiple highly-ranked epitopes from the ranked list that share at least one common sequence capable of triggering a T-cell response;
- e) incorporating the selected highly-ranked epitopes to prepare a personalized vaccine;
- and
- f) administering the personalized vaccine to the subject.
Dependencies are inferred from the claim text.