Bioinformatics

A device for tumour antigen identification comprising:

• a microfluidic device comprising at least one flow-through channel containing a plurality of micropillars arranged in an array to which there is attached at least one molecule, or at least one complex, that has bound thereto at least one anti-MHC antibody or at least one anti-pan-Human Leukocyte Antigen (HLA) antibody whereby a pMHC in a sample flowing through said channel can be extracted from said sample using said at least one antibody;
• and
• a processor adapted for identifying said peptide bound to said Major Histocompatibility Complex and comparing said peptide of said bound pMHC with a library of pathogen-derived peptide antigens to determine if said peptide bound or that was bound to said Major Histocompatibility Complex shows homology/affinity with at least one pathogenic antigen, or part thereof, and where greater than 60% homology/affinity exists;
• indicating said peptide bound or that was bound to said Major Histocompatibility Complex as a tumour-specific antigen for use in cancer therapy.

A method of stratifying patients for checkpoint inhibitor cancer treatment comprising:

• i) taking a sample of tumour from a patient;
• ii) dissolving or suspending the sample in a fluid;
• iii) passing said fluid through a microfluidic device for tumour-specific antigen identification comprising:
• at least one flow-through channel containing a plurality of micropillars arranged in an array to which there is attached at least one molecule, or at least one complex, that has bound thereto at least one anti-MHC antibody or at least one anti-pan-Human Leukocyte Antigen (HLA) antibody whereby a pMHC in a sample flowing through said channel can be extracted from said sample using said at least one antibody;
• iv) binding to said at least one antibody at least one pMHC in said sample;
• v) removing said at least one bound pMHC of part iv) from said device;
• vi) comparing said peptide of said bound pMHC with a library of human pathogen antigens to determine if said peptide shows homology/affinity with at least one human pathogenic antigen, or part thereof, and where greater than 60% homology/affinity exists;
• vii) identifying said peptide as a tumour-specific antigen;
• and
• viii) when said peptide is found, administering an effective amount of at least one checkpoint inhibitor (ICI) to said patient.

A method of stratifying patients for adenoviral cancer treatment comprising:

• i) taking a sample of tumour from a patient;
• ii) dissolving or suspending the sample in a fluid;
• iii) passing said fluid through a microfluidic device for tumour-specific antigen identification comprising:
• at least one flow-through channel containing a plurality of micropillars arranged in an array to which there is attached at least one molecule, or at least one complex, that has bound thereto at least one anti-MHC (Major Histocompatibility Complex) antibody or at least one anti-pan-Human Leukocyte Antigen (HLA) antibody whereby a pMHC in a sample flowing through said channel can be extracted from said sample using said at least one antibody;
• iv) binding to said at least one antibody at least one pMHC in said sample;
• v) optionally, removing said at least one bound pMHC of part iv) from said device;
• vi) comparing said peptide of said bound pMHC with a library of human pathogenic antigens to determine if said peptide shows homology/affinity with at least one human pathogenic antigen, or part thereof, and where greater than 60% homology/affinity exists;
• vii) identifying said peptide as a tumour-specific antigen;
• and
• viii) when said peptide is found, attaching said peptide to the capsid of an adenoviral vector and administering an effective amount of said adenoviral vector to said patient.

A method of treating cancer comprising:

• i) taking a sample of tumour from a patient;
• ii) dissolving or suspending the sample in a fluid;
• iii) passing said fluid through a microfluidic device for tumour-specific antigen identification comprising:
• at least one flow-through channel containing a plurality of micropillars arranged in an array to which there is attached at least one molecule or at least one complex that has bound thereto at least one anti-MHC antibody or at least one anti-pan-Human Leukocyte Antigen (HLA) antibody whereby a pMHC in a sample flowing through said channel can be extracted from said sample using said at least one antibody;
• iv) binding to said at least one antibody at least one pMHC in said sample;
• v) optionally, removing said at least one bound pMHC of part iv) from said device;
• vi) comparing said peptide of said bound pMHC with a library of human pathogenic antigens to determine if said peptide shows homology/affinity with at least one human pathogenic antigen, or part thereof, and where greater than 60% homology/affinity exists;
• vii) identifying said peptide as a tumour-specific antigen;
• and
• viii) administering an effective amount of said peptide to said patient to stimulate or activate T-cells against the tumor-specific antigen and so the cancer from which the sample was taken;
• or using said tumour-specific antigen to expand a population of T-cells active against said tumour antigen and then administering said T-cells to said patient.