Antigen-specific cells, methods of generating these cells and uses thereof
First Claim
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1. A method of identifying a polynucleotide fragment of a gene that encodes an antigen recognized by an immune effector cell, comprising:
- (a) providing a first cell that expresses an antigen recognized by the immune effector cell and having an identified major histocompatibility complex (MHC) restriction and one or more second cells having a compatible major histocompatibility complex (MHC) to the first cell but which does not express antigen;
(b) identifying polynucleotides encoding a peptide sequence motif in the antigen displayed by antigen presenting cells and recognized by the immune effector cell;
(c) identifying polynucleotides which are aberrantly expressed by the first cells as compared to one or more second cells; and
(d) comparing the polynucleotides identified in step (c) with the polynucleotides motifs identified in step (b) to identify the fragment of the gene encoding the antigen recognized by the immune effector cell.
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Abstract
The present invention provides methods for identifying antigens recognized by immune effector cells. In one embodiment, the methods combine identifying amino acid sequence motifs of such antigens and the DNA sequences that potentially encode the identified amino acid motifs and the DNA sequences which are aberrantly expressed in the cells. By comparison of these sequences, novel antigens that are recognized by immune effector cells are identified.
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24 Claims
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1. A method of identifying a polynucleotide fragment of a gene that encodes an antigen recognized by an immune effector cell, comprising:
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(a) providing a first cell that expresses an antigen recognized by the immune effector cell and having an identified major histocompatibility complex (MHC) restriction and one or more second cells having a compatible major histocompatibility complex (MHC) to the first cell but which does not express antigen;
(b) identifying polynucleotides encoding a peptide sequence motif in the antigen displayed by antigen presenting cells and recognized by the immune effector cell;
(c) identifying polynucleotides which are aberrantly expressed by the first cells as compared to one or more second cells; and
(d) comparing the polynucleotides identified in step (c) with the polynucleotides motifs identified in step (b) to identify the fragment of the gene encoding the antigen recognized by the immune effector cell. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
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2. The method of identifying a fragment of one or more genes encoding an antigen recognized by an immune effector cell, comprising:
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(a) generating a first set of polynucleotide primers corresponding to peptide sequence motifs displayed by an antigen expressing cell and recognized by immune effector cells in a manner restricted by the major histocompatability complex of the antigen expressing cell;
(b) generating a second set of polynucleotide primers corresponding to the unique identifier sequences (SAGE tags) of transcripts differentially expressed in the same antigen expressing cells as described in part (a) above when compared to other antigen expressing cells that are not recognized by the same immune effector cells as in part (a) above but possess a compatible major histocompatability complex;
(c) combining the first and second sets of primers in a combinatorial fashion and identifying the transcripts representative of one or more genes encoding antigens recognized by immune effector; and
(d) amplifying cDNA obtained from the first group of cells recognized by the immune effector cells with the combined primers and analyzing the amplified products, thereby identifying one or more fragments of genes encoding antigens recognized by immune effector cells.
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Specification