Simplified Exome Mining Technique Identifies Mutated Antigens Recognized by Adoptively Transferred Tumor-Reactive T Cells

Cancer researchers have used advanced exome mapping technology to characterize mutated proteins expressed in patient tumors and then used peptides from these mutant proteins to isolate tumor-infiltrating lymphocytes (TILS) suitable for therapeutic use.

Substantial regressions of metastatic lesions have been observed in up to 70% of patients with melanoma who received adoptively transferred autologous TILs in phase 2 clinical trials. In addition, 40% of patients treated in a recent trial experienced complete regressions of all measurable lesions for at least five years following TIL treatment.

To evaluate the potential association between the ability of TILs to mediate durable regressions and their ability to recognize potent antigens that presumably include mutated gene products, investigators at the Moffitt Cancer Center (Tampa, FL, USA) developed a new screening approach involving mining whole-exome sequence data to identify mutated proteins expressed in patient tumors.

The exome is the part of the genome formed by exons, nucleotide sequences encoded by a gene that remain present within the final mature RNA product of that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. The exome of the human genome consists of roughly 180,000 exons constituting about 1% of the total genome, or about 30 megabases of DNA. Though comprising a very small fraction of the genome, mutations in the exome are thought to harbor 85% of disease-causing mutations.

After identifying mutated proteins expressed in patient tumors, the investigators synthesized and evaluated candidate mutated T cell epitopes that were identified using a major histocompatibility complex–binding algorithm for recognition by TILs. Using this approach, they identified mutated antigens expressed on autologous tumor cells that were recognized by three bulk TIL lines from three individuals with melanoma that were associated with objective tumor regressions following adoptive transfer.

This simplified approach for identifying mutated antigens recognized by T cells avoided the need to generate and laboriously screen cDNA libraries from tumors and may represent a generally applicable method for identifying mutated antigens expressed in a variety of tumor types.

“Our new technique allowed us to more quickly and easily identify mutated gene antigens recognized by T-cells in the immune system,” said contributing author Dr. Jamie K. Teer, assistant member of the cancer biology and evolution program at Moffitt Cancer Center. “Work such as this was previously done by generating and laboriously screening DNA libraries from tumors. The same screening technique may be applicable for identifying mutated antigens in a variety of tumor types.”

The study was published in the May 5, 2013, online edition of the journal Nature Medicine.

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