Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

Abstract

• Tumor neoantigens are a promising class of immunogens based on exquisite tumor specificity and the lack of central tolerance against them.• Massively parallel DNA sequencing with class I prediction enables systematic identification of tumor neoepitopes (including from CLL).Genome sequencing has revealed a large number of shared and personal somatic mutations across human cancers. In principle, any genetic alteration affecting a protein-coding region has the potential to generate mutated peptides that are presented by surface HLA class I proteins that might be recognized by cytotoxic T cells. To test this possibility, we implemented a streamlined approach for the prediction and validation of such neoantigens derived from individual tumors and presented by patient-specific HLA alleles. We applied our computational pipeline to 91 chronic lymphocytic leukemias (CLLs) that underwent whole-exome sequencing (WES). We predicted ∼22 mutated HLA-binding peptides per leukemia (derived from ∼16 missense mutations) and experimentally confirmed HLA binding for ∼55% of such peptides. Two CLL patients that achieved long-term remission following allogeneic hematopoietic stem cell transplantation were monitored for CD8 1 T-cell responses against predicted or confirmed HLA-binding peptides. Long-lived cytotoxic T-cell responses were detected against peptides generated from personal tumor mutations in ALMS1, C6ORF89, and FNDC3B presented on tumor cells. Finally, we applied our computational pipeline to WES data (N 5 2488 samples) across 13 different cancer types and estimated dozens to thousands of predicted neoantigens per individual tumor, suggesting that neoantigens are frequent in most tumors. (Blood. 2014;124(3):453-462) IntroductionRecent progress in the development of potent vaccine adjuvants, clinically effective vaccine delivery systems, and agents that overcome tumor-induced immunosuppression strongly support the possibility that long-awaited effective therapeutic cancer vaccines are feasible. [1][2][3][4] Past cancer vaccine efforts have lacked efficacy that may stem from their focus on overexpressed or selectively expressed tumor-associated native antigens as vaccine targets that require overcoming the challenging hurdles of breaking central and peripheral tolerance while risking the generation of autoimmunity. [4][5][6] The rare examples of successful cancer vaccines in humans have targeted foreign pathogen-associated antigens 7 or a mutated growth factor receptor 8 or are idiotype vaccines derived from patient-specific rearranged immunoglobulins. 9 These studies point to the importance of selecting immunogens distinct from self, where central/peripheral tolerance can be overcome and the risk of autoimmunity is minimal.A hallmark of tumorigenesis is the accumulation of mutations in cancer cells. These mutations are found as both driver and passenger events 10 and collectively provide an opportunity to specifically target tumor cells through the creation of tumor-specific novel immunogenic peptides (neoantigens). ...

Tumor neoantigens: building a framework for personalized cancer immunotherapy

“…Whereas SYFPEITHI (65), Rankpep (66), and BIMAS (67) were the first such tools to be developed, more accurate prediction algorithms have now come on line, and some have been incorporated into the Immune Epitope Database and Analysis Resource (IEDB) (68). A subset of these algorithms predicts peptide binding to different MHCI variants based on artificial neural networks (ANN), providing predicted IC 50 as an output (69). In this category, NetMHC (70) is one of the most commonly used and best validated prediction programs (71,72).…”

Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells

“…Likewise, in two patients with chronic lymphocytic leukemia, in vitro priming revealed T-cell responses against 12% (3/25) of mutations tested (although MHC class I processing and presentation was assessed for only one of these peptides; ref. 40). Thus, although the sample sizes are small in each of these studies, the combined results suggest that, by using sensitive methods that allow detection of na€ ve and/or rare T cells, one can identify T-cell responses to a larger proportion of mutations than previously appreciated.…”

The next steps in next-gen sequencing of cancer genomes

“…Nonetheless, recent studies confirm the utility of exome sequencing for discovery of tumor neoantigens, although it should be noted that the majority of neoantigens identified are in genes that are absent in current targeted exon-sequencing panels (54,55). Overall, it seems likely that the integration of other genomic platforms such as RNA sequencing and platforms such as proteomics and polychromatic flow cytometry will allow for a more comprehensive "immune portrait" of tumors, including the molecular assessment of lymphocyte clonality and diversity (56) as well as the assessment of other key microenvironmental components such as tumor-associated fibroblasts and endothelial cells, which may be key predictors of response to both immune and antiangiogenic therapies (refs.…”