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Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens.

Gubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Toebes M, Vesely MD, Lam SS, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Schumacher TN, Aebersold R, Rammensee HG, Melief CJ, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD - Nature (2014)

Bottom Line: Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression.Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits-including durable responses--to patients with different malignancies.These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.

ABSTRACT
The immune system influences the fate of developing cancers by not only functioning as a tumour promoter that facilitates cellular transformation, promotes tumour growth and sculpts tumour cell immunogenicity, but also as an extrinsic tumour suppressor that either destroys developing tumours or restrains their expansion. Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression. In many individuals, immunosuppression is mediated by cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1), two immunomodulatory receptors expressed on T cells. Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits-including durable responses--to patients with different malignancies. However, little is known about the identity of the tumour antigens that function as the targets of T cells activated by checkpoint blockade immunotherapy and whether these antigens can be used to generate vaccines that are highly tumour-specific. Here we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T-cell rejection antigens following anti-PD-1 and/or anti-CTLA-4 therapy of mice bearing progressively growing sarcomas, and we show that therapeutic synthetic long-peptide vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Although mutant tumour-antigen-specific T cells are present in progressively growing tumours, they are reactivated following treatment with anti-PD-1 and/or anti-CTLA-4 and display some overlapping but mostly treatment-specific transcriptional profiles, rendering them capable of mediating tumour rejection. These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

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Mutations in Lama4 and Alg8 form top predicted d42m1-T3 epitopesa, Growth of d42m1-T3 or F244 tumours in 5-mouse cohorts treated with αPD-1 (closed circles), αCTLA-4 (open circles), αPD-1+αCTLA-4 (open triangle) or control mAb (closed triangle). b, Potential H-2Kb binding epitopes predicted by in silico analysis of all missense mutations in d42m1-T3. c, Median affinity values for the top 62 predicted H-2Kb epitopes. d, Median affinity values of H-2Kb epitopes after filtering. e, Screening for specificities of CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice using H-2Kb tetramers loaded with top 62 H-2Kb epitopes. f, IFN-γ and TNF-α induction in CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice following culture with irradiated splenocytes pulsed with the top 62 H-2Kb peptides. Data are presented as per cent CD8+ TILs expressing IFN-γ, TNF-α or for both. Data are representative of two independent experiments.
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Figure 1: Mutations in Lama4 and Alg8 form top predicted d42m1-T3 epitopesa, Growth of d42m1-T3 or F244 tumours in 5-mouse cohorts treated with αPD-1 (closed circles), αCTLA-4 (open circles), αPD-1+αCTLA-4 (open triangle) or control mAb (closed triangle). b, Potential H-2Kb binding epitopes predicted by in silico analysis of all missense mutations in d42m1-T3. c, Median affinity values for the top 62 predicted H-2Kb epitopes. d, Median affinity values of H-2Kb epitopes after filtering. e, Screening for specificities of CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice using H-2Kb tetramers loaded with top 62 H-2Kb epitopes. f, IFN-γ and TNF-α induction in CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice following culture with irradiated splenocytes pulsed with the top 62 H-2Kb peptides. Data are presented as per cent CD8+ TILs expressing IFN-γ, TNF-α or for both. Data are representative of two independent experiments.

Mentions: In this study, we used two distinct progressor MCA sarcoma cell lines (d42m1-T3 and F244) and asked whether they expressed sufficient immunogenicity to be controlled by checkpoint blockade immunotherapy. Both sarcoma lines were rejected in wild type (WT) mice treated therapeutically with αPD-1- and/or αCTLA-4 (Fig. 1a). Rejection was immunologic since it (a) was ablated by administration of mAbs that either deplete CD4+ or CD8+ cells or neutralize IFN-γ; (b) did not occur in Rag2−/− mice lacking T, B, and NKT cells or Batf3−/− mice lacking CD8α+/CD103+ dendritic cells required for tumour antigen cross-presentation to CD8+ T cells (Extended Data Fig. 1a); and (c) induced a memory response that protected mice against rechallenge with the same tumour cells that had been injected into naïve mice (Extended Data Fig. 1b,c).


Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens.

Gubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Toebes M, Vesely MD, Lam SS, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Schumacher TN, Aebersold R, Rammensee HG, Melief CJ, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD - Nature (2014)

Mutations in Lama4 and Alg8 form top predicted d42m1-T3 epitopesa, Growth of d42m1-T3 or F244 tumours in 5-mouse cohorts treated with αPD-1 (closed circles), αCTLA-4 (open circles), αPD-1+αCTLA-4 (open triangle) or control mAb (closed triangle). b, Potential H-2Kb binding epitopes predicted by in silico analysis of all missense mutations in d42m1-T3. c, Median affinity values for the top 62 predicted H-2Kb epitopes. d, Median affinity values of H-2Kb epitopes after filtering. e, Screening for specificities of CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice using H-2Kb tetramers loaded with top 62 H-2Kb epitopes. f, IFN-γ and TNF-α induction in CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice following culture with irradiated splenocytes pulsed with the top 62 H-2Kb peptides. Data are presented as per cent CD8+ TILs expressing IFN-γ, TNF-α or for both. Data are representative of two independent experiments.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4279952&req=5

Figure 1: Mutations in Lama4 and Alg8 form top predicted d42m1-T3 epitopesa, Growth of d42m1-T3 or F244 tumours in 5-mouse cohorts treated with αPD-1 (closed circles), αCTLA-4 (open circles), αPD-1+αCTLA-4 (open triangle) or control mAb (closed triangle). b, Potential H-2Kb binding epitopes predicted by in silico analysis of all missense mutations in d42m1-T3. c, Median affinity values for the top 62 predicted H-2Kb epitopes. d, Median affinity values of H-2Kb epitopes after filtering. e, Screening for specificities of CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice using H-2Kb tetramers loaded with top 62 H-2Kb epitopes. f, IFN-γ and TNF-α induction in CD8+ TILs from αPD-1 treated, d42m1-T3 tumour bearing mice following culture with irradiated splenocytes pulsed with the top 62 H-2Kb peptides. Data are presented as per cent CD8+ TILs expressing IFN-γ, TNF-α or for both. Data are representative of two independent experiments.
Mentions: In this study, we used two distinct progressor MCA sarcoma cell lines (d42m1-T3 and F244) and asked whether they expressed sufficient immunogenicity to be controlled by checkpoint blockade immunotherapy. Both sarcoma lines were rejected in wild type (WT) mice treated therapeutically with αPD-1- and/or αCTLA-4 (Fig. 1a). Rejection was immunologic since it (a) was ablated by administration of mAbs that either deplete CD4+ or CD8+ cells or neutralize IFN-γ; (b) did not occur in Rag2−/− mice lacking T, B, and NKT cells or Batf3−/− mice lacking CD8α+/CD103+ dendritic cells required for tumour antigen cross-presentation to CD8+ T cells (Extended Data Fig. 1a); and (c) induced a memory response that protected mice against rechallenge with the same tumour cells that had been injected into naïve mice (Extended Data Fig. 1b,c).

Bottom Line: Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression.Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits-including durable responses--to patients with different malignancies.These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.

ABSTRACT
The immune system influences the fate of developing cancers by not only functioning as a tumour promoter that facilitates cellular transformation, promotes tumour growth and sculpts tumour cell immunogenicity, but also as an extrinsic tumour suppressor that either destroys developing tumours or restrains their expansion. Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression. In many individuals, immunosuppression is mediated by cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1), two immunomodulatory receptors expressed on T cells. Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits-including durable responses--to patients with different malignancies. However, little is known about the identity of the tumour antigens that function as the targets of T cells activated by checkpoint blockade immunotherapy and whether these antigens can be used to generate vaccines that are highly tumour-specific. Here we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T-cell rejection antigens following anti-PD-1 and/or anti-CTLA-4 therapy of mice bearing progressively growing sarcomas, and we show that therapeutic synthetic long-peptide vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Although mutant tumour-antigen-specific T cells are present in progressively growing tumours, they are reactivated following treatment with anti-PD-1 and/or anti-CTLA-4 and display some overlapping but mostly treatment-specific transcriptional profiles, rendering them capable of mediating tumour rejection. These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

Show MeSH
Related in: MedlinePlus