Low-dose interferon-alpha preconditioning and adoptive cell therapy in patients with metastatic melanoma refractory to standard (immune) therapies: a phase I/II study

BACKGROUND

Adoptive cell therapy (ACT) with tumor-reactive T cells has shown consistent clinical efficacy. We evaluated the response to ACT in combination with interferon alpha (IFNa) preconditioning in patients with stage IV metastatic melanoma, most of which were progressive on cytotoxic T-lymphocyte-associated protein 4 and/or programmed cell death protein 1 checkpoint blockade therapy.

METHODS

Thirty-four patients were treated with ex vivo expanded tumor reactive T cells, derived from mixed lymphocyte autologous tumor cultures, or with autologous tumor-infiltrating lymphocytes and evaluated for clinical response. Clinical and immunological parameters associated with response were also evaluated.

RESULTS

Best overall response defined as clinical benefit, comprising either complete response, partial response or stable disease >6 months, was observed in 29% of the patients. Forty-three per cent of the 14 immunotherapy-naïve patients and 20% of the 20 patients progressive on prior immunotherapy benefited from ACT. The overall survival (OS) was 90% versus 28.6% at 1 year and 46.7% versus 0% at 3 years follow-up, of responder and non-responder patients, respectively. Median OS was 36 versus 7 months, respectively. IFNa pretreatment resulted in leukopenia, neutropenia and lymphopenia, which was sustained during the treatment in clinical responders and associated with response. Differences in antigen specificity, but not in phenotype, cytokine profile or CD8+ T cell number of the ACT products correlated with clinical response. Cross-reactivity of the ACT products to one or more allogeneic human leukocyte antigen-matched melanoma cell lines was associated with short OS after treatment while the ACT products of very long-term survivors showed no cross-reactivity but recognized patient-specific neoantigens.

CONCLUSION

This study demonstrates that ACT in combination with a mild IFNa preconditioning regimen can induce clinical benefit even in immunotherapy pretreated patients, although with lower success than in immunotherapy-naïve patients. ACT products comprising neoantigen reactivity may be more effective.

Abstract PR11: Neo-antigen landscape dynamics during human melanoma-T cell interactions

Recognition of the neo-antigens that are formed as a consequence of DNA damage is likely to be a major driving force behind the clinical activity of T cell checkpoint blockade and adoptive T cell therapy for treatment of non-virally induced solid cancers. Consequently, strategies to selectively enhance T cell reactivity against genetically defined neo-antigens are currently under development. In mouse models, T cell pressure has been shown to sculpt the antigenicity of tumors through selection of tumor cell variants that do not express the relevant neo-antigens. However, it is unclear whether the T cell-recognized neo-antigen repertoire is constant over time in human cancers. To address this issue, we analyzed the stability of neo-antigen specific T cell responses and the antigens they recognize in stage IV melanoma patients treated by adoptive T cell transfer. Fresh tumor tissue resected before and after treatment was used to establish autologous melanoma cell lines, to culture tumor-infiltrating lymphocytes (TIL) and to generate T-cell infusion products by autologous mixed lymphocyte tumor cell cultures using peripheral blood lymphocytes. Material from 2 patients with objective clinical responses after infusion of autologous tumor-specific CD4+ and CD8+ T cells was analyzed by whole exome and RNA sequencing. Subsequently, 31-mer peptides covering all the non-synonymous somatic mutations were used to test the reactivity of both the T-cell infusion products and TIL isolated from subsequent tumor lesions by ELISA and flow cytometry. The expression of genes encoding T cell-recognized neo-antigens was then analyzed within the tumor cell lines and within the corresponding paraffin-embedded tumor tissue, by real-time PCR analysis, a competitive allele-specific PCR assay, and by analysis of heterozygosity and next generation amplicon sequencing. Analysis of the infusion products showed that 50-80% of T cells reacted to autologous tumor cells, with only a very low percentage of these cells recognizing known shared tumor-associated epitopes. Instead, tumor reactivity was predominantly mediated by CD4+ and CD8+ T cells recognizing clonally expressed neo-antigens formed by private mutations. CD8+ T cells within the infusion products and within TIL populations generated from subsequent tumor lesions of these two patients recognized a total of 6 different neo-antigens, and analysis of these neo-antigens in both the index lesion and subsequent lesions revealed profound alterations in the T cell-recognized neo-antigen landscape. In particular, in 2 cases, the mutant allele was lost from a subsequent tumor, in one case, expression of the mutant gene was substantially reduced in a recurring lesion, and in another case expression of the mutant gene was increased approx. 40-fold in a subsequent tumor. Notably, in 4 out of 4 cases these changes in neo-antigen expression were paralleled by loss or gain of the respective neo-antigen specific T cell response. Collectively, our data demonstrate that under conditions in which a high frequency of tumor-specific T cells is present, tumor cell variants with reduced or lost neo-antigen expression can emerge, similar to what has been observed in mice. This, and the observation of concurrent acquisition of novel T cell reactivity, reveal the dynamics of T cell - neo-antigen interaction in human cancer, and indicate that immunotherapies that maximize the capacity to respond to an altering neo-antigen landscape may offer the highest chance to achieve long-term tumor control.

Citation Format: Els M.E. Verdegaal, Noel de Miranda, Marten Visser, Tom Harryvan, Marit van Buuren, Rikke Andersen, Sine Hadrup, Caroline van der Minne, Remko Schotte, Hergen Spits, John Haanen, Ellen Kapiteijn, Ton Schumacher, Sjoerd H. Van Der Burg. Neo-antigen landscape dynamics during human melanoma-T cell interactions [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR11.