Signatures of mutational processes in human cancer.

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy

Biomarkers in cancer immunotherapy

Antibodies against T cell checkpoint molecules have started to revolutionize cancer treatment. Nevertheless, less than half of all patients respond to these immunotherapies. Recent work supports the potential value of biomarkers that predict therapy outcome and inspires the development of assay systems that interrogate other aspects of the cancer-immunity cycle

Resilient flood risk strategies: Institutional preconditions for implementation

There is a growing recognition of resilience enhancement as an additional objective for adaptation. This will typically involve enhancing the preparedness and capacity to respond to the impacts of climate change. Within flood risk practice, resilient strategies focus on reducing impacts from flooding through better prevention and preparedness. Such strategies will not only reduce existing risk levels, but could also make the social-ecological system more robust for extreme flood events. This is because they seek to prevent those impacts on the system from which recovery is extremely difficult without outside help. Besides that, resilient strategies increase the prospect for the realization of cobenefits, particularly when measures are selected within the spatial domain. Implementing resilient strategies, however, faces many difficulties, particularly in countries like the Netherlands and Poland where prevalent governance arrangements are aimed to facilitate resistant strategies, focusing exclusively on flood protection. We analyzed these implementation difficulties for the Island of Dordrecht, which is a front-runner case of resilient flood risk governance in the Netherlands. A theoretical framework based on relevant issues regarding governance arrangements was used to reflect on the identified gaps and barriers. Although all issues played a role in the case study, there seem to be no generic institutional design parameters that have to be applied for implementing resilient strategies. Even in the current institutional regime, it is possible to find ways of implementing a resilient strategy. The more general institutional precondition has to do with the political willingness to allow for collaboration and experimentation and to enable a more flexible use of current principles and rules

Tumor infiltrating lymphocytes (TIL) therapy in metastatic melanoma: boosting of neoantigen-specific T cell reactivity and long-term follow-up

Purpose Execute a phase I/II feasibility study with TIL therapy in metastatic melanoma at the Netherlands Cancer Institute, with the goal to assess feasibility and potential value of a randomized phase III trial.Experimental Ten patients were treated with TIL therapy. Infusion products and peripheral blood samples were phenotypically characterized and neoantigen reactivity was assessed. Here, we present long-term clinical outcome and translational data on neoantigen reactivity of the T cell products.Results Five out of 10 patients, who were all anti-PD-1 naïve at time of treatment, showed an objective clinical response, including two patients with a complete response that are both ongoing for more than 7 years. Immune monitoring demonstrated that neoantigen-specific T cells were detectable in TIL infusion products from three out of three patients analyzed. For six out of the nine neoantigen-specific T cell responses detected in these TIL products, T cell response magnitude increased significantly in the peripheral blood compartment after therapy, and neoantigen-specific T cells were detectable for up to 3 years after TIL infusion.Conclusion The clinical results from this study confirm the robustness of TIL therapy in metastatic melanoma and the potential role of neoantigen-specific T cell reactivity. In addition, the data from this study supported the rationale to initiate an ongoing multicenter phase III TIL trial

Neoantigen landscape dynamics during human melanoma-T cell interactions

Recognition of neoantigens that are formed as a consequence of DNA damage is likely to form a major driving force behind the clinical activity of cancer immunotherapies such as T-cell checkpoint blockade and adoptive T-cell therapy(1-7). Therefore, strategies to selectively enhance T-cell reactivity against genetically defined neoantigens(1,8-11) are currently under development. In mouse models, T-cell pressure can sculpt the antigenicity of tumours, resulting in the emergence of tumours that lack defined mutant antigens(12,13). However, whether the T-cell-recognized neoantigen repertoire in human cancers is constant over time is unclear. Here we analyse the stability of neoantigen-specific T-cell responses and the antigens they recognize in two patients with stage IV melanoma treated by adoptive T-cell transfer. The T-cell-recognized neoantigens can be selectively lost from the tumour cell population, either by overall reduced expression of the genes or loss of the mutant alleles. Notably, loss of expression of T-cell-recognized neoantigens was accompanied by development of neoantigen-specific T-cell reactivity in tumour-infiltrating lymphocytes. These data demonstrate the dynamic interactions between cancer cells and T cells, which suggest that T cells mediate neoantigen immunoediting, and indicate that the therapeutic induction of broad neoantigen-specific T-cell responses should be used to avoid tumour resistanc