Discussion
cancer, tumors
CANCER, SOLID TUMORS, MALIGNANCIES, METASTATIC MELANOMA, TUMORS, SOMATIC MUTATIONS
The NIBIT-M4 trial has been the first Phase Ib epigenetic immunomodulation study testing the association of the HMA guadecitabine with ICI in solid malignancies. Treatment of metastatic melanoma patients with guadecitabine combined with ipilimumab was found to be safe, feasible, and tolerable, with initial signs of clinical and immunologic activityOur aim here was to exploit the longitudinal multi-omics profiling of the NIBIT-M4 cohort in conjunction with the 5 years follow-up to shed light on the effect of the combination during treatment and to identify early biomarkers of response. To this end, we have first individually interrogated the available omics platforms taking advantage of the accurate longitudinal sampling. Then we developed computational multi-omics integration approaches to evaluate the effect of the adopted demethylation agent on boosting the adaptive and innate immune-mediated cancer rejection. The five-year follow-up showed that our multi-omics classification based on the ICR/GIE index is a better prognostic factor than best overall response (BOR). Therefore, the analysis reported here can serve as a guide for improved patient stratification and selection strategies in combination therapies involving ICI and immunomodulatory agents, including HMA.Longitudinal WES and transcriptomic analysis contributed to shed light on molecular factors impacting clinical response and on long-term outcome after guadecitabine plus ipilimumab. At the mutational profile level, strong consistency across biopsies obtained at three-time points in a 12-week time frame allowed us to identify significant associations of somatic mutations with response/resistance even with the small number of patients enrolled in the NIBIT-M4 trial.Even if the impact of the genomic landscape is difficult to be linked to the HMA rather than to ipilimumab, our results confirm and extend evidence of resistance obtained in ICB-only trials. First, we found that Mutations in genes belonging to the EMT were enriched in NR patients. EMT is associated with a less favorable outcome in patients with cancerInterrogating the longitudinal gene expression data was also useful in evaluating how the immune context evolves during therapy. The differential activity of these pathways tends to increase during therapy, suggesting that immune surveillance promoted by ICI represses cell cycle genes together with differentiation pathways. We have shown an increased expression of the guadecitabine-specific signature that we had previously definedThe transcriptional effects that could be ascribed to guadecitabine and could contribute to explain clinical benefit in this combinatorial trial, were assessed by considering tumor-specific antigens derived from transposable elementsWe evaluated several transcription-based signatures for response prediction to ICI. No difference was observed at the baseline. This suggests that additional factors contribute to clinical response, beyond the process of development of adaptive immunity, captured by these signatures. We reasoned that an immune-based stratification approach taking into account: a) the evidence of expression of genes associated with ICR and b) the amount of immunoediting measured as the ratio of observed versus expected neoantigens (GIE) could improve our ability to understand response and resistance to treatment. The presence of an adaptive immune response within tumors is accounted by the ICRThe inference of changes in gene expression programs needs to account for the cellular composition at different time points. The actual profiling platform, with half of the cases lacking the normal reference, is not ideal for an accurate estimation of the purity. Single-cell profiling will be performed on this cohort in future studies to address this point. Moreover, the low number of analyzed cases, even with longitudinal multi-omics profiling, represents a limitation in our study, though its results help to guide further development of HMA/ICI combinations in solid tumors. Additionally, the application of the ICR/GIE to multiple contexts at a pan-cancer level is needed to further validate the clinical relevance of our approach and findings. Collectively, though limited by the still scarce number of completed trials and enrolled patients, the available clinical results suggest and support further development of combinatorial approaches of HMA with ICI in cancer therapy in randomized clinical trials with extensive translational endpoints.