Melanoma is the most lethal malignancy of the skin. Immunotherapy has contributed to improved survival in melanoma patients, yet the mechanisms explaining differences in efficacy have not been elucidated. In previous studies our group found an immune signature that predicts response to antiPD1 immunotherapy. On the other hand, melanoma genomics have been extensively studied, but data regarding protein expression are still scarce. We have performed a genomics plus proteomics analysis of advanced melanoma samples aiming to find mechanisms of resistance to antiPD1.
53 formalin-fixed, paraffin-embedded (FFPE) melanoma samples were analyzed using a high-throughput proteomics approach based on mass-spectrometry. Using the same 53 FFPE samples we performed RNA-seq of 2000 preselected genes through SeqCap® RNA Choice Probes. Both proteomics and RNA-seq data will be analyzed using probabilistic graphical models (PGM) and sparse-k means plus consensus cluster algorithm, independently and joint together.
53 advanced melanoma patients treated with anti-PD1 immunotherapy were recruited. Proteomics analyses allowed the identification and quantification of 1605 proteins passing quality criteria (two unique peptides and less than 50% of missing values). A PGM, including these 1605 proteins was built, and the resulting graph was processed to seek for functional structures. Successive sparse k-means and consensus cluster algorithm were performed to find the different informative layers. We found an informative layer composed of 102 proteins that divide patients in two groups; these two groups had prognostic value. On the other hand, a PGM including the 2000 genes will be also built (experiments already ongoing). Finally, results from both proteomics and genomics approach will be combined looking for anti-PD1 resistance mechanisms.
The integration of different omics will lead us to a better understanding of the resistance mechanisms to anti-PD1 immunotherapy in advanced melanoma.
The authors.
Has not received any funding.
G. Prado Vázquez, L. Trilla Fuertes, A. Zapater Moros, E. López Camacho: Full/Part-time employment: biomedica Molecular Medicine. A. Gámez Pozo, J.A. Fresno Vara, E. Espinosa: Shareholder/Stockholder/Stock options: biomedica Molecular Medicine. All other authors have declared no conflicts of interest.