While anti-CTLA4 immunotherapy (IT) improves survival in metastatic melanoma patients, it manifests with severe toxicity. Recently, we identified serum antibody signatures associated with toxicity outcomes following anti-CTLA4 IT. In this study, capitalizing on our recent data showing that the expression of autoimmunity risk genes is controlled by germline genetic variation in melanoma survival, we tested whether antibody profiles linked with IT-related toxicity are impacted by underlying genetic variation.
We have integrated serum data from 37 anti-CTLA4 IT-treated patients, profiled by HuProt human proteome array with germline whole-exome sequencing (WXS), comparing 28 patients with none/mild toxicity (CTCAE score 0-2) and 9 patients with severe toxicity (CTCAE score 3-5). The associations between toxicity and germline genetic variation were assessed by gene-burden analysis (SKAT). SKAT was integrated with differential proteome analysis of toxicity to identify individual proteins coded by genes and/or pathway enrichment putatively controlled by genetic variation associated with anti-CTLA4 related toxicity.
The proteomic analysis identified 915 proteins that were differentially expressed (p < 0.05) in non/mild versus sever toxicity outcomes in anti-CTLA4 IT. SKAT analysis of genetic variation identified 1947 significant genes (p < 0.05) associated with toxicity, of which 78 were also significant (p < 0.05) in the proteomic analysis. The functional pathway analysis of 78 proteins showed enrichment for the regulation of interferon production, and a significant enrichment was observed for molecular pathways involved in autoimmunity.
We present a novel framework integrating germline genetic information and serum protein expression levels to identify associations with toxicity in anti-CTLA4 IT. We found enrichment for interferon production and pathways involved in autoimmunity controlled by genetic variation. The data strongly support the importance of genetic variation in immune system regulation and its effect on IT-related toxicity. The effect of genetic variants on protein expression is currently further tested in the context of toxicity response to IT treatment.
Clinical trial identification
Legal entity responsible for the study
S. Hu: Scientist at CDI laboratories. J.S. Weber: Consulting or advisory role: Celldex, Ichor Medical Systems, cCam Biotherapeutics, Lion Biotechnologies, Pieris Pharmaceuticals, Altor BioScience, Bristol-Myers Squibb, Merck, Genentech, Roche, Amgen, AstraZeneca, GlaxoSmithKline, Daiichi Sankyo, Abbvie, Eisai, CytomX Therapeutics, Nektar, Novartis, Medivation, Sellas Life Sciences, WindMIL; Stock and ownership options: Altor BioScience, Celldex, CytomX Therapeutics, Biond. All other authors have declared no conflicts of interest.