Castelo, R. | Search bioRxiv

bioRxiv2024

Predicting immunotherapy response in advanced bladder cancer: a meta-analysis of six independent cohorts

Advanced bladder cancer patients show very variable responses to immune checkpoint inhibitors (ICIs) and effective strategies to predict response are still lacking. Here we integrate mutation and gene expression data from 707 advanced bladder cancer patients treated with anti-PD-1/anti-PD-L1 to build highly accurate predictive models. We find that, in addition to tumor mutational burden (TMB), enrichment in the APOBEC mutational signature, and the abundance of pro-inflammatory macrophages, are major factors associated with the response. Paradoxically, patients with high immune infiltration do not show an overall better response. We show that this can be explained by the activation of immune suppressive mechanisms in a large portion of these patients. In the case of non-immune-infiltrated cancer subtypes, we uncover specific variables likely to be involved in the response. Our findings provide novel information for advancing precision medicine in patients with advanced bladder cancer treated with immunotherapy.

cancer biology↗

bioRxiv2023

Non-canonical ORFs are an important source of tumor-specific antigens in a liver cancer meta-cohort

The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Antigens that have been used as cancer vaccines are those originated by non- synonymous mutations and those derived from cancer/testis antigens. However, the first class is predominantly patient-specific, preventing the development of therapies than can benefit multiple patients, and the second one offers a limited set of actionable targets. A possible alternative is the use of peptides derived from non-canonical ORFs (ncORFs). While many ncORFs have been shown to be translated in cancer cells, their tumor-specificity and patient distribution remains to be determined. Here we analyze RNA sequencing data 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue, together with ribosome profiling data from an additional 10 HCC tumors, to answer these open questions. Combining HLA-epitope binding predictions and experimental validation experiments we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs in lncRNAs, including two peptides that can trigger an immune response in mice. We identify a subset of 33 tumor-specific lncRNAs expressing novel cancer antigens shared by more than 10% of the HCC analyzed, which could be combined to target a large proportion of the patients. The results of the study open new avenues for extending the range of anti-cancer vaccines.

genomics↗