Garcia-Soriano, J. C. | bioRxiv Science

bioRxiv2026

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

Classical cancer germline-antigens (CGAs) are proteins that are expressed in the male germinal line but not in somatic tissues, and that can also become expressed in tumors. However, the vast majority of testis-specific transcripts are long non-coding RNAs (lncRNAs) rather than protein-coding genes. Since recent studies have shown that many lncRNAs contain non-canonical open reading frames (ncORFs) that are translated into small proteins, or microproteins, there could be a large class of non-canonical cancer-germline antigens (ncCGAs) that remains to be discovered. Here, we integrate ribosome profiling from human testis and cancer cell lines with paired tumor/normal transcriptomes from 917 patients across eight common cancer types to define a comprehensive catalog of ncCGAs. This set comprises 235 ncCGAs encoded by lncRNAs or mRNA untranslated regions (5UTRs and 3UTRs), compared to 192 canonical CGAs (cCGAs) with similar expression patterns. We show that ncCGAs are evolutionary young, consistent with recent de novo emergence in the rapidly evolving male germline. Moreover, a large fraction is expressed across multiple patients and cancer types, indicating recurrent reactivation mechanisms in tumors. We further find that ncCGAs are frequently located in cancer-amplified regions or associated with MYC or E2F-regulated pathways, which may explain their expression in cancer. Finally, we provide strong evidence that a subset of ncCGAs give rise to potentially immunogenic HLA class I bound peptides. Together, our results describe a previously unexplored class of tumor-restricted antigens with potential applications in cancer immunotherapy.

cancer biology↗

bioRxiv2026

Oncogenes and tumor suppressor genes are enriched in stop-loss mutations generating protein extensions

Cancer genomes tend to accumulate a large number of mutations, and even rare mutations such as those causing the loss of a stop codon can be observed in a significant fraction of the tumors. Stop-loss mutations extend protein translation into the 3 untranslated region (3 UTR), generating altered proteins carrying extra amino acid sequences. These C-terminal extensions can potentially have consequences for tumorigenesis and immune recognition. To investigate the prevalence of stop-loss mutations in cancer, and to identify recurrent mutations with a possible tumor-promoting effect, we have interrogated mutation data from the tumor samples of 20,801 patients. This search has resulted in the annotation of 3,757 stop-loss mutations in 3,249 different protein-coding genes. Around 11% of the mutated genes contain recurrent stop-loss mutations, occurring in more than one patient. The protein extensions created by the mutations tend to be hydrophobic and/or positively charged, and these features are associated with an increased propensity to generate MHC I-bound peptides. We have also found that cancer-related genes contain 37% more stop-loss mutations than non-cancer-related genes, with both oncogenes and tumor suppressor genes showing similar enrichments. Furthermore, three out of the four genes with the highest number of stop-loss recurrences, PTMA, PCDH9 and SOX9, are cancer-related. In PTMA, the gene with the largest number of stop-loss mutations (14 patients), the mutation results in an extension of 9 amino acids. We provide experimental evidence that the mutation is associated with impaired cleavage of thymosin alpha 1, a peptide with immunostimulatory functions that is generated from the N-terminal part of the PTMA protein. The study provides evidence that stop-loss mutations are enriched in cancer-associated genes and constitutes a valuable resource for further studies on the effects of stop-loss mutations in cancer.

genomics↗