Pan-cancer Cell-level Expression of Alternative Stop Codon Transcripts from Single Cell RNA Sequencing Data
Open AccessBackground: Alternative stop codons can result from mutations creating a new or destroying an existing stop codon (stop codon mutations). Stop-codon mutations have been associated with numerous genetic disorders, including cancer. Disease phenotypes caused by stop codon mutations are often more severe, as these mutations frequently result in a complete loss of protein function. In recent studies, most alternative stop codons have been analyzed from bulk sequencing datasets, which can obscure cell-level information. The current study aims to establish a methodology for exploring the expression of alternative stop codon variants at single-cell resolution in cancer and normal scRNA-seq datasets generated on the widely used platform 10x-Genomics.Method: Twenty-eight publicly available cancer and normal single-cell RNA-sequencing datasets were used to demonstrate our pipeline. The SCExecute tool, in conjunction with GATK and Strelka2, was used for cell-level variant calling. After annotation, the alignments at the stop codon locus were visually examined using the Integrative Genomics Viewer (IGV) package. Potential effects of the stop-codon variants on their harboring genes were assessed using Deseq2. Downstream analyses on pathway and gene-network alterations associated with the stop-codon variants were performed using the String package, and the PANTHER classification system. Results: We identified a large number of expressed alternative stop codon transcripts more than 70% of which were novel (not previously described). We exemplify our analyses with a novel stop gain mutation W109* expressed in a gene encoding ubiquitin conjugating enzyme E2 C gene (UBE2C). UBE2CW109* is found in different cancer and normal embryo samples and shows significantly higher cell frequency and more pronounced effects in cancer samples such as cholangiocarcinoma. Conclusion: Our study uncovered a previously unrecognized collection of cell-level expressed stop codon variants. Some of these variants show potential pathogenic effects on their harboring gene, as well as on other related genes. Analyses as the one demonstrated here are essential for better understanding of the stop codon mutations effects in normal and cancer tissues.
- All rights reserved
Notice to Authors
If you are the author of this work and you have any questions about the information on this page, please use the Contact form to get in touch with us.