An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome

Patricio Yankilevich*, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Mouse tumour models are extensively used as a pre-clinical research tool in the field of oncology, playing an important role in anticancer drugs discovery. Accordingly, in cancer genomics research, the demand for next-generation sequencing (NGS) is increasing, and consequently, the need for data analysis pipelines is likewise growing. Most NGS data analysis solutions to date do not support mouse data or require highly specific configuration for their use. Here, we present a genome analysis pipeline for mouse tumour NGS data including the whole-genome sequence (WGS) data analysis flow for somatic variant discovery, and the RNA-seq data flow for differential expression, functional analysis and neoantigen prediction. The pipeline is based on standards and best practices and integrates mouse genome references and annotations. In a recent study, the pipeline was applied to demonstrate the efficacy of low dose 6-thioguanine (6TG) treatment on low-mutation melanoma in a pre-clinical mouse model. Here, we further this study and describe in detail the pipeline and the results obtained in terms of tumour mutational burden (TMB) and number of predicted neoantigens, and correlate these with 6TG effects on tumour volume. Our pipeline was expanded to include a neoantigen analysis, resulting in neopeptide prediction and MHC class I antigen presentation evaluation. We observed that the number of predicted neoepitopes were more accurate indicators of tumour immune control than TMB. In conclusion, this study demonstrates the usability of the proposed pipeline, and suggests it could be an essential robust genome analysis platform for future mouse genomic analysis.

Original languageEnglish
Article number22
JournalCancer Immunology, Immunotherapy
Volume73
Issue number2
Number of pages10
ISSN0340-7004
DOIs
Publication statusPublished - Feb 2024

Keywords

  • 6-Thioguanine (6TG) treatment
  • Immune-checkpoint inhibitors (ICI)
  • Mouse genome analysis pipeline
  • Mouse tumour models
  • Neoantigen analysis
  • Tumour mutational burden

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