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Updated: Jul 16, 2025
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Published on: February 26, 2015
Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments
Benjamin S Strope1,2, Katherine E Pendleton1,2,3, William Z Bowie1,2
1Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
Abstract:
Xenograft models are attractive models that mimic human tumor biology and permit one to perturb the tumor microenvironment and study its drug response. Spatially resolved transcriptomics (SRT) provide a powerful way to study the organization of xenograft models, but currently there is a lack of specialized pipeline for processing xenograft reads originated from SRT experiments. Xenomake is a standalone pipeline for the automated handling of spatial xenograft reads. Xenomake handles read processing, alignment, xenograft read sorting, quantification, and connects well with downstream spatial analysis packages. We additionally show that Xenomake can correctly assign organism specific reads, reduce sparsity of data by increasing gene counts, while maintaining biological relevance for studies.
Insights
Xenomake is a new pipeline for processing spatial xenograft data. It automates analysis, improves gene counts, and maintains biological relevance for tumor microenvironment studies.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Xenograft models are crucial for studying human tumor biology and drug responses within the tumor microenvironment.
- Spatially resolved transcriptomics (SRT) offers powerful insights into xenograft model organization.
- A specialized bioinformatics pipeline is lacking for processing SRT data from xenografts.
Approach:
- Developed Xenomake, a standalone, automated pipeline for handling spatial xenograft reads.
- Xenomake integrates read processing, alignment, xenograft read sorting, and quantification.
- The pipeline seamlessly connects with downstream spatial analysis packages.
Key Points:
- Xenomake effectively assigns organism-specific reads in mixed xenograft samples.
- The pipeline reduces data sparsity by increasing gene counts.
- Xenomake maintains the biological relevance of the data for downstream studies.
Conclusions:
- Xenomake provides an automated solution for analyzing SRT data in xenograft models.
- This pipeline enhances data quality and facilitates deeper biological insights.
- Xenomake supports comprehensive studies of the tumor microenvironment and drug responses.
