Pipelines¶
Various computational biology approaches can be used to study and optimize adoptive cellular immunotherapies. For example, single-cell multi-omics technologies enable the study of heterogeneity within immune cell populations, but also within the tumor sample. In combination with V(D)J sequencing of T or B cell receptors and profiling of cell surface protein expression, a more comprehensive understanding of the immune diversity and clonal expansion of the tumor cell can be achieved.
Since CAR T cells, as genetically engineered cells, are very different from normal cells, it is essential to ensure their safety and efficacy. One critical aspect is the monitoring of the integration sites of the inserted CAR gene, which can be achieved by integration site analysis. This technique allows precise mapping of the CAR transgene integration site and can be used to determine clonality or to assess the potential risk of secondary malignancies.
As CAR T cell therapies continue to expand, careful monitoring and tailored computational approaches will be essential for refining these treatments and for advancing other emerging therapies such as T-cell receptor (TCR) therapy and natural killer (NK) cell-based therapies. In light of this, we provide tailored pipelines for the study and optimisation of adoptive cellular immunotherapies, with a focus on CAR T-cell therapy.
Explore the Pipelines¶
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CERTOMICS
Purpose: Multi-omics single-cell pipeline specifically tailored to CAR-engineered cell products.
Supports: Optimized Nextflow pipeline compatible with 10x Genomics single cell technologies such as gene expression (5' and 3'), VDJ-T, VDJ-B, cell surface protein detection. Includes CAR-specific detection and mutli-modal quality control.
Output: Seurat object with integrated single-cell multi-omic RNA-seq data ready for downstream analysis, together with an interactive webpage that consolidates cross-sample and CAR-specific quality metrics.
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LivingDrugSpace (in progress)
Here we will provide a Nextflow pipeline which processes spatial transcriptomics data generated by Visium (HD) technology.
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Integration Site Analysis (in progress)
Integration site analysis enables precise mapping of CAR transgene insertion sites to assess clonality and safety risks.
Read more about our unbiased whole-genome based approach in our publication: Braun et. al 2024
CERTOMICS