CERTOMICS : Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adoptive Cellular Immunotherapies

Adoptive cellular immunontherapies, such as chimeric antigen receptor (CAR) T cell therapy, have transformed cancer treatment, yet challenges such as resistance, relapse, and high costs limit their efficacy and accessibility. A comprehensive understanding of cellular heterogeneity and molecular profiles is essential to improve these therapies. Advanced single-cell multiomics technologies have the power to analyze the complex interactions between CAR-engineered cells, immune cells, and tumor cells. However, standardized single-cell multiomics computational pipelines specifically tailored to CAR-engineered cell products are lacking. Due to the synthetic nature of CAR transgenes, additional steps are required for the identification and characterization of CAR-positive cells within single-cell multiomics data, which are not included in standard pipelines. To address this, we present CERTOMICS , a Nextflow-based pipeline offering enhanced CERT ainty in immunophenotyping and data interpretation, tailored for single-cell multi OMICS profiling of adoptive cellular immunotherapies. The pipeline standardizes processing 10x Genomics single-cell multiomics data and integrates CAR-specific identification and quality control. Additionally, a curated repository of CAR construct sequences and annotation data is provided, serving as a resource to support the analysis and development of CAR T cell therapies.