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201 Discovering next-generation biomarkers through integrating single-cell ‘omics and artificial intelligence
  1. Corinne Solier and
  2. Sarah Carl
  1. Scailyte AG, Basel, Switzerland
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Single-cell technologies have revolutionized the generation of extensive data from human tissues, providing unprecedented resolution. Although numerous cell atlas initiatives have made significant progress in describing and cataloging cellular complexity, fully harnessing the potential of single-cell data for biomarker discovery and clinical applications remains a challenge.

Methods Scailyte has developed an innovative approach that combines multi-omic single-cell analysis, integration of clinical data, and a tailored supervised machine learning platform called ScaiVision (figure 1). This platform enables targeted and sensitive biomarker discovery, transcending specific indications and cell types. By leveraging data augmentation and a cluster-free approach, ScaiVision extracts relevant information while preserving single-cell resolution throughout the analysis. These distinctive features yield remarkably high success rates in discovery of rare cell populations and features from a limited number of samples, providing actionable insights for assay development.

Results We emphasize the unique advantages of our methodology compared to standard single-cell analysis approaches, particularly its successful application in biomarker discovery projects spanning various disease areas. Utilizing scRNAseq data from CAR T cell infusion products, we have trained AI models and identified complex biosignatures that predict the development of severe neurotoxicities and response to CAR T therapy in lymphoma patients.

Conclusions Our approach offers a rapid and efficient end-to-end pipeline for extracting relevant biosignatures from single-cell data, elucidating efficacy, toxicity, and therapeutic mechanisms. These discoveries de-risk drug development programs and serve as the foundation for companion diagnostics and in-vitro diagnostic assay prototypes on widely adopted clinical platforms.

Abstract 201 Figure 1

Toxicity prediction: ScaiVision identifies T cell signature predictive of neurotoxicity in CAR-T cell therapy of DLBCL.

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