Vanhille L, Kassambara A, Hamdad C, Mercadal M, Papadopoulos A, Outters P, Vasse T, Leca V, Galon J, Fieschi J. Veracyte Biopharma Atlas for colorectal cancer: Combining multi-parameter approach and machine learning to capture the complexity of the tumor immune contexture. Cancer Research. 2023. Poster #5476, AACR Annual Meeting. View Abstract
Summary of the Study
Understanding immune mechanisms in colorectal cancer (CRC) is critical to improving the response to immunotherapies, which benefit only a minority of patients. The Veracyte Biopharma Atlas represents a multi-omics framework combining transcriptomics, spatial proteomics (Brightplex®), and genomics to decode the tumor immune microenvironment (TME).
Key contributions of the study:
Developed a multi-parameter atlas using machine learning tools:
- Multimodal Factor Analysis (MOFA)
- Self-Organizing Maps (SOMs)
Applied to 47 FFPE CRC samples, revealing patient clusters with:
- High immune cell infiltration (T cells, macrophages) and immune gene expression
- Poorly infiltrated tumors with elevated M2/M1 macrophage ratios
The atlas serves as a foundational map to later:
- Project new patient data
- Build Immunograms to support personalized treatment strategies
In this study, Alboukadel Kassambara was the first author of the poster presentation and second author of the abstract submission. He contributed to the design and implementation of the multi-omics integration toolbox, performed the bioinformatics analyses and data visualizations, and contributed to the construction of the Veracyte Biopharma Atlas for colorectal cancer, integrating transcriptomics, genomics, and spatial proteomics to map immune contexture.
Citation
Presentation: Poster at AACR Annual Meeting, Abstract #5476
Date: April 4, 2023
Type: Poster Presentation
PDF: View Abstract
Scientific Contributions
Here are more scientific abstracts authored or co-authored by Alboukadel Kassambara. These contributions span computational biology, bioinformatics, biostatistics, machine learning, and multi-omics, with a focus on immuno-oncology and translational research.
