Chemotherapy (CT) remains the cornerstone of colorectal cancer (CRC) treatment worldwide; however, many patients experience disease progression despite therapy. Although conventional markers aim to account for CRC heterogeneity to guide treatment decisions, they often yield inconsistent results, leading to overtreatment of low-risk patients and undertreatment of high-risk individuals. Despite the recognized therapeutic potential of the tumor microenvironment (TME), clinical decisions, actionable biomarker discovery, and drug development continue to focus primarily on the CRC epithelial compartment. This limited approach may explain why many patients do not respond to standard therapies and why new drugs frequently fail in clinical trials.

In this study, we will investigate the TME heterogeneity and plasticity, particularly in response to CT, to identify stromal and immune factors influencing treatment efficacy. We will develop the first spatially resolved CRC atlas integrating transcriptomic, proteomic, and elemental data to capture cellular and molecular dynamics as well as CT bioaccumulation upon treatment. With this approach, we aim to reveal new predictive biomarkers within cancer-associated fibroblasts (CAFs) and immune cell populations in the TME. Using in vivo models and advanced immunocompetent cancer-in-a-dish systems, we will simulate patient-specific interactions between CRC cells and the TME to explore how CAF heterogeneity and immune cell interactions drive treatment resistance. We will leverage our expertise to reengineer CT drugs, minimizing their extensive adverse effects on the TME while enhancing specificity for CRC cells. Our interdisciplinary study holds the potential to shift clinical practice towards precision oncology by identifying TME factors that shape therapy responses. Expected outcomes include refined diagnostic tools to guide treatment choices, and therapies tailored to the unique attributes of CRC cells and their TME.

The project leading to these results has received funding from “la Caixa” Foundation under the project code [LCF/PR/HRXX/ HR25-00861].

ROLE OF CNAG

CNAG will generate the first spatially resolved single-cell atlas of colorectal tumors collected before and after chemotherapy. Using CosMx Spatial Molecular Imager, we will apply advanced spatial transcriptomics on 40 patient tumor samples to map gene expression programs across hundreds of thousands of individual cells. This technology allows us to precisely visualize how cancer, immune, and stromal cells, including cancer-associated fibroblasts  (CAFs), are organized inside the tumor and how they interact. These experiments will be complemented by immunohistochemistry to validate key findings directly in tissue.

We will also lead the computational integration of transcriptomic, proteomic, elemental, and clinical data using dedicated in-house analysis pipelines. This will enable us to identify druggable molecular pathways altered by chemotherapy, track changes in cell-to-cell communication, and discover spatially resolved biomarkers that may predict treatment response or resistance. By combining cutting-edge multiomics with deep computational analysis, our contribution will be essential for revealing how chemotherapy reshapes the tumor microenvironment and for uncovering new strategies to improve personalized therapies for colorectal cancer.

 

COORDINATOR

Hospital del Mar Research Institute