Digital Spatial Profiling in Muscle-Invasive Bladder Cancer - Expert Commentary
The investigators collected samples from transurethral resection in 34 patients and used the GeoMx platform using the Whole Transcriptome Atlas (WTA) panel of over 18,000 RNA probes. Three regions of interest (ROIs) were defined: tumor, stroma, and immune infiltrated. There was a clear separation in transcriptional profiles between different regions. Immune-infiltrated regions were enriched for epithelial markers, while stroma regions were enriched for genes related to the extracellular matrix. Both regions were enriched for immune genes. Differential analysis revealed that tumor regions were enriched for genes involved in translation elongation and specific signaling pathways. In contrast, immune-infiltrated ROIs were enriched for genes involved in neutrophil degranulation, Class I MHC processing, regulation of inflammation, and HER-2 signaling. In terms of cell types, tumor ROIs harbored malignant and urothelial cells, while stroma ROIs mainly contained myofibroblast cancer-associated fibroblasts (MyoCAFs). B-cells represented the most abundant immune cell in the stroma and immune infiltrated ROIs. Tumor ROIs exhibited similar proportions of basal and luminal subtypes to those expected based on bulk sequencing datasets. Basal and luminal subtypes exhibited distinct enriched genes, indicating that the technique can identify cellular and molecular changes associated with basal versus luminal subtypes.
Since one of the major advantages of this technique is that spatial links between cells are captured, the researchers subsequently measured the presence of ligands and target genes in adjacent regions. This uncovered a network of active ligand signaling in bladder cancer, in which fifteen stroma ligands were found to have targets in the stroma or tumor and nineteen ligands signaled from the tumor regions. Notably, tumor targets were genes involved in cell proliferation, cell cycle transition, and inhibition of apoptosis. Stroma targets were enriched for genes involved in extracellular matrix disorganization and disassembly. B-cells, endothelial cells, and MyoCAFs were identified as potential sources for these ligands. Nine ligands were identified in the immune infiltrated ROIs, which were involved in immune reactions, stress response, angiogenesis, and hypoxia.
The DSP technique is highly promising for characterizing molecular and cellular underpinnings of bladder cancer. Importantly, the archived tumor samples used were 16 to 22 years old, indicating a major opportunity for profiling available tissues with no loss in data quality and suggesting the potential for exploring larger archival datasets.
Written by: Bishoy M. Faltas, MD, Director of Bladder Cancer Research, Englander Institute for Precision Medicine, Weill Cornell Medicine
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