Single-Cell Study Reveals Resistance Mechanisms to Trastuzumab Deruxtecan in HER2-Positive Gastric Cancer
Single-cell RNA sequencing of nearly 92,000 cells from the DESTINY-Gastric06 trial reveals distinct primary and acquired resistance mechanisms to trastuzumab deruxtecan in HER2-positive gastric cancer, including MUC3A and CST3 as key drivers.
Researchers from Peking University Cancer Hospital and collaborating institutions have identified molecular drivers of resistance to trastuzumab deruxtecan in HER2-positive gastric cancer, publishing their findings on December 19, 2025 in Precision Clinical Medicine. Analyzing tumor biopsies from patients enrolled in the phase II DESTINY-Gastric06 trial, the team applied single-cell RNA sequencing to track how cancer cells and their surrounding immune environment evolve during treatment.
The researchers profiled nearly 92,000 individual cells from gastric cancer biopsies collected before treatment, during response, and after resistance emerged. By dissecting epithelial tumor cells at single-cell resolution, they identified distinct transcriptional programs linked to different resistance stages.
Tumors showing primary resistance were enriched for metabolic pathways associated with glycolysis and lipid metabolism. Among these, MUC3A stood out as a key marker: high expression predicted shorter progression-free survival and experimentally reduced sensitivity to trastuzumab deruxtecan by limiting drug binding to HER2-positive cells.
In contrast, acquired resistance followed a different trajectory. As treatment progressed, tumor cells downregulated HER2 and cell-cycle genes while upregulating CST3, a natural inhibitor of lysosomal proteases required to cleave the drug's linker and release its cytotoxic payload. Functional assays confirmed that CST3 dampens drug activation, allowing tumor cells to survive despite continued therapy.
Beyond tumor-intrinsic changes, the study revealed dynamic remodeling of the tumor microenvironment. Initial treatment enhanced immune-cell infiltration and antigen presentation, but resistant tumors shifted toward an immunosuppressive state marked by reactivation of transforming growth factor-beta signaling and increased PD-1 expression on immune cells.
The findings suggest several clinical strategies. Measuring MUC3A expression could help identify patients unlikely to benefit from trastuzumab deruxtecan upfront, enabling more precise treatment selection. Targeting CST3 or restoring lysosomal drug processing may help overcome acquired resistance. The observed shift toward immune suppression supports combining trastuzumab deruxtecan with immunotherapies or agents targeting TGF-β signaling.