Integrated Single-Cell Proteomic and Morphometric Analysis Reveals Heterogeneous Drug-Resistant Subpopulations

Investigating the heterogeneous responses of individual cancer cells to chemotherapeutic drugs is crucial for deciphering the mechanisms of cancer drug resistance. In recent years, single-cell proteomics has demonstrated its significant capability in exploring drug response in cancer cells. Meanwhile, there are increasing reports suggesting that the cellular morphology is potentially associated with drug resistance. However, integrating the single-cell proteomic results with morphological information remains challenging. Here, we present a morphology-aware single-cell proteomic analysis (Morp-SCP) platform to precisely capture cells of interest with real-time and high-resolution imaging, and to conduct deep proteomic analysis at the single-cell level, providing multidimensional information on the target single cells. The Morp-SCP platform was applied for exploring the time-dependent proteomic alterations of human nonsmall cell lung cancer cells (A549) upon cisplatin exposure. Subpopulations of drug-resistant A549 cells were identified, which exhibited distinct proteomic and morphological patterns when resisting cell death induced by cisplatin exposure. By revealing the proteomics-morphology relationship, the Morp-SCP platform offers an effective strategy to provide insights into the heterogeneity of drug resistance at the single-cell level.