High-throughput single-cell density measurements enable dynamic profiling of immune cell and drug response from patient samples.

Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. This approach achieves a precision of 0.03% (0.0003 g ml) for cells larger than 12 μm in diameter. In human lymphocytes, we discover that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we find that the ex vivo density response of primary tumour cells to drug treatment can predict the in vivo tumour growth response. Our method reveals unexpected behaviour in molecular crowding during cell state transitions and suggests density as a biomarker for functional precision medicine.