Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique

Fluorescence-activated
cell sorting (FACS) is a specialized technique
to isolate specific cell subpopulations with a high level of recovery
and accuracy. However, the cell sorting procedure can impact the viability
and metabolic state of cells. Here, we performed a comparative study
and evaluated the impact of traditional high-pressure charged droplet-based
and microfluidic chip-based sorting on the metabolic and phosphoproteomic
profile of different cell types. While microfluidic chip-based sorted
cells more closely resembled the unsorted control group for most cell
types tested, the droplet-based sorted cells showed significant metabolic
and phosphoproteomic alterations. In particular, greater changes in
redox and energy status were present in cells sorted with the droplet-based
cell sorter along with larger shifts in proteostasis. 13C-isotope tracing analysis on cells recovering postsorting revealed
that the sorter-induced suppression of mitochondrial TCA cycle activity
recovered faster in the microfluidic chip-based sorted group. Apart
from this, amino acid and lipid biosynthesis pathways were suppressed
in sorted cells, with minimum impact and faster recovery in the microfluidic
chip-based sorted group. These results indicate microfluidic chip-based
sorting has a minimum impact on metabolism and is less disruptive
compared to droplet-based sorting.