Assessing proteomic drift in cell passages using single cell proteomic analysis of acute myeloid leukemia
Acute myeloid leukemia (AML) is the most lethal form of leukemia with a 5-year survival rate of 29.5%. Additionally, 75% of patients will experience a relapse in AML following standard treatment with chemotherapy. AML is a disease that arises due to genomic aberrations in hematopoietic stem cells, leading to defects in cell cycling, proliferation, and apoptosis. AML tumor cells display highly heterogeneous behavior with presence of distinct sub-clones with different immunophenotypes. We used single cell proteomics (SCP) to measure the proteome drift between two AML cell lines, MOLM-13 and MV-4-11, after subsequent passages. This revealed changes in cellular mechanisms between subclones of AML cells. Simultaneously, we utilized two SCP multiplexing techniques, mTRAQ and tandem mass tags (TMT), and assessed their performance with the goal of increasing throughput. Using nano-proteomic sample preparation (nPOP), cells were isolated and labeled with one of the two multiplexing methods. We found that there is evidence of minor proteome drift occurring between passages of MV-4-11, and found the later passage separating into two subpopulations. By increasing throughput with TMT multiplexing we identified 37% more protein identifications on average while maintaining a higher throughput. This allowed for the acquisition of 140 more single cell samples per day compared to mTRAQ. SCP revealed distinct subpopulations within the cell lines, which would not have been possible with bulk proteomics, and shows promise for future patient experiments.
