Phosphoproteomic study of the effect of ALK inhibition alongside DUSP6 gene inactivation in KELLY neuroblastoma cells

The hypothesis behind this research was that the DUSP6 phosphatase regulates signaling from the ALK tyrosine kinase in neuroblastoma cells, and loss of DUSP6 would enhance the effectiveness of ALK inhibitors in these cancer cells. The phosphoproteomics study was carried out to understand which phosphopeptides change in neuroblastoma cells when DUSP6 is lost, and how these are affected by co-treatment with lorlatinib.
KELLY tumour cells were previously engineered to express Cas9 and a DUSP6-targeting guide RNA. KELLY parental cells and derived cells lacking DUSP6 expression were then treated with 30nM lorlatinib for 1 hr and cell extracts processed for phosphopeptide analysis using mass spec. Samples were made as quadruplicate biological replicates.
The data provide an indication of novel protein effectors of DUSP6 (not determined if direct or indirect substrates) in these tumour cells and how some of these may be co-regulated by ALK. It is found that DUSP6 does not significantly impinge on ERK signaling as it is does in other cell types, but may be a co-regulator of pathways involving N-Myc and EE2FK.
The data can be mined for further information concerning how DUSP6 functions in KELLY tumour cells, what the signaling effect is of lorlatinib in these cells, and how the two pathway interact. The work is part of the PhD thesis of Elliott Thompson, to be found in UCL Discovery (https://discovery.ucl.ac.uk/id/eprint/10148906/).