A Targeted Proteomic Approach for Heat Shock Proteins Reveals DNAJB4 as a Suppressor for Melanoma Metastasis

Heat
shock proteins are molecular chaperones that are involved
in protein folding. In this study, we developed a targeted proteomic
method, relying on LC-MS/MS in the parallel-reaction monitoring (PRM)
mode, for assessing quantitatively the human heat shock proteome.
The method facilitated the coverage of approximately 70% of the human
heat shock proteome and displayed much better throughput and sensitivity
than the shotgun proteomic approach. We also applied the PRM method
for assessing the differential expression of heat shock proteins in
three matched primary/metastatic pairs of melanoma cell lines. We
were able to quantify ∼45 heat shock proteins in each pair
of cell lines, and the quantification results revealed that DNAJB4
is down-regulated in the three lines of metastatic melanoma cells
relative to the corresponding primary melanoma cells. Interrogation
of The Cancer Genome Atlas data showed that lower levels of DNAJB4
expression conferred poorer prognosis in melanoma patients. Moreover,
we found that DNAJB4 suppresses the invasion of cultured melanoma
cells through diminished expression and activities of matrix metalloproteinases
2 and 9 (MMP-2 and MMP-9). Together, we established, for the first
time, a high-throughput targeted proteomics method for profiling quantitatively
the human heat shock proteome and discovered DNAJB4 as a suppressor
for melanoma metastasis.