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Objective To investigate the expression and significance of NFATc3 in different malignant melanoma (MM) tissues and cells. Methods The metastatic (11 cases) and non-metastatic (20 cases) MM tissues and adjacent tissues (3 cases) were collected in paraffin sections. MM cell lines with different malignancy were compared and transfected with Crispr/Cas9 knock-down plasmid. The effects of NFATc3 expression on the proliferation, apoptosis and invasion of MM cells were observed by immunohistochemical staining, qPCR, Western blotting, CCK-8 assay and flow cytometry. Results ① NFATc3 was highly expressed in MM tissues, but hardly seen in the adjacent tissues (P < 0.01). Its expression at mRNA and protein levels was obviously up-regulated in the Mel-RM cells when compared with the A375 cells (P < 0.01). ②After NFATc3 knock-down, the cell survival rate of NFATc3 knock-down group was significantly decreased (P < 0.05). The proportion of Caspase-3 positive fluorescent cells was significantly increased (P < 0.01). Flow cytometry and TUNEL staining showed an increased proportion of apoptotic cells in the knock-down group (P < 0.05), and further Western blot assay confirmed that the expression of activated Caspase-3 (17×103) and Caspase-8 (18×103) proteins were increased. ③The number of invaded and migrated cells in the knock-down group were significantly reduced by wound healing test and Transwell test (P < 0.01). Conclusion NFATc3 is highly expressed in metastatic MM, and its expression level is correlated to the malignancy. NFATc3 knockdown can induce the apoptosis and inhibit the invasion and migration abilities of MM cells.