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Dietary marine lipids enriched in ω-3 polyunsaturated fatty acids (PUFAs) are spotlighted for favorable effects in neurodegenerative conditions and tumor cell proliferation. Commercial marine oils, with high EPA and DHA content, consist of non-polar lipids constituted by triacylglycerols or polar oils composed of phospholipids. Both classes have shown different activities to significantly inhibit proliferation and migration, and induce apoptosis in cancer cells. This work was aimed at testing marine oils' associated effects on neuroblastoma (NB) and glioblastoma (GB). Commercial non-polar and polar marine oils were studied in 3D spheroid models developed with human neuroblastoma, GB, and non-nervous embryonic kidney cell lines. This study also included results provided by a new sustainable polar marine oils source: fishery side-streams. Cell viability and mitochondrial activity assessments demonstrated that both marine oils dramatically reduced NB cells' metabolism, proliferation, and viability. Effects on GB and epithelial cells were different, including a metabolic increase. Marine oils also induce cell differentiation and selectively modulate the activity of neurons and glia, depending on the oils' chemical form. Sustainable polar oil showed bioactive characteristics similar to commercial krill oil. We propose that marine oils rich in triacylglycerols and phospholipids with high EPA and DHA levels may be a useful tool in NB antiproliferative therapies.