Integrated transcriptomic and proteomic profiling reveals alteration of oxidative phosphorylation in omega-3 polyunsaturated fatty acid-mediated inhibition of Candida albicans biofilm formation

Abstract

Candida albicans biofilms are highly tolerant to conventional antifungals, posing a major clinical challenge. Omega-3 polyunsaturated fatty acids (PUFAs), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), exhibit antibiofilm activity, but their mechanisms remain incompletely understood. Integrated transcriptomic and proteomic approaches were used to investigate the antibiofilm activity of DHA and EPA against C. albicans ATCC 90028. Biofilm inhibition was assessed by crystal violet staining and XTT reduction assays. Biofilm cells treated with 1 mM DHA or EPA (sub-MIC, both MICs > 1 mM) were subjected to RNA‑seq and DIA proteomics. Differentially expressed genes (DEGs) and proteins (DEPs) were identified, and integrated KEGG pathway analysis was conducted. Both DHA and EPA inhibited biofilm formation at 1 mM without affecting planktonic growth. DHA altered 1787 transcripts (750 up, 1037 down) and 554 proteins (170 up, 384 down). EPA altered 905 transcripts (446 up, 459 down) and 259 proteins (104 up, 155 down). DHA suppressed ribosome biogenesis and oxidative phosphorylation at both mRNA and protein levels. In contrast, EPA transcriptionally down-regulated DNA replication genes while affecting oxidative phosphorylation predominantly via post-transcriptional mechanisms. Integrated analysis identified oxidative phosphorylation and central carbon metabolism as core convergent targets, with DHA showing more extensive metabolic disruption than EPA. DHA and EPA suppress C. albicans biofilms through distinct regulatory modes that converge on pathways linked to mitochondrial energy metabolism. These findings provide a molecular framework for omega-3 PUFA-based antibiofilm strategies and underscore the value of multi-omics integration in generating insights into complex drug mechanisms.