NMR-based metabolomics analysis in breast cancer patients from Saudi Arabia: a pilot study

In breast cancer (BC), metabolomic profiles have largely focused on Western and East Asian groups, with limited data from the Middle East. Population-specific studies are required to better understand metabolite alterations due to regional, environmental and genetic heterogeneity. This exploratory pilot study aimed to evaluate serum metabolic alterations in breast cancer patients and their associations with disease stage using NMR-based metabolomics in the Saudi Arabian cohort. A total of 30 female breast cancer patients and 30 healthy controls were included. Patient samples showed higher levels of ketoglutarate, glutamine, lipids, and branched-chain amino acids, while acetate, creatine, and glucose were lower in the patient group (all FDR q < 0.05). Ketoglutarate (AUC = 0.85), glutamine (AUC = 0.84), and lipids (AUC = 0.82) demonstrated discriminatory ability. A combined model incorporating acetate and ketoglutarate achieved an AUC of 0.91. With advancing disease stage, lactate (p-trend = 0.005), leucine (p-trend = 0.044), and glutamate (p-trend = 0.033) showed decreasing trends. Lactate, choline, and glucose were each independently associated with more advanced disease in multivariable models. Unsupervised principal component analysis (PCA), supervised partial least squares-discriminant analysis (PLS-DA), and orthogonal PLS-DA (OPLS-DA) showed metabolic separation between patients and controls. Permutation testing indicated that class separation exceeded random classification; however, overfitting remains possible due to reliance on internal validation. The negative Q² value (- 0.577) indicates poor predictive generalizability. In conclusion, this study identifies candidate metabolite signatures associated with breast cancer in a Saudi cohort. These findings require validation in independent cohorts before clinical application.