biostudies-arrayexpressRohit DnyansagarHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16979The ketogenic diet (KD) has demonstrated anti-proliferative effects across multiple tumor types, yet the underlying metabolic and transcriptomic mechanisms remain incompletely understood. This study employed integrated multi-omics analysis combining targeted metabolomics and RNA-sequencing to elucidate KD-induced metabolic reprogramming in BRAF/NRAS wild-type, BRAF mutant, and NRAS mutant melanoma xenografts, which showed delayed tumor growth when treated with KD. Despite pronounced metabolic and transcriptional heterogeneity across models with minimal overlap in individual KD-responsive genes, pathway-level analysis revealed convergent biological signatures. Using correlation-based integration and supervised latent variable modeling (mixOmics DIABLO), we identified consistent KD-associated alterations in cancer-related pathways including PI3K-Akt and MAPK signaling, as well as sphingolipid, HIF-1, and shigellosis pathways. Mechanistically, KD enhanced sphingomyelin and ceramide levels in addition to the expression of ceramide synthesis genes while reducing ceramide breakdown. Moreover, KD induced downregulation of critical tumor regulators including PI3K, AKT, HIF, MEK, and ERK. These findings demonstrate that despite metabolic and transcriptomic heterogeneity, KD drives coordinated metabolic reprogramming at the pathway level, shifting lipid metabolism toward pro-apoptotic ceramides and attenuating key oncogenic signaling cascades. Our results provide mechanistic insights into KD's anti-tumor efficacy and identify metabolic nodes amenable to therapeutic intervention in melanoma. This record contains the count matrix generated with the RNA-seq experiment.biostudies-arrayexpressLibrary Construction - Sequencing libraries were prepared at the Genomics Core Facility of the Medical Univer-sity of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module, and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to manu-facturer’s protocol (New England Biolabs, Ipswich, MA, USA). The libraries were QC-checked on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) using a high sensitiv-ity DNA kit for correct insert size, and quantified using a Qubit dsDNA HS Assay (Invi-trogen, Eugene, OR, USA).Sample Collection - Melanoma xenograft-bearing mice were established and treated as published previously [PMID: 35851093 ]. In brief, the human melanoma cell lines A375, WM47, WM3311, and WM3000 were used to establish melanoma xenografts in 5- to 7-week-old female CD-1 nude mice. Once the tumor volume reached 100 mm3, mice were equally assigned to the standard diet (SD) or a long-chain triglyceride-based ketogenic diet (KD). All diets were given ad libitum. Once tumors reached humane endpoints, tumor tissue was harvested, snap frozen in liquid nitrogen, and stored at -80 °C for RNA extraction and bulk RNA-Seq.Sequencing - The pooled libraries were sequenced on two flow cells of a NextSeq500 instrument (Illu-mina, San Diego, CA, USA) in 1 × 75 bp single-end sequencing mode. Per sample, an av-erage of 25 million reads were generated.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Two normalization protocols were used at two different stages. 1. DESeq2’s median of ratios counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene 2. For multi-omics integration we used TPM (transcripts per kilobase million) normalization which normalize for gene length, and later normalize for sequencing depth.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAHomo sapiensDaniela WeberRohit DnyansagarfalseIntegrative Multi-Omics Reveal Metabolic Reprogramming by Ketogenic Diet in Melanoma XenograftsThe ketogenic diet (KD) has demonstrated anti-proliferative effects across multiple tumor types, yet the underlying metabolic and transcriptomic mechanisms remain incompletely understood. This study employed integrated multi-omics analysis combining targeted metabolomics and RNA-sequencing to elucidate KD-induced metabolic reprogramming in BRAF/NRAS wild-type, BRAF mutant, and NRAS mutant melanoma xenografts, which showed delayed tumor growth when treated with KD. Despite pronounced metabolic and transcriptional heterogeneity across models with minimal overlap in individual KD-responsive genes, pathway-level analysis revealed convergent biological signatures. Using correlation-based integration and supervised latent variable modeling (mixOmics DIABLO), we identified consistent KD-associated alterations in cancer-related pathways including PI3K-Akt and MAPK signaling, as well as sphingolipid, HIF-1, and shigellosis pathways. Mechanistically, KD enhanced sphingomyelin and ceramide levels in addition to the expression of ceramide synthesis genes while reducing ceramide breakdown. Moreover, KD induced downregulation of critical tumor regulators including PI3K, AKT, HIF, MEK, and ERK. These findings demonstrate that despite metabolic and transcriptomic heterogeneity, KD drives coordinated metabolic reprogramming at the pathway level, shifting lipid metabolism toward pro-apoptotic ceramides and attenuating key oncogenic signaling cascades. Our results provide mechanistic insights into KD's anti-tumor efficacy and identify metabolic nodes amenable to therapeutic intervention in melanoma. This record contains the count matrix generated with the RNA-seq experiment.2026-07-01T00:00:00Z2026-07-01T01:04:21.806Z2026-04-30T12:46:02.309ZE-MTAB-16979ERP190961EFO_0004170EFO_0003816EFO_0005518EFO_0003738EFO_0004184