Multi-Omics Profiling of Genes, Proteins & Metabolites in Cancer

Cancer is a complex disease, driven by the interplay of genes, proteins, metabolites and signaling networks. Understanding how these layers connect is essential for identifying vulnerabilities and therapeutic targets.

Single-omics analyses provide powerful knowledge into specific layers of cancer biology. However, complex drivers like KRAS operate across multiple layers. Panome Bio’s Integrated Multi-Omics Platform combines metabolism, with protein expression, phosphorylation, and gene regulation. Tens of thousands of data points are distilled into hundreds of high impact biomarkers, delivering a unified, functional view of cancer biology.

In a case study using Panome Bio’s Integrated Multi-Omics platform, HCT-116 colorectal cancer cells harboring the KRAS^G13D mutation were compared to a matched KRAS^G13D allele deletion. Integrating metabolomics, proteomics, phosphoproteomics, and transcriptomics, more than 30,000 data points were distilled into a focused network of fewer than 100 high-impact biomarkers, revealing how KRAS^G13D coordinates growth, metabolism, and survival. This integrated analysis provides a detailed molecular profile to guide precision oncology.

Omics Data to Guide Cancer Research and Targeting

Single ‘Omics Layer	Key Molecular Shift	Practical Value
Metabolomics	2,776 compounds identified Increased oxidative markers and altered mitochondrial function in allele KO cells Potential shift of cancer cells to a less aggressive, more vulnerable cell type	Metabolic Targets: Highlight metabolic weak points to guide therapies that disrupt the tumor’s energy supply using Panome Bio’s Next-Generation Metabolomics.
Phosphoproteomics	<10,000 phosphopeptides identified Phosphorylation of proteins important in growth, survival and stress response KRASG13D fuels oncogenic signaling	Drug Development Guidance: Identify active signaling nodes to support precise kinase inhibitor strategies that interfere with tumor signaling.
Proteomics	6,654 protein groups were available for analysis KRASG13D loss altered key proteins in gene regulation, splicing and cellular metabolism Reflects adaptive tumor behavior	Functional Mechanisms: Show how KRAS deletion reshapes cellular machinery, illuminating tumor behavior and resistance patterns to inform more durable treatment.
Transcriptomics	<15, 000 genes were quantified Allele loss disrupted genes involved in glucose metabolism	Gene-Level Mapping: Highlight disruptions in glucose utilization to direct therapies toward nutrient uptake and gene-level targets.

Integrated Results: Mapping KRAS’s Core Network via Multi-Omics Integration

To understand the full molecular impact of KRAS^G13D allele deletion, an Integrated Multi-Omics analysis combining all four ‘omics datasets were performed. This approach provides a connected view of cellular regulation that single-omics methods can’t achieve.

Multi-Omics Pathway Enrichment Reveals How KRAS^G13D Deletion Rewires Cancer

• Mitochondrial protein degradation is the most enriched pathway, driven by proteomic and transcriptomic changes.
• Aspartate and asparagine metabolism is upregulated, driven by metabolite and gene-level shifts.
• Multi-omics integration amplifies insights: combined pathway enrichment exceeds any single-omics layer.
• Metabolic pathways upregulated: respiratory electron transport, branched-chain amino acid catabolism, triglyceride biosynthesis.
• Growth and signaling pathways downregulated: collagen synthesis, transcriptional pathways, IGF transport, IL-4/IL-13 signaling.

KRAS Biology Revealed Through Network Modules Uncovered

• >390 disrupted pathways and >1,000 analytes distilled into <100 key molecules.
• Five core modules: collagen biosynthesis, mitochondrial metabolism, phospholipid regulation, DNA repair, and cell cycle control.
• Integrated network links genes, proteins, phosphopeptides, and metabolites, exposing coordinated shifts invisible to single-omics.
• Provides a connected map of KRAS-driven biology for discovery and therapeutic insights.

Panome Bio’s Integrated Multi-Omics profiled over 30,000 biomolecules to reveal a connected story of KRAS^G13D allele deleted cancer cells

• Comprehensive molecular rewiring: Metabolomics showed the largest changes, followed by phosphoproteomics, transcriptomics, and proteomics, highlighting KRAS’s role in metabolism and signaling.
• Pathway-level shifts: 194 dysregulated pathways were identified, along with additional molecular patterns that complement single-omics studies, including mitochondrial metabolism, amino acid catabolism, and growth signaling.
• Network connection: Central modules link collagen biosynthesis, glycolysis, and growth pathways, while amino acid transport and respiration increased.
• Biological guidance: Reveals how KRAS balances energy and proliferation, providing targets for precision oncology.

Why Multi-Omics Enhances Your Research

• Broad coverage: Measure metabolites, proteins, phosphopeptides, and transcripts in a single experiment.
• High resolution: Detect low-abundance molecules, structural variants, and subtle signaling changes.
• Integrated biology: Combine multiple molecular layers to uncover pathway and network relationship that complement single-omics findings.
• Research-ready data: Results are robust, reproducible and easily integrated into downstream studies.