Methionine Cycle in Cancer Metabolism and Tumor Progression

The methionine cycle is a fundamental metabolic pathway that plays a critical role in cellular function, particularly in methylation reactions, redox balance, and protein biosynthesis. This cycle is essential for maintaining normal cellular homeostasis, yet its dysregulation has been increasingly linked to cancer progression.

Cancer cells exhibit a heightened dependency on methionine, a phenomenon known as methionine auxotrophy. This metabolic adaptation supports tumor growth, alters gene expression, and shapes the tumor microenvironment. Understanding the methionine cycle's role in cancer metabolism provides key insights into tumor biology and potential vulnerabilities.

Methionine Cycle Dysregulation in Cancer Cells

Cancer cells exhibit fundamental alterations in methionine metabolism. Unlike normal cells, which efficiently recycle methionine and regulate its utilization, many tumors rely on increased methionine uptake and exhibit deficiencies in methionine salvage. This metabolic adaptation supports rapid proliferation, epigenetic remodeling, and survival under stress.

Methionine Auxotrophy and Metabolic Reprogramming

Methionine auxotrophy, the excessive dependence on exogenous methionine, is a hallmark of many cancer types. Normal cells maintain methionine homeostasis by converting homocysteine to methionine via methionine synthase (MTR) and remethylation pathways. In contrast, cancer cells show a diminished ability to regenerate methionine from homocysteine, necessitating increased uptake from the extracellular environment.

Key Features of Methionine Dependence in Cancer:

• Upregulated Methionine Transporters: Many tumors overexpress SLC7A5 (LAT1), a high-affinity transporter responsible for methionine import. Increased LAT1 expression correlates with aggressive tumor phenotypes, including higher proliferation rates and resistance to metabolic stress.
• Elevated S-Adenosylmethionine (SAMe) Production: Methionine is converted to SAMe, the primary methyl donor for cellular methylation reactions. Cancer cells exhibit enhanced flux through this pathway, supporting epigenetic modifications that promote tumorigenesis.
• Dysregulated Methionine Salvage Pathway: In some tumors, enzymes such as methylthioadenosine phosphorylase (MTAP), involved in methionine recycling, are deleted or downregulated. This deletion is frequently observed in glioblastoma, pancreatic adenocarcinoma, and certain sarcomas. The loss of MTAP disrupts methionine homeostasis, reinforcing reliance on external methionine sources.

Methionine cycle regulates SAM levels facilitating m6A methylation of NR4A2 mRNA and tumor growth (Tassinari et al., 2014).

Epigenetic and Gene Expression Alterations

Methionine metabolism is tightly linked to epigenetic regulation through its role in methylation. SAMe, generated from methionine, donates methyl groups for DNA, RNA, and histone modifications. Changes in SAMe availability directly influence gene expression and chromatin structure, contributing to oncogenesis.

DNA and Histone Methylation:

• Tumor-Specific DNA Hypermethylation: Many cancers exhibit hypermethylation at CpG islands within promoter regions of tumor suppressor genes, leading to transcriptional silencing. This process is particularly evident in colorectal, lung, and breast cancers, where genes involved in apoptosis and DNA repair are frequently silenced.
• Altered Histone Modifications: Methylation of histone lysine residues, particularly H3K9 and H3K27, influences chromatin accessibility. Increased SAMe levels enhance histone methyltransferase (HMT) activity, reinforcing oncogenic transcriptional programs.

RNA Methylation and Post-Transcriptional Regulation:

• N6-Methyladenosine (m6A) Modifications: m6A is a prevalent RNA modification that affects mRNA stability and translation. Dysregulated methionine metabolism alters m6A deposition on oncogenic transcripts, promoting tumor growth and metastasis.
• Non-Coding RNA Modulation: Methylation-dependent regulation of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) influences pathways related to proliferation, stemness, and immune evasion.

Interaction with One-Carbon and Folate Metabolism

The methionine cycle is functionally linked to folate-mediated one-carbon metabolism. This interplay supports nucleotide biosynthesis, redox balance, and amino acid metabolism—processes that are critical for sustaining rapid tumor growth.

Key Interactions Between Methionine and Folate Cycles:

• Serine-Driven One-Carbon Flux: Many tumors upregulate serine hydroxymethyltransferase (SHMT) to enhance one-carbon unit production, fueling purine and thymidine synthesis. This increases the availability of methyl donors for methionine metabolism, reinforcing epigenetic reprogramming.
• Thymidylate and Purine Synthesis: The folate cycle provides substrates for DNA replication. Increased methionine metabolism supports this process by ensuring a continuous supply of methyl groups for nucleotide production.
• Mitochondrial One-Carbon Metabolism: In cancer cells, mitochondrial folate metabolism interacts with the methionine cycle to optimize energy production and biosynthesis. This metabolic coordination is particularly active in highly proliferative tumors such as hepatocellular carcinoma and leukemia.

Metabolic processes elicited by methionine: the one carbon metabolism (Tassinari et al., 2014).

Methionine Cycle and the Tumor Microenvironment

The tumor microenvironment (TME) is a complex ecosystem composed of cancer cells, immune cells, fibroblasts, endothelial cells, and extracellular matrix (ECM) components. It plays a crucial role in supporting tumor progression, immune evasion, and metabolic adaptation. The methionine cycle influences this microenvironment through its impact on cellular metabolism, methylation status, and intercellular signaling. Changes in methionine availability and processing shape the behavior of both tumor cells and surrounding stromal components, creating conditions that favor malignancy.

Influence on Immune Cells and Immune Evasion

Cancer cells exploit methionine metabolism to suppress immune responses, creating an immunosuppressive TME. T cells, macrophages, and dendritic cells are particularly sensitive to methionine availability, which affects their activation, differentiation, and function.

T Cell Suppression Through Methionine Depletion

• Activated T cells require methionine for protein synthesis, proliferation, and methylation-dependent gene regulation. Methionine is essential for generating S-adenosylmethionine (SAMe), which regulates T cell receptor (TCR) signaling and cytokine production.
• Tumor cells upregulate methionine-consuming pathways, depleting extracellular methionine and limiting T cell function. Reduced methionine levels impair histone methylation at key loci involved in T cell activation, leading to dysfunctional and exhausted T cell states.
• Methionine restriction particularly affects cytotoxic CD8+ T cells, reducing their ability to mount effective anti-tumor responses. Regulatory T cells (Tregs), in contrast, exhibit greater metabolic flexibility, allowing them to persist under low-methionine conditions and further suppress immune activity.

Macrophage Polarization and Methionine Metabolism

• Tumor-associated macrophages (TAMs) exist in different functional states, ranging from pro-inflammatory (M1-like) to immunosuppressive (M2-like). Methionine metabolism influences macrophage polarization, favoring the M2-like phenotype, which supports tumor progression.
• High SAMe levels in macrophages promote DNA and histone methylation patterns associated with an immunosuppressive phenotype. This epigenetic programming enhances the production of anti-inflammatory cytokines such as IL-10 and TGF-β.
• Methionine-derived metabolites also regulate the arginase pathway in macrophages, which depletes arginine, further suppressing T cell responses.

Dendritic Cell Function and Antigen Presentation

• Dendritic cells (DCs) rely on methionine metabolism for proper antigen processing and presentation. SAMe availability influences MHC class I and II expression, which affects the ability of DCs to activate naïve T cells.
• Tumor-induced methionine depletion leads to dysfunctional antigen presentation, reducing anti-tumor immune surveillance.

Methionine's Role in Fibroblast Activation and ECM Remodeling

Cancer-associated fibroblasts (CAFs) are key regulators of the TME. They produce ECM components, secrete growth factors, and modulate immune cell infiltration. Methionine metabolism contributes to fibroblast activation and ECM remodeling, processes that enhance tumor progression and metastasis.

Fibroblast Activation and Secretome Modulation

• CAFs exhibit increased methionine metabolism, supporting the production of SAMe for methylation-dependent gene expression changes.
• Methionine-derived methylation regulates fibroblast contractility, ECM deposition, and secretion of pro-tumorigenic cytokines such as IL-6 and CXCL12.
• Enhanced methylation activity in CAFs drives the activation of pro-fibrotic signaling pathways, including TGF-β and Hedgehog signaling, leading to ECM stiffening and tumor-promoting inflammation.

Extracellular Matrix Remodeling and Tumor Invasion

• ECM remodeling is critical for cancer cell invasion and metastasis. Methionine metabolism influences the expression and activity of matrix metalloproteinases (MMPs), which degrade ECM components and facilitate tumor cell migration.
• Collagen methylation affects ECM structure, altering mechanical properties that promote invasive behavior.
• Methionine metabolism also supports the synthesis of sulfated glycosaminoglycans, which regulate growth factor availability and cell-cell interactions within the TME.

Angiogenesis and Vascular Adaptation

Tumor growth requires the formation of new blood vessels to supply oxygen and nutrients. Methionine metabolism contributes to angiogenesis by regulating endothelial cell function and vascular remodeling.

Endothelial Cell Function and Methionine Metabolism

• Endothelial cells use methionine metabolism to support epigenetic regulation of pro-angiogenic genes, including VEGFA and ANGPT2.
• SAMe availability influences histone methylation at promoter regions of angiogenesis-related genes, enhancing their expression in response to hypoxia and growth factor signaling.
• Methionine-derived polyamines contribute to endothelial cell proliferation and tube formation, key steps in new blood vessel formation.

Hypoxia-Induced Metabolic Shifts

• In hypoxic conditions, tumors rewire methionine metabolism to sustain angiogenic signaling.
• Hypoxia-inducible factors (HIFs) modulate methionine metabolism to promote vascular endothelial growth factor (VEGF) secretion, enhancing endothelial cell migration and vessel formation.

Methionine Cycle and Redox Balance in the TME

The TME is characterized by oxidative stress, which influences tumor progression and therapy resistance. Methionine metabolism plays a role in maintaining redox homeostasis through glutathione (GSH) synthesis and methylation-dependent antioxidant responses.

Glutathione Production and ROS Detoxification

• Methionine metabolism provides precursors for GSH, a major antioxidant that neutralizes reactive oxygen species (ROS).
• Tumor cells enhance methionine flux into the transsulfuration pathway, increasing GSH synthesis to counteract oxidative stress. This adaptation supports survival under conditions of hypoxia and inflammation.

Epigenetic Control of Redox Enzymes

• DNA and histone methylation regulate the expression of antioxidant genes such as SOD2 (superoxide dismutase 2) and GPX4 (glutathione peroxidase 4).
• High SAMe levels reinforce antioxidant defense mechanisms, reducing oxidative damage and supporting tumor cell viability.

Methionine Cycle Analysis in Cancer Research

The methionine cycle is a central hub in cellular metabolism, integrating nutrient availability, epigenetic regulation, and redox homeostasis. Its dysregulation is a defining feature of many cancer types, making methionine metabolism a key focus in oncological research. Advanced analytical approaches allow for precise characterization of methionine cycle activity, providing critical insights into tumor biology, metabolic vulnerabilities, and potential biomarkers.

Metabolic Flux Analysis of the Methionine Cycle

Metabolic flux analysis (MFA) enables the quantification of methionine utilization and pathway activity in cancer cells. Stable isotope-labeled tracers, such as ¹³C-methionine or deuterium-labeled methionine (²H₄-Met), are widely used to track methionine incorporation and downstream metabolite distribution.

Key Insights from MFA Studies:

• Differential Methionine Flux in Cancer vs. Normal Cells: Tumor cells exhibit increased flux from methionine to S-adenosylmethionine (SAMe) and elevated transmethylation activity, supporting widespread epigenetic modifications.
• Integration with One-Carbon Metabolism: MFA studies reveal a strong connection between methionine metabolism and folate-dependent pathways, linking methionine flux to nucleotide synthesis and redox regulation.
• Methionine Salvage Pathway Activity: In MTAP-deleted tumors, flux analysis demonstrates impaired methionine recycling, increasing reliance on extracellular methionine uptake.

Transcriptomic and Proteomic Profiling of Methionine Cycle Enzymes

RNA sequencing (RNA-seq) and proteomic analyses provide comprehensive views of methionine metabolism at the gene and protein levels. Differential expression analysis identifies key regulatory enzymes that are altered in cancer.

Key Findings in Cancer:

• Upregulation of Methionine Transporters: Many aggressive cancers overexpress SLC7A5 (LAT1), enhancing methionine import to support proliferation and survival.
• Dysregulation of Methionine Synthase (MTR) and Methionine Adenosyltransferase (MAT): Altered expression of these enzymes influences SAMe availability, leading to widespread changes in DNA and histone methylation patterns.
• Methionine Cycle Adaptation to Hypoxia: Under hypoxic conditions, tumors modulate methionine metabolism by upregulating enzymes involved in transsulfuration, enhancing antioxidant defenses.

Spatial Metabolomics of Methionine Utilization

Spatial metabolomics reveals methionine metabolism heterogeneity in tumors. Techniques like mass spectrometry imaging (MSI) and MALDI imaging map methionine-related metabolites in tissue sections, highlighting metabolic interactions between cancer and stromal cells.

Key Findings:

• Intratumoral Heterogeneity: Hypoxic regions increase transsulfuration for glutathione synthesis, while proliferative zones show high SAMe levels for methylation.
• Stromal Adaptations: Cancer-associated fibroblasts (CAFs) and endothelial cells alter methionine metabolism, affecting ECM remodeling and angiogenesis.
• Immune Suppression: Methionine depletion in lymphocyte-rich areas impairs T cell activation, promoting immune evasion.

Methionine-Related Biomarkers in Cancer

Methionine metabolism generates potential biomarkers for cancer detection and prognosis. Circulating methionine levels, SAMe/SAH ratios, and methylation signatures serve as indicators of metabolic reprogramming in tumors.

Promising Methionine-Related Biomarkers:

• Elevated Plasma Methionine and SAMe Levels: Increased systemic methionine flux is observed in highly proliferative cancers such as hepatocellular carcinoma and glioblastoma.
• Global DNA Methylation Patterns: Hypomethylation of repetitive elements (LINE-1, Alu) and hypermethylation of specific promoter regions correlate with disease progression.
• Methylation-Dependent RNA Modifications (m6A/m5C): Altered RNA methylation signatures influence transcript stability and translation efficiency in tumors.

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