Subcellular one-carbon metabolism, S-Adenosylmethionine availability and cancer

PROJECT SUMMARY
Pancreatic Ductal Adenocarcinoma (PDAC) stands as the most common and one of the deadliest forms of
pancreatic cancer, largely due to liver metastasis and the lack of effective targeted treatments. Emerging
evidence comparing primary and metastatic cancer lesions suggests that key steps of metastasis are controlled
by reversible epigenetic mechanisms, specifically DNA methylation and Histone Post Translational Modifications
(PTMs). These epigenetic changes are intricately linked to metabolic networks, which supply the essential
substrates and cofactors for these modifications, thereby potentially playing a crucial role in metastasis
adaptation. To explore this interplay between metabolism and epigenetics in PDAC, we leveraged the DepMap
database to identify metabolic dependencies in pancreatic cancer cells. Our unbiased analysis revealed
Methionine Adenosyltransferase 2A (MAT2A) as a specific vulnerability. MAT2A is a key enzyme in the One
Carbon Metabolism (OCM), a pathway fundamental for transferring single-carbon units to various substrates.
Crucially, OCM is integral to DNA and histone methylation processes by generating S-adenosylmethionine
(SAM), the universal methyl donor whose availability is tightly regulated by MAT2A itself. Further characterization
of MAT2A revealed its nuclear localization in metastatic liver lesions compared to primary tumors. Additionally,
untargeted metabolomic analysis of human liver metastases revealed that most one-carbon metabolism (OCM)
intermediates, including SAM, are downregulated, indicating a high demand for these metabolites in metastatic
cells. To mimic these conditions, we developed a Metastasis-like Media (MLM), and our in vitro experiments
confirmed that under these conditions, MAT2A translocates to the nucleus, binds to chromatin and is required to
sustain histone methyltransferase (HMT) activity, forming a previously unrecognized nuclear network. To
elucidate MAT2A's role in metastasis, we propose in Aim 1 to use CUT&RUN and chromatin immunoprecipitation
followed by LC-MS to identify MAT2A's chromatin binding sites and interactors. This will enhance understanding
of its chromatin interactions in metastasis and identify potential therapeutic targets. In aim 2, to advance next-
generation cancer metabolic drugs, we aim to determine the specific metabolic requirements of metastatic PDAC
at a subcellular level by measuring SAM levels across compartments using newly developed in-house methods.
Next, we will Assess how diet-induced metabolic changes affect metastasis, MAT2A localization, and metabolic
fluxes in vivo using a PDAC mouse model and 13C_3-serine labeling. Lastly in aim 3, we will develop new
therapeutic strategies for metastatic PDAC using an in vivo orthotopic model, combining dietary interventions,
MAT2A inhibitors, and genetic disruption of MAT2A's chromatin network. Targeting MAT2A's nuclear activity,
including its chromatin binding and interactions with chromatin-associated proteins, offers a novel therapeutic
approach for metastatic PDAC. This proposal aims to uncover how one-carbon metabolism shapes DNA and
histone methylation, paving the way for metabolism-targeted therapies to improve PDAC patient outcomes.

Grant Number: 1K99CA296774-01A1
NIH Institute/Center: NIH
Principal Investigator: Tiziano Bernasocchi