Exploratory studies of cellular resistance to MTA-cooperative PRMT5 inhibitors in MTAP-loss tumors.

PROJECT SUMMARY/ABSTRACT
MTAP is deleted in approximately 15% of all human malignancies and co-occurs in 80-90% of all CDKN2A-
/CDKN2B-deleted cancers, including but not limited to cancers of the lung, gastric system, brain, breast, urinary
tract, and skin. The inhibition of PRMT5, an arginine methyltransferase (PRMT), is synthetic lethal to cancer cells
with MTAP loss. MTAP loss elevates the level of intracellular methylthioadenosine (MTA), which binds and
potently inhibits PRMT5 activity via competing with S-adenosylmethionine (SAM) binding. This creates a state
whereby MTAP-loss cancer cells are particularly vulnerable to further inhibition of PRMT5. The 1st-generation
PRMT5 inhibitors (PRMT5i) bind to either apo or SAM-bound PRMT5 abundantly available in both tumor and
normal cells. These agents thus fail to selectively impact the viability of tumor cells and exhibit mechanism-based
toxicities due to their inability to bind and inactivate MTA-complexed PRMT5, specifically found in MTAP-loss
tumor cells. On the other hand, the 2nd-generation MTA-cooperative PRMT5i (MTA:PRMT5i) targets MTA-bound
PRMT5 and demonstrated significantly improved selectivity for MTAP loss in preclinical models. Ongoing early-
phase clinical trials confirmed promising activity of MTA:PRMT5i monotherapy in MTAP-loss solid tumors, with
a favorable safety profile. Despite these positive outcomes, response assessment across different patients
indicated that 40-60% of MTAP-loss cases showed minimal or no tumor shrinkage, suggesting innate resistance
(IR). Moreover, 20-30% of patients showed a degree of acquired resistance (AR), where the tumors were initially
responsive to the compound but eventually progressed. These lines of evidence suggest a critical challenge in
the treatment of patients with MTAP-loss solid tumors due to IR and/or AR to MTA:PRMT5i.
Our long-term goal is to develop effective strategies for patient stratification and combinational therapy to
overcome resistance to MTA:PRMT5i treatment. In the proposed project, we will conduct exploratory studies to
generate valuable resources and information to facilitate the understanding of resistance mechanism(s) and the
development of therapeutic approaches. We propose 2 Specific Aims. First, we will establish and test prototype
in vitro and in vivo models of MTAP-loss solid tumors that recapitulate the phenotype of IR and/or AR to
MTA:PRMT5i. This will be achieved based on a selected panel of cholangiocarcinoma (CCA) and non-small cell
lung cancer (NSCLC) cell lines and patient samples collected from clinical trials. To demonstrate the use of these
models, we will evaluate combined treatment with MTA:PRMT5i and MEK inhibitors (MEKi) on the AR models,
where MEKi was identified as a potential combination agent from high-throughput drug screens (HTDS) in our
preliminary study. Second, we will perform a pilot study to identify vulnerability and molecular signatures
associated with IR and/or AR. This will be achieved by the integrative analysis of HTDS, whole-exome
sequencing, and RNA-seq performed on 11 CCA and NSCLC cell lines of various resistant phenotypes. Together,
the research outcomes of the 2 aims will set up a foundation for achieving our long-term goal.

Grant Number: 1R21CA296234-01A1
NIH Institute/Center: NIH
Principal Investigator: Jordi Ahnert