# Linking Genetic, Epigenetic and Signaling Mechanisms of Oncogene Addiction

> **NIH NIH R01** · UNIVERSITY OF VIRGINIA · 2024 · $54,269

## Abstract

PROJECT SUMMARY
Our long-term goal is to build a network-level and single-cell understanding of the interplay between genetic,
epigenetic and signaling mechanisms that determine the state of MAP kinase (MAPK) pathway dependency in
tumor cells. Such understanding will be key to our ability to predict and ultimately improve the responsiveness
of tumor cells to therapeutic inhibitors of MAPK signaling. Our focus, in this application, is on BRAFV600
mutated cancers, particularly melanomas, where hyperactivation of MAPK signaling has motivated the clinical
evaluation of MAPK-targeted therapies, but they often lead to variable responses and no durable cure in most
patients. While genetic alterations are associated with late resistance, epigenetic heterogeneity associated with
tumor differentiation state or tissue lineage and its adaptive plasticity within a tumor influence the dynamic
state of BRAF/MAPK dependency, thereby diminishing the therapeutic efficacy of MAPK inhibitors. Here, we
propose a systems pharmacology approach to test the hypothesis that heterogeneity in the state of MAPK
dependency may result from a subset of key epigenetic variations across tumor cells of heterogeneous
differentiation states. To identify regulator of such variations, we screened 276 small-molecule epigenetic
modulators individually or in combination with BRAF/MEK kinase inhibitors in melanoma cell lines that
represent a wide spectrum of differentiation states. Integrating multiplexed single-cell analysis with multivariate
statistical modeling and genetic experiments, we identified three classes of inhibitors that target seemingly
distinct epigenetic states in melanoma cells: (1) a lysine demethylase 1A (KDM1A)-dependent state associated
with undifferentiated (AXLHigh), MAPK inhibitor-resistant (p-ERKHigh) cells, (2) a Jumonji histone demethylase
(Jmj-KDM)-dependent state associated with neural crest-like (NGFRHigh/AXLLow) cells, and (3) a state induced
by BET bromodomain inhibitors in NGFRHigh cells, which substantially enhances their requirement for MAPK
signaling. Single-cell analysis shows that these states might co-exist in different combinations and frequencies,
highlighting mutual epigenetic vulnerabilities among genetically diverse melanoma cell populations. In this
proposal, we aim to: (1) examine the molecular specificity of the identified small molecule inhibitors as well as
mechanisms that govern each of the phenotypically consequential epigenetic states, (2) identify predictors of
epigenetic switching in BRAF-mutated cell lines and patient-derived tumors, and (3) test new epigenetic
strategies to overcome heterogeneous populations of MAPK inhibitor-tolerant cells in vitro and in vivo. This will
be achieved through a systems pharmacology approach, combining genetic experiments, high-throughput
single-cell imaging, proteomic measurements, and network-level computational modeling. We will use these
tools as a means to measure, model, modulate and ultimately ...

## Key facts

- **NIH application ID:** 10815704
- **Project number:** 5R01CA249229-04
- **Recipient organization:** UNIVERSITY OF VIRGINIA
- **Principal Investigator:** Mohammad Fallahi-Sichani
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $54,269
- **Award type:** 5
- **Project period:** 2021-05-01 → 2027-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10815704

## Citation

> US National Institutes of Health, RePORTER application 10815704, Linking Genetic, Epigenetic and Signaling Mechanisms of Oncogene Addiction (5R01CA249229-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10815704. Licensed CC0.

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