Evolution of gliomas during treatment and resistance

Project Abstract
Despite decades of research into targeted therapeutics, the most effective treatments in glioma remain DNA
damaging agents: radiation and the alkylating agents temozolomide and nitrosureas like CCNU. In this project’s
prior cycle, we found that mismatch repair deficiency (MMRd) is a common source of temozolomide resistance;
and that unlike other cancers, gliomas that gain temozolomide resistance through MMRd tend not to respond to
immune checkpoint inhibition. But they often do respond to CCNU. We hypothesize that a fuller understanding
of the different resistance mechanisms to TMZ and CCNU will enable 1) improved knowledge of when and how
to use these agents, including clinically useful biomarkers, and 2) optimization of combined strategies using
targeted and immunotherapies developed over the last decade.
Although extensive work has been done to understand how CCNU damages DNA and to detect genes and
pathways involved in repairing this damage, the field lacks a unified understanding of how CCNU effects vary
across gliomas with different DNA damage response (DDR) characteristics, how resistance arises, and how the
effects of CCNU interact with other agents including DNA damaging agents such as temozolomide and radiation,
as well as therapeutics targeting specific DDR functions and pathways. As a result, we lack biomarkers that can
accurately guide clinicians to prescribe CCNU to patients who are likely to respond, do not know the optimal
combined therapeutic approaches involving CCNU, and clinical practice varies widely.
We propose to pursue a systematic evaluation of the genomic effects and potential therapeutic roles of
CCNU. A major innovation in our proposal is our systematic approach to evaluating the effects of CCNU on
cancer survival and proliferation and genome integrity: when used alone and in combination with temozolomide,
RT, and agents targeting DNA damage response pathways; and across a wide variety of DNA damage response
contexts. For this, we will leverage a living tissue biobank of over 250 gliomas in vivo and in vitro models and
state-of-the-art technologies for functional genomics and genome characterization across treatment conditions
and DDR backgrounds. Our Aims are: Aim 1: Test the hypothesis that MMRd based resistance to TMZ within a
GBM indicates relative sensitivity to CCNU and RT and can be detected through plasma cell-free DNA. Aim 2:
Test the hypothesis that defects in proteins involved in repair of CCNU-induced ICLs determine resistance to
CCNU and strategies to overcome. Aim 3: Test the hypothesis that intentional manipulation of mutational profiles
and clonal dynamics by coordinating TMZ, CCNU, RT, and DDR pathway inhibition can increase the
effectiveness of immunotherapy. DNA damaging agents remain the most effective agents in glioma and all other
cancers, the unified understanding of their effects in isolation and combination across the varied DDR contexts
in this proposal will shape the use of these agents in clinical practice and guide the development of new
biomarker-driven combinations with novel DDR targets.

Grant Number: 5R01CA188228-10
NIH Institute/Center: NIH
Principal Investigator: RAMEEN BEROUKHIM