Elucidating and Targeting tumor dependencies and drug resistance determinants at the single cell level

Cancer targets fall into two major categories: oncoproteins that elicit tumor essentiality due to their direct role in
tumorigenesis or tumor maintenance (oncogene dependencies) and proteins that elicit synthetic lethality with
oncogene mutations but are not themselves mutated (non-oncogene dependencies). Unfortunately, clonal
selection and inherent cancer cell plasticity—as well as the ability of cancer cells to undergo adaptation and
reprogramming to drug resistant states, following treatment—are currently challenging the concept of
individual proteins as effective therapeutic targets for an entire tumor mass—especially if identified from
bulk tissue analyses. Indeed, despite several successes, only 5% – 11% of cancer patients benefit from
targeted therapy, based on progression free survival, often with no substantial overall survival differences; while
promising, immune therapy is also subject to selective response and relapse. To address these challenges, our
proposal will study a more universal class of mutation-agnostic, non-oncogene dependencies implemented
by tightly-autoregulated sets of Master Regulator (MR) proteins that we have called Tumor Checkpoint (TC)
modules. We have shown that MR proteins mechanistically implement a tumor cell’s transcriptional state by
canalizing the effect of mutations and aberrant signals in their upstream pathways. As such, within the context
of a transcriptionally-distinct tumor subtype, they represent largely mutation-agnostic dependencies. Our
proposal will thus focus on the elucidation and pharmacological targeting of MRs and TC-modules at the
single cell level, within molecularly distinct, yet co-existing tumor subpopulations. This will lead to design
of successful combination therapy approaches and will help elucidate and pharmacologically target mechanisms
of drug resistance and cell adaptation. To accomplish these goals, we will extend a highly successful, network-
based framework developed by our CTD2 Center, for the elucidation, validation, and pharmacological targeting
of MR proteins and TC-modules. Indeed, we have shown that genetic or pharmacological targeting of this new
class of tumor dependencies can induce collapse of TC-module activity and induce loss of tumor viability in a
wide range of malignancies, ranging from glioblastoma, neuroblastoma, and neuroendocrine tumors, to prostate
and breast adenocarcinoma, among many others. In particular, analysis of 25 TCGA cohorts has identified 112
transcriptionally distinct tumor subtypes, each one regulated by a distinct subtype-specific TC-module, which
was independent of patient-specific mutations. These methodologies are especially relevant in rare, aggressive
tumors—including several pediatric malignancies—where cohort size may be too small to support correlative
analyses. Critically, these studies have led to the development of two NY/CA Dpt. of Health approved, CLIA-
compliant tests, OncoTarget and OncoTreat, whose predictions have spurred several clinical trials. These
approaches will be extended to elucidate TC-module dependencies and to develop drug sensitivity biomarkers
at the single cell level.

Grant Number: 5U01CA272610-04
NIH Institute/Center: NIH
Principal Investigator: ANDREA CALIFANO