Abstract A007: Pancreatic cancer comprises co-existing transcriptional states regulated by distinct master regulator programs

Despite extensive efforts, reproducible assessment of pancreatic ductal adenocarcinoma (PDA) heterogeneity and plasticity at the single cell level remains elusive. Systematic, network-based analysis of single cell RNA-seq profiles showed that most PDA tumors comprise three coexisting lineages whose aberrant transcriptional state is mechanistically controlled by distinct regulatory programs. These lineages were characterized by the aberrant activation of either gastrointestinal lineage markers (GLS), transcriptional effectors of morphogen pathways (MOS) and acinar to ductal metaplasia markers (ALS). Each lineage was characterized by cells in two different cell states determined by the differential activation of MEK signaling (M+/M-) and high cellular plasticity. These states were confirmed in multiple cohorts, cell lines, PDX models and harmonized with bulk profile analyses. Master regulators (MRs) of GLS and MOS state were predictive of patient’s survival in bulk profiles. Cross-state plasticity was confirmed by lineage tracing assays, while pooled CRISPR/Cas9 assays confirmed the essentiality of identified MR proteins. Finally, mechanistic MR-mediated cell state control was confirmed by MR expression-mediated reprogramming of MOS cells to a GLS state. Our work provided a mechanistic model of pancreatic cancer heterogeneity and testable hypothesis to target cell state-specific pancreatic cancer dependencies.

Citation Format: Pasquale Laise, Mikko Turunen, Hans Carlo Maurer, Alvaro Curiel Garcia, Ela Elyada, Bernhard Schmierer, Lorenzo Tomassoni, Jeremy Worley, Mariano J. Alvarez, Jordan Kesner, Xiangtian Tan, Somnath Tagore, Ester Calvo Fernandez, Kelly Wong, Alexander L. E. Wang, Sabrina Ge, Alina C. Iuga, Aaron T. Griffin, Winston Wong, Gulam A. Manji, Faiyaz Notta, David A. Tuveson, Kenneth P. P. Olive, Andrea Califano. Pancreatic cancer comprises co-existing transcriptional states regulated by distinct master regulator programs [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A007.

Abstract 1421: Targeting cell-adaptive mechanisms of drug resistance in lethal prostate cancer

Precision oncology therapies are significantly hindered by the emergence of genetically or epigenetically-distinct cellular sub-populations, presenting either pre-existing or acquired drug resistance. For example, patients affected by advanced prostate cancer (PC), which is initially driven by aberrant activation of androgen receptor (AR) signals, often respond to Androgen Deprivation Therapy (ADT). Unfortunately, long-term treatment leads to the emergence of ADT-resistant tumors, termed Castration Resistant Prostate Cancer (CRPC), and poor outcome. Next-generation AR inhibitors extend CRPC patient survival, but frequently lead to the emergence of an even more aggressive Neuroendocrine PC (NEPC) phenotype, with exceedingly poor prognosis. Progression to NEPC is often determined by epigenetic-mediated reprogramming, rather than genomic alterations, resulting in cell-adaptive resistance, driven by aberrant activation of a handful of Master Regulator (MR) proteins. Consequently, better and more mechanistic understanding of cell-adaptive resistance is necessary to develop effective therapeutic strategies for CRPC. To address this challenge, we devised an RNA-based, high-throughput methodology, to systematically elucidate drug resistance mechanisms with single-cell resolution, and we applied it to study diverse, clonal populations that emerge following long-term treatment of PC LnCAP cells with next-generation AR inhibitors. Specifically, we identified Master Regulator (MR) proteins leading to the emergence of drug resistance, as well as clinically-available inhibitors able to reversing their activity, which were experimentally validated. We used PLATE-Seq, a low-cost, high-throughput RNA-Seq technology to profile more than 80 clonal, ADT-resistant populations, with single-cell resolution, and the VIPER algorithm to elucidate the MR proteins that mechanistically regulate their cell-adaptation programs. Our analysis revealed distinct cell-adaptive responses, associated with profound epigenetic reprogramming of prostate cancer cells. We used OncoTreat to prioritize a list of more than 400 FDA-approved and late-stage investigational drugs. Sensitivity to predicted drugs was confirmed in vitro and in vivo studies, in xenograft models derived from ADT- resistant clones are underway. We propose that this framework may represent a relevant advance to the study of cell-adaptive mechanism of drug resistance. Critically, this methodology is not limited to prostate cancer and can be applied to study arbitrary drug-resistance phenotypes.

Citation Format: Prem Subramaniam, Alessandro Vasciaveo, Juan Arriaga, Jordan Kesner, Cory Abate-Shen, Andrea Califano. Targeting cell-adaptive mechanisms of drug resistance in lethal prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1421.

The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State

Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1^-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming.

Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization

Cytosolic sensing of nucleic acids initiates tightly regulated programs to limit infection. Oocyte fertilization represents a scenario wherein inappropriate responses to exogenous yet non-pathogen-derived nucleic acids would have negative consequences. We hypothesized that germ cells express negative regulators of nucleic acid sensing (NAS) in steady state and applied an integrated data-mining and functional genomics approach to identify a rheostat of DNA and RNA sensing-the inflammasome component NLRP14. We demonstrated that NLRP14 interacted physically with the nucleic acid sensing pathway and targeted TBK1 (TANK binding kinase 1) for ubiquitination and degradation. We further mapped domains in NLRP14 and TBK1 that mediated the inhibitory function. Finally, we identified a human nonsense germline variant associated with male sterility that results in loss of NLRP14 function and hyper-responsiveness to nucleic acids. The discovery points to a mechanism of nucleic acid sensing regulation that may be of particular importance in fertilization.

Millimeter-wave radiometer diagnostics of harmonic electron cyclotron emission in the Levitated Dipole Experiment

A 110/137 GHz radiometer pair with collimated antenna pattern is being used to diagnose optically thin harmonic electron cyclotron emission from hot electrons in LDX. Signal levels of 0.1-1 keV and 110/137 ratios of 2-4 stationary with ECRH power have been observed. The large plasma core magnetic field gradient causes all relevant harmonics to be simultaneously viewed over a angle(k,B) angular range of 0°-90° representing a unique geometry for interpretation of ECE in terms of hot electron temperature and density.