Abstract A022: Cell state-directed integrated functional genomics reveals TAB1 as a central controller of the neuroblastoma chemoresistant mesenchymal cell state

Abstract

Resistance to conventional chemotherapies is a major cause of cancer patient relapse and subsequent death. The fundamental biological properties of tumor cells are not only driven by acquired genetic mutations, but also by aberrant epigenetic regulation leading to corresponding changes in the expressed transcriptome. Plasticity in the transcriptome creates intratumoral malignant heterogeneity, imparting new phenotypic properties to cancer cells such as chemoresistance, aberrant proliferation and invasion. High-risk neuroblastoma (NB) demonstrates transcriptional plasticity with defined cell states and a low mutational burden. NB cells exist primarily in two genetically identical but epigenetically and transcriptionally distinct states: a chemosensitive adrenergic state (ADRN) and a less common drug-tolerant persister cell state, the mesenchymal (MES) state. MES cells are enriched at relapse, suggesting that cells may switch to this state under therapeutic pressure. Despite a myriad of approaches to treating high risk NB, relapsed patients have extremely poor survival. Unfortunately, the mechanisms by which NB cells switch to and maintain this more chemoresistant MES cell state are poorly understood. We hypothesized that dissecting pathways promoting NB cell state plasticity may reveal new approaches to drive cell state interconversions, facilitating chemosensitivity. We used a recently developed novel fluorescent reporter system of the NB MES cell state to perform whole exome-CRISPR-cas12 knockout screening to identify master controllers of MES cell state maintenance. Integrated pathway analysis demonstrated multiple conserved pathway modules involved in maintaining cells in the MES cell state, including a prominent role for inflammatory signaling pathways. To dissect state interconversion mechanisms, we next performed fluorophore-based transcription factor overexpression library screens in ADRN cells. These data demonstrated a prominent role for transcription factors downstream of inflammatory signaling pathways in driving the formation of the MES cell state. Intersecting these data, we identified central nodes for targeting to disrupt maintenance and formation of the MES state. A prominent central node identified was the TAK1-binding protein 1 gene (TAB1). Consistent with a role in maintaining the MES state, TAB1 protein interactors were more highly expressed in MES-dominant cell lines and primary tumors than in ADRN-dominant models. Targeted CRISPR knockout of TAB1 in highly MES cell lines resulted in profound loss of MES-related gene expression. TAB1 knockout cell pools showed increased chemosensitivity to several chemotherapy agents across various classes used in treating neuroblastoma. Cell state switching is an intriguing paradigm by which NB cells can evade conventional therapies. We have identified candidate genes, including TAB1, that play an important role in maintaining the MES cell state in NB. Continued interrogation of these fundamental mechanisms represents a new approach that may potentially be leveraged for therapeutic gain.