Chromatin remodeling in neuroblastoma: BAF complex links epigenetics to metastasis

Carlos G. Jiménez Jiménez

Miguel F. Segura Ginard

Neural Tumor Laboratory of the Translational Research Group on Cancer in Childhood and Adolescence

Epigenetic programming of cells during embryonic development is essential for the determination and maintenance of different cell lineages and tissue homeostasis. Embryonic tumors originate from molecular alterations during developmental stages that result in aberrant transcriptional programs controlled by altered epigenetic profiles. In the case of neuroblastoma, neural crest progenitors destined to become cells of the sympathetic nervous system aberrantly block their natural differentiation course and initiate a neoplastic process that leads to a potentially aggressive and metastatic pediatric oncological disease. Therefore, the study of the epigenetic regulators that determine, interpret or execute these oncogenic gene expression networks is crucial to fully understand the behavior of this type of tumor, as well as to develop new therapies based on epigenetics. This doctoral thesis presents a systematic and functional analysis of the ATP-dependent chromatin remodeling complex mSWI/SNF in neuroblastoma cells. This chromatin remodeler acts at the genome-wide level by translating epigenetic signals into open chromatin states, facilitating the interaction of transcription factors and other regulatory elements with DNA. Neuroblastoma cells contain all three major subtypes of mSWI/SNF complexes, but only the BAF complex is relevant for their proliferation. Disruption of the BAF complex by silencing the key and specific subunits ARID1A and ARID1B produces an epigenetic reprogramming in these cells that affects genes related to cell cycle progression and the process of metastasis. Disruption of the assembly of this complex results in a strong cell cycle arrest as well as a reduction in extracellular matrix adhesion and invasion capacity in vitro, in addition to drastically reducing metastasis formation in vivo, extending the survival of murine models of metastatic neuroblastoma. Finally, a drug binding susceptibility analysis and subsequent virtual molecular screening were performed on the ARID1A structure, identifying candidate molecules for pharmacological disruption of the BAF complex by inhibiting protein-protein interactions. One of these candidates appears to exert effects on the molecular target of interest and a strong inhibition of neuroblastoma cell proliferation. These results represent a promising starting point for the development of a pioneering therapeutic strategy based on the disruption of the BAF complex for the treatment of high-risk metastatic neuroblastoma.

The main strength of this project is the impact that the results generated once developed will have in multiple areas. On the one hand, the product generated will have a clear impact on society, since it will represent a new class of drugs without precedents, especially relevant for thousands of patients for whom effective treatments are still lacking, such as metastatic neuroblastoma. This is of particular relevance for diseases considered orphan, including pediatric cancers. However, patients with a wide variety of diseases where the SWI/SNF complex has also been identified as a therapeutic target of interest, such as melanoma, colon cancer or ovarian cancer, may also benefit. On the other hand, it will be an economic stimulus for the biotechnology sector, since it will represent an opportunity to cover a market that demands specific inhibitors of a very specific therapeutic target, exploitable in numerous diseases, and against which different studies show that current inhibitors, directed at partial functions of the complex, are not sufficient. A product like the one we propose, a pioneer in its class as a structural disruptor of a chromatin remodeling complex, will undoubtedly provide assured economic value to the industry. In short, the results obtained in my doctoral thesis have generated a new and promising line of research that will allow the development of a new class of commercially exploitable pharmacological inhibitors. This new drug will allow the simultaneous inhibition of multiple signaling pathways, allowing the exploitation of the proliferative and metastatic vulnerability of neuroblastoma cells revealed during my doctorate

Epigenetic Programming; Embryonic Development; Cell Lineages; Tissue Homeostasis; Embryonic Tumors; Molecular Alterations; Aberrant Transcriptional Programs; Altered Epigenetic Profiles; Neuroblastoma; Neural Crest Progenitors; Sympathetic Nervous System; Neoplastic Process; Aggressive Pediatric Oncological Disease; Metastatic Pediatric Oncological Disease; Epigenetic Regulators; Oncogenic Gene Expression Networks; New Epigenetic Therapies; ATP-dependent Chromatin Remodeling Complex mSWI/SNF; Systematic Functional Analysis; Chromatin Remodeler; Genome-wide Level; Epigenetic Signals; Open Chromatin States; Transcription Factors; Regulatory Elements; DNA Interaction; mSWI/SNF Complex Subtypes; BAF Complex; Proliferation; ARID1A; ARID1B; Epigenetic Reprogramming; Cell Cycle Progression; Metastasis Process; Cell Cycle Arrest; Extracellular Matrix Adhesion; Invasion Capacity In Vitro; Metastasis Formation In Vivo; Murine Models; Metastatic Neuroblastoma; Drug Binding Susceptibility Analysis; Virtual Molecular Screening; ARID1A Structure; Candidate Molecules; Pharmacological Disruption; Protein-Protein Interactions Inhibition; Molecular Target; Neuroblastoma Cell Proliferation Inhibition; Pioneering Therapeutic Strategy; High-Risk Metastatic Neuroblastoma.