Identification of the SOX2 Interactome by BioID Reveals EP300 as a Mediator of SOX2-dependent Squamous Differentiation and Lung Squamous Cell Carcinoma Growth

Abstract

Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma. Thus, anti-SOX2 targeting strategies could help treat early and/or advanced disease. Because SOX2 itself is not readily druggable, we sought to characterize SOX2 binding partners, with the hope of identifying new strategies to indirectly interfere with SOX2 activity. We now report the first use of proximity-dependent biotin labeling (BioID) to characterize the SOX2 interactome We identified 82 high confidence SOX2-interacting partners. An interaction with the coactivator EP300 was subsequently validated in both basal cells and SQCCs, and we demonstrate that EP300 is necessary for SOX2 activity in basal cells, including for induction of the squamous fate. We also report that copy number gains are common in SQCCs and that growth of lung cancer cell lines with 3q gains, including SQCC cells, is dependent on EP300. Finally, we show that EP300 inhibitors can be combined with other targeted therapeutics to achieve more effective growth suppression. Our work supports the use of BioID to identify interacting protein partners of nondruggable oncoproteins such as SOX2, as an effective strategy to discover biologically relevant, druggable targets.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

“…Low-CNA C5A and B tumors were enriched for mutations in (1) epigenetic modifiers EP300 , MLL4 , and CTCF ; (2) mitogen pathway components EPHA2 , HRAS , MAPK1 , and RAC1 ; and (3) cell death mediator caspase CASP8 (Figures 1A, 1B, and S2B). Intriguingly, EP300 is a chromatin modifier recently linked to the enhancement of target gene activation by stemness transcription factor SOX2 , which is amplified on 3q in higher CNA SCCs (Kim et al, 2017), and these alterations tended toward mutual exclusivity in CNA versus quiet subtypes (p = 0.004). Mutations in EPHA2 , HRAS , MAPK1 , and RAC1 cumulatively affected ~27% and 46% of C5 and C5A tumors, with EPHA2 and HRAS mutations tending toward mutual exclusivity across all C5 samples (Figure S2B; p = 0.037).…”

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology

“…TFs have sometimes been classified as initiating or elongating factors. However, they are often found to interact with a wide range of cofactors and regulators (Dingar et al, 2015;Kim et al, 2017;Carnesecchi et al, 2020), and it is therefore likely that they modulate multiple processes albeit with different strengths. Hence, we next considered a more general scenario where each TF can enhance any of the transitions to different extents (Fig.…”

Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders

“…Biotinylation allows the labeling of nearby proteins that can be pulled down using affinity chromatography against biotin and run through the mass spectrometer. APEX and BioID have mainly been used to identify the proteins in cellular compartments or signaling pathways in mammalian cells lines such as HEK293 cells [80][81][82][83][84][85][86]. Only two studies have used APEX on cultured cortical neurons, focusing on the identification of proteins in the synaptic cleft or the identification of the RNA localized to different cellular compartments [87,88].…”