Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

Abstract

Small cell lung cancer (SCLC) is a devastating disease because of its tendency to early invasion and refractory relapse after initial treatment response. These aggressive traits have been associated with phenotypic heterogeneity, which however remains incompletely understood. To fill this knowledge gap, we inferred a set of 33 transcription factors (TFs) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes. The topology of this SCLC TF network was derived from prior knowledge and simulated using Boolean modeling. These simulations predicted that the network settles into attractors (TF expression patterns) correlated with NE or ML phenotypes, suggesting that TF network dynamics underlie emergence of heterogeneous SCLC phenotypes in an epigenetic landscape. However, several cell lines and patient samples did not correlate with either the NE or ML attractors. Flow cytometry indicated that single cells within these cell lines simultaneously express surface markers of both NE and ML differentiation, revealing existence of a “hybrid” phenotype. Upon exposure to standard-of-care cytotoxic drugs or epigenetic modifiers, NE and ML cell populations converged toward the hybrid state, suggesting a possible escape route from treatment. Our findings indicate that SCLC phenotypic heterogeneity can be specified dynamically by attractor states of a master regulatory TF network. Thus, SCLC heterogeneity may be best understood as states within an epigenetic landscape. Understanding phenotypic transitions within this landscape could provide insights to clinical applications.

Small cell lung cancer tumors and preclinical models display heterogeneity of neuroendocrine phenotypes

“…Figure 9 is a summary of the main differences between the NE high and low subtypes. As shown in a GEM (11) or in a SCLC cell lines (33), this process is a dynamic one, with transition from NE high to NE low phenotype or toward a hybrid state. Whether changes in the opposite direction (NE low to NE high) can occur is currently unknown.…”

A Mechanism for Epithelial-Mesenchymal Heterogeneity in a Population of Cancer Cells

“…Subpopulations of cells exhibiting a stem cell-like phenotype have been reported in multiple cancer types including leukemia (Lapidot et al, 1994), breast cancer (Al-Hajj et al, 2003), colorectal cancer (O'Brien et al, 2007;Ricci-Vitiani et al, 2007), brain cancer (Singh et al, 2004), and prostate cancer (Collins et al, 2005). Tumor cell populations in triple-negative breast cancer can consist of luminal, basal, immunomodulatory, mesenchymal, and stem-like cells (Lehmann et al, 2011), while those in small cell lung cancer are composed of neuroendocrine and non-neuroendocrine cells (Calbo et al, 2011;Udyavar et al, 2016). Intra-tumoral heterogeneity has been associated with poor prognosis across cancer types (Stanta and Bonin, 2018).…”

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers

“…However, several groups have found evidence for non-NE variants within SCLC tumors [10][11][12], as well as an NE 57 variant driven by MYC overexpression and NEUROD1 overexpression, instead of ASCL1 [13-15]. We previously described 58 SCLC cell lines with hybrid expression of both NE and non-NE markers [16], and proposed they could serve as a resistant 59 niche since drug perturbations shifted most cell lines towards hybrid phenotype(s). Taken together, these observations 60 indicate the existence of a complex landscape of SCLC phenotypes that may form a tumor microenvironment robust to 61 perturbations and treatment [10,17].…”