Multivalent State Transitions Shape the Intratumoral Composition of Small Cell Lung Carcinoma

Small cell lung carcinoma (SCLC) is an aggressive, tobacco-associated tumor characterized by rapid growth, early metastases, and initial response followed by almost invariable resistance to chemotherapy. Studies to date have not resolved the extent that diverse transcriptional programs drive SCLC and contribute to its lethality. We combined patient-derived xenograft (PDX) (n = 64) resources with multi-omic profiling, single-cell fluorescence tracking of ex vivo tumor cells, and mathematical and statistical models to study the topology of the SCLC transcriptional state space and its plasticity. ]]>
Human tumor material and associated clinical data were obtained after informed written consent on an IRB-approved prospective registry study. Patients with a pathological diagnosis of small cell lung carcinoma and a successfully engrafted PDX were selected for further evaluation. A total of 64 patients met our eligibility criteria.]]>
SCLC tumors are substantially more heterogeneous than previously appreciated, with most samples retaining two or more subpopulations marked by Ascl1, NeuroD1, or Yap1. Using single-cell RNA-seq profiling, we showed that the relative frequency of each state varied across tumors and tumor composition impacted clinical treatment response trajectories (e.g. Ascl1 high tumors were more likely to progress after chemotherapy and concomitantly had a worse overall survival). We measured the kinetics of state transitions using single-cell fluorescence tracking of ex vivo cells and associated single-cell dynamics with overall population trends using stochastic transition theory (i.e. Markov chains). Our results indicate that the transition rates in individual tumors were largely governed by probabilistic rules with autonomous tendencies that are critical for configuring intratumoral proportions. In conclusion, we elucidated a spectrum of states in SCLC cells and quantified their dynamics, identifying cellular programs that recapitulate neuroendocrine, neural, and mesenchymal development. Our work advances a model of cellular states and program diversity in SCLC and nominates new therapeutic strategies designed to limit the plasticity, and hence the versatility, of this lethal cancer. ]]>