MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate.

Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of ASCL1, NEUROD1, POU2F3, or YAP1. Here, we use mouse and human models with a time-series single-cell transcriptome analysis to reveal that MYC drives dynamic evolution of SCLC subtypes. In neuroendocrine cells, MYC activates Notch to dedifferentiate tumor cells, promoting a temporal shift in SCLC from ASCL1+ to NEUROD1+ to YAP1+ states. MYC alternatively promotes POU2F3+ tumors from a distinct cell type. Human SCLC exhibits intratumoral subtype heterogeneity, suggesting that this dynamic evolution occurs in patient tumors. These findings suggest that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

[1]  Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data , 2019, Nature Reviews Cancer.

[2]  R. Kageyama,et al.  Significance of proneural basic helix-loop-helix transcription factors in neuroendocrine differentiation of fetal lung epithelial cells and lung carcinoma cells. , 2001, Histology and histopathology.

[3]  V. Seshan,et al.  FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing , 2016, Nucleic acids research.

[4]  I. Huijbers,et al.  Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells , 2014, EMBO molecular medicine.

[5]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[6]  William C Hahn,et al.  Lentivirus-delivered stable gene silencing by RNAi in primary cells. , 2003, RNA.

[7]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[8]  P. Jänne,et al.  Five‐Year Survival in EGFR‐Mutant Metastatic Lung Adenocarcinoma Treated with EGFR‐TKIs , 2016, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[9]  Kristofer C. Berrett,et al.  MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. , 2017, Cancer cell.

[10]  T. Jacks,et al.  Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase , 2009, Nature Protocols.

[11]  A. Letai,et al.  MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer , 2019, Nature Communications.

[12]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[13]  Carlos F. Lopez,et al.  Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers , 2019, PLoS Comput. Biol..

[14]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[15]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[16]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[17]  Martin Vingron,et al.  Comprehensive genomic profiles of small cell lung cancer , 2015, Nature.

[18]  Jun Zhu,et al.  Classic oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer , 2020 .

[19]  Robert Langer,et al.  CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling , 2014, Cell.

[20]  Cole Trapnell,et al.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.

[21]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[22]  Ann B. Lee,et al.  Geometric diffusions as a tool for harmonic analysis and structure definition of data: multiscale methods. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  M. Lawrence,et al.  Combination Olaparib and Temozolomide in Relapsed Small Cell Lung Cancer. , 2019, Cancer discovery.

[24]  Aaron T. L. Lun,et al.  Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R , 2017, Bioinform..

[25]  A. Sweet-Cordero,et al.  Loss of p130 accelerates tumor development in a mouse model for human small-cell lung carcinoma. , 2010, Cancer research.

[26]  M. German,et al.  Hes6 Promotes Cortical Neurogenesis and Inhibits Hes1 Transcription Repression Activity by Multiple Mechanisms , 2003, Molecular and Cellular Biology.

[27]  M. Sos,et al.  Family matters: How MYC family oncogenes impact small cell lung cancer , 2017, Cell cycle.

[28]  Andrew J. Hill,et al.  Single-cell mRNA quantification and differential analysis with Census , 2017, Nature Methods.

[29]  P. Robson,et al.  Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer , 2020, Nature Cancer.

[30]  A. Gazdar,et al.  Genetic requirement for Mycl and efficacy of RNA Pol I inhibition in mouse models of small cell lung cancer , 2016, Genes & development.

[31]  N. Girard,et al.  Advanced-Stage Non-Small Cell Lung Cancer: Advances in Thoracic Oncology 2018. , 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[32]  Nicholas T. Ingolia,et al.  MYC-Driven Small-Cell Lung Cancer is Metabolically Distinct and Vulnerable to Arginine Depletion , 2019, Clinical Cancer Research.

[33]  L. Girard,et al.  A biobank of small cell lung cancer CDX models elucidates inter- and intratumoral phenotypic heterogeneity , 2020, Nature Cancer.

[34]  C. Rudin,et al.  Targeting NOTCH activation in small cell lung cancer through LSD1 inhibition , 2019, Science Signaling.

[35]  Jiaoti Huang,et al.  Prostate epithelial cell of origin determines cancer differentiation state in an organoid transformation assay , 2016, Proceedings of the National Academy of Sciences.

[36]  Hiroshi I. Suzuki,et al.  YAP and TAZ modulate cell phenotype in a subset of small cell lung cancer , 2016, Cancer science.

[37]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[38]  V. Velcheti,et al.  Reciprocal expression of INSM1 and YAP1 defines subgroups in small cell lung cancer , 2017, Oncotarget.

[39]  K. Nackaerts,et al.  Randomized Phase II Study of Paclitaxel plus Alisertib versus Paclitaxel plus Placebo as Second-Line Therapy for Small-Cell Lung Cancer: Primary and Correlative Biomarker Analyses. , 2020, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[40]  Virginia Savova,et al.  Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. , 2019, Immunity.

[41]  R. Cardiff,et al.  Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell of origin model for prostate cancer heterogeneity , 2013, Nature Cell Biology.

[42]  Robert Gentleman,et al.  Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer , 2012, Nature Genetics.

[43]  M. Krasnow,et al.  New approaches to small cell lung cancer therapy : from the laboratory to the clinic. , 2020, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[44]  J. Minna,et al.  Small cell lung cancer tumors and preclinical models display heterogeneity of neuroendocrine phenotypes. , 2018, Translational lung cancer research.

[45]  Fabian J. Theis,et al.  destiny: diffusion maps for large-scale single-cell data in R , 2015, Bioinform..

[46]  D. Spector,et al.  POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer , 2018, Genes & development.

[47]  Steven J. M. Jones,et al.  Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.

[48]  M. Roussel,et al.  The Interaction of Myc with Miz1 Defines Medulloblastoma Subgroup Identity. , 2016, Cancer cell.

[49]  A. Berns,et al.  Cell of origin of small cell lung cancer: inactivation of Trp53 and Rb1 in distinct cell types of adult mouse lung. , 2011, Cancer cell.

[50]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[51]  H. Bolouri,et al.  Crebbp Loss Drives Small Cell Lung Cancer and Increases Sensitivity to HDAC Inhibition. , 2018, Cancer discovery.

[52]  Peter Chen,et al.  Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis , 2018, Cell reports.

[53]  K. Cibulskis,et al.  Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer , 2012, Nature Genetics.

[54]  J. Battey,et al.  Changes in the phenotype of human small cell lung cancer cell lines after transfection and expression of the c-myc proto-oncogene. , 1986, The Journal of clinical investigation.

[55]  R. Deberardinis,et al.  Inosine Monophosphate Dehydrogenase Dependence in a Subset of Small Cell Lung Cancers. , 2018, Cell metabolism.

[56]  Yan Liu,et al.  Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. , 2014, Cancer cell.

[57]  Volker Hovestadt,et al.  Resolving medulloblastoma cellular architecture by single-cell genomics , 2019, Nature.

[58]  P. Meltzer,et al.  SCLC_CellMiner: Integrated Genomics and Therapeutics Predictors of Small Cell Lung Cancer Cell Lines based on their genomic signatures , 2020, bioRxiv.

[59]  Luc Girard,et al.  ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs. , 2016, Cell reports.

[60]  N. Neff,et al.  Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seq , 2014, Nature.

[61]  Sarah A Teichmann,et al.  Computational assignment of cell-cycle stage from single-cell transcriptome data. , 2015, Methods.

[62]  M. Krasnow,et al.  Rare Pulmonary Neuroendocrine Cells Are Stem Cells Regulated by Rb, p53, and Notch , 2019, Cell.

[63]  Jun Zhu,et al.  Classic oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer , 2019, bioRxiv.

[64]  Alex H. Wagner,et al.  Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer , 2018, Nature Communications.

[65]  K. Geisinger,et al.  Use of Monoclonal Antiestrogen Receptor Antibody to Evaluate Estrogen Receptor Content in Fine Needle Aspiration Breast Biopsies , 1986, Annals of surgery.

[66]  A. McKenna,et al.  Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing , 2014, Cell.

[67]  Akinobu Matsumoto,et al.  Fbxw7-dependent Degradation of Notch Is Required for Control of “Stemness” and Neuronal-Glial Differentiation in Neural Stem Cells* , 2011, The Journal of Biological Chemistry.

[68]  Kwok-Kin Wong,et al.  Characterization of the cell of origin for small cell lung cancer , 2011, Cell cycle.

[69]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[70]  Jing Wang,et al.  Protein expression of TTF1 and cMYC define distinct molecular subgroups of small cell lung cancer with unique vulnerabilities to aurora kinase inhibition, DLL3 targeting, and other targeted therapies , 2017, Oncotarget.

[71]  K. Garcia,et al.  Intratumoral heterogeneity generated by Notch signaling promotes small cell lung cancer , 2017, Nature.

[72]  Levi Garraway,et al.  Nuclear factor I/B is an oncogene in small cell lung cancer. , 2011, Genes & development.

[73]  A. Berns,et al.  Induction of small cell lung cancer by somatic inactivation of both Trp53 and Rb1 in a conditional mouse model. , 2003, Cancer cell.

[74]  Pan Tong,et al.  CHK1 Inhibition in Small-Cell Lung Cancer Produces Single-Agent Activity in Biomarker-Defined Disease Subsets and Combination Activity with Cisplatin or Olaparib. , 2017, Cancer research.

[75]  Zachary T Herbert,et al.  The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis , 2019, Genes & development.

[76]  G. Bepler,et al.  Establishment and identification of small cell lung cancer cell lines having classic and variant features. , 1985, Cancer research.

[77]  John T. Poirier,et al.  DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2 , 2015 .

[78]  G. Wahl,et al.  Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development , 2018, Cell reports.

[79]  J. Minna,et al.  Characterization of variant subclasses of cell lines derived from small cell lung cancer having distinctive biochemical, morphological, and growth properties. , 1985, Cancer research.

[80]  T. Jacks,et al.  Caspase-2-mediated cleavage of Mdm2 creates a p53-induced positive feedback loop. , 2011, Molecular cell.

[81]  C. Rudin,et al.  A DLL3-targeted antibody-drug conjugate eradicates high-grade pulmonary neuroendocrine tumor-initiating cells in vivo , 2015, Science Translational Medicine.

[82]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[83]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[84]  J. Marioni,et al.  Pooling across cells to normalize single-cell RNA sequencing data with many zero counts , 2016, Genome Biology.