Project description: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 lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. We developed an in vitro model of MYC-driven SCLC tumor cell progression, and performed a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4RPM tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. With the single-cell RNA sequencing of this human SCLC liver biopsy, along with IHC on a panel of 21 human biopsies, we show that human SCLC exhibits intratumoral SCLC subtype heterogeneity, suggesting this dynamic evolution occurs in patient tumors. Together, these single-cell RNA sequencing data support our conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
Project description:Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. We perform bulk RNA-sequencing on SCLC tumors from RPM and Rb1/Trp53/Rbl2 (RPR2) GEMMs, initiated by CGRP-Cre, to complement time-series analysis of single-cell transcriptome profiling and reveal that MYC drives the dynamic evolution of SCLC subtypes. MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Sequenced RPM tumors driven by MycT58A, in comparison to RPR2 tumors associated with high Mycl, have increased intratumoral subtype heterogeneity by bulk-seq, single-cell RNA seq, and IHC compared to RPR2 tumors. In RPM tumors with high MYC, tumors are able to proceed to non-NE subtypes resembling the NEUROD1+ and YAP1+ human SCLC subtypes. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
Project description:Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. To study transcriptional dynamics of MYC-driven tumor evolution and compare transcriptional states to human SCLC tumors, we performed bulk and single-cell RNA-sequencing on various timepoints of Rb1/Trp53/MycT58A (RPM) tumor cells (from Ad-Cgrp-Cre infected mice) as they progress in culture, and on RPM bulk tumors. Here, to complement these analyses we performed ~30X whole-genome sequencing (WGS) of early (day 4) and late (day 23) time-point RPM tumor cells from culture, along with a matching normal blood control to confirm complete loss of expected regions of Rb1 and Trp53. WGS analyses revealed no detectable copy number variations (CNVs), and SNV analysis suggests that minimal clonal and subclonal evolution occurs in vitro. Together, these data ultimately reveal that MYC drives the dynamic evolution of SCLC subtypes. We find that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
Project description:Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. To study transcriptional dynamics of MYC-driven tumor evolution and compare transcriptional states to human SCLC tumors, we performed bulk RNA-sequencing on various timepoints of Rb1/Trp53/MycT58A (RPM) tumor cells (from Ad-Cgrp-Cre infected mice) as they progress in culture. These bulk RNA-seq data of the RPM time-series cells complement time-series analysis of single-cell transcriptome profiling of similar timepoints and ultimately reveal that MYC drives the dynamic evolution of SCLC subtypes. We find that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
Project description: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 lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. Here, we develop an in vitro model of MYC-driven SCLC tumor cell progression and perform a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an Ascl1-to-Neurod1-to-Yap1+ state from a neuroendocrine cell of origin. They also support our findings that MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4 bulk Rb1/Trp53/MycT58A (RPM) tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. Together, these single-cell RNA sequencing data place 3 of 4 SCLC subtypes on a defined trajectory and suggest that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
Project description:Small cell lung cancer (SCLC) is an aggressive subtype of lung cancer whose biology is still poorly understood. Using a multiplexed inhibitor beads assay, we identified active kinases in SCLC. Among those, we found that PKA is critical for the expansion of SCLC in culture and in vivo. PKA promotes the neuroendocrine epithelial state associated with SCLC tumor-initiating cells. Phosphoproteomics analyses identify ~200 PKA substrates and show that PKA controls multiple facets of SCLC growth. Notably, the PP2A phosphatase counteracts the oncogenic effects of PKA, and PP2A activators inhibit SCLC as single agents and with chemotherapy. Our data uncover key signaling networks in SCLC and indicate that targeting the PKA/PP2A pathway may help inhibit this lethal neuroendocrine cancer.
Project description:Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.
Project description:Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.
Project description:Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.
Project description:Lung cancer is comprised of distinct histological subtypes including lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC). Although histological subtypes of lung cancer are often mutually exclusive, patients can present with combined LUAD and SCLC histology tumors. Moreover, LUADs can histologically transform to SCLC through lineage plasticity as a mechanism of resistance to targeted therapies, which most often occurs in EGFR-Mutant LUAD with concurrent RB1 and TP53 inactivation after treatment with EGFR inhibitors. The mechanisms that promote LUAD to SCLC histological transformation are poorly understood. Expression of genes associated with PRC2 activity increase during LUAD to SCLC histological transformation, but it is unknown whether PRC2 is a causative driver of histological transformation in lung cancer. To study the role of the PRC2 complex in SCLC tumorigenesis, we used CRISPR-based somatic gene editing to make SCLC genetically-engineered mouse models (GEMMs) deficient for PRC2 through inactivation of EED; PRC2’s core scaffolding subunit. Strikingly, EED inactivation caused complete histological transformation from ASCL1-positive SCLC to LUAD through an intermediate NEUROD1-positive/NCAM-positive cell state. Mechanistically, SCLC to LUAD histological transformation is initiated when PRC2 inactivation de-represses bivalent genes marked by both H3K27me3 and K3K4me3 including RAS, PI3K, and MAPK pathway genes as well as NEUROD1. Lastly, we developed an EGFR-Mutant LUAD GEMM with concurrent RB1 and TP53 inactivation where EGFR inhibition can promote SCLC transformation and a metastatic phenotype; both of which are completely abrogated by EED inactivation. Together, these findings show that the PRC2 complex is required to drive ASCL1-positive neuroendocrine SCLC with its loss promoting the LUAD phenotype nominating PRC2 inhibition as a therapeutic strategy to block SCLC transformation.