Abstract 156: Integrated exome and transcriptome sequencing of primary lung cancers and paired distant metastases

Background: The precise molecular mechanisms underlying metastasis of nonsmall cell lung cancers (NSCLC) are largely unknown. Two recent studies comparing genomic landscapes of primary NSCLC tumors and paired brain metastases suggested branched evolution, where all metastatic and primary tumors shared a common ancestor yet continued to evolve independently. The integrated genomic and transcriptomic profiles of primary NSCLC and metastases have not been studied in any details.

Methods: We performed whole exome sequencing (WES) and RNA sequencing (RNA-seq) of surgically resected primary tumors and paired distant metastases from 7 patients with NSCLC.

Results: Totally, 6,945 somatic mutations, including 1,702 non-silent (stop-gain, stop-loss, frameshift, splicing site and nonsynonymous) mutations were identified by WES. Metastases trended to have larger mutation burdens compared to paired primary tumors, although the difference was not statistically different (average 595 mutations per tumor in primary tumors versus 852 mutations per tumor in metastases, respectively, p = 0.54). On average, 51% of all mutations (24% to 93%) were shared between primary tumors and metastases. We identified 14 canonical cancer gene mutations in this cohort of patients, defined as mutations that lead to amino acid changes identical to those found previously in cancer genes or disrupting mutations in tumor suppressor genes, all of which were shared between primary tumors and paired distant metastases. In addition, metastases resembled paired primary NSCLC tumors closely in regard to somatic copy number aberration profiles and mutation signatures. Pathway analysis from RNA-seq data demonstrated that 25 of the 35 signal transduction pathways that were significantly down regulated in metastases relative to primary NSCLC tumors were related to immune activation. Validation study with a larger patient cohort is in progress.

Conclusions: Although branched evolution is a common phenomenon during metastasis of NSCLC, majority of canonical cancer gene mutations are probably early molecular events likely acquired before metastasis initiates. Mutation mechanism may be determined early during carcinogenesis and preserved during cancer evolution even at the metastatic sites. Immune suppression may be one characteristic feature of cancer cells of metastatic capacity.

Citation Format: Jianjun Zhang, Chia-Chin Wu, Jianhua Zhang, Junya Fujimoto, Xingzhi Song, Xizeng Mao, Huadong Sun, Sahil Seth, Rebecca Thornton, Marcus Coyle, Latasha Little, Curtis Gumbs, Carmen Behrens, Chi-Wan Chow, Erik Sulman, Ganesh Rao, Stephen Swisher, Ignacio Wistuba, John Heymach, Andrew Futreal, Daniel Gomez. Integrated exome and transcriptome sequencing of primary lung cancers and paired distant metastases. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 156.

Abstract 2815: Antitumor activity of CDK4/6 inhibition in combination with radiation therapy on glioblastoma stem cells

Almost 80% of glioblastoma tumors have alterations in the CNKN2A-CDK-Rb pathway. Cyclin dependent kinases 4 and 6 (CDK4/6) act as cell cycle regulators and have been recognized as therapeutic targets for glioblastoma (GBM). In the current study, we determined the antitumor activity of CDK4/6 inhibition (palbociclib and abemaciclib) alone and in combination with radiation on a panel of glioblastoma stem cells (GSCs). The GSCs were molecularly characterized using multiple ‘omimcs’ techniques and Western blots identified specific phospho- and total protein levels. Approximately 50% of cell lines have homozygous deletion of CDKN2A although CDK4 and CDK6 protein expression was significantly elevated in most of the GSCs. RB protein was constitutively phosphorylated in only a subset (45%): GSC11, GSC262, GSC231, GSC304 and GSC7-2. In our panel of GSCs, there were total of three cell lines with CDKN2A loss, RB phosphorylation and CDK4/6 overexpression (GSC262, GSC11 and GSC231). Our data showed that GSC262, GSC11, GSC231 (CDKN2A deletion, RB intact), GSC7-2 and GSC300 (CDKN2A WT, RB intact) were sensitive to CDK4/6 treatment (IC50 ≤ 1μM). CDK4/6 inhibitor treated GSCs showed G1 cell cycle arrest and decreased phospho-RB levels in GSC262 and GSC7-2 cells. We next determined whether CDK4/6 inhibition combined with radiation has additive or synergistic antitumor effect. A clonogenic assay demonstrated that neurosphere formation was significantly decreased by CDK4/6 inhibition in combination with radiation compared to either treatment in GSC262 (resistant to radiation treatment) or GSC7-2 (sensitive to radiation treatment) cell lines. The radiation resistant GSC (GSC262) treated with radiation and CDK4/6 inhibitor became sensitive to radiation therapy whereas radiation sensitive GSC (GSC7-2) had a significant decrease in colony formation compared to radiation alone. CDK4/6 combined with radiation increased γ-H2AX protein expression levels and decreased cyclin D1 protein expression in a time dependent manner compared to single drug treatment. These data indicate synergistic antitumor effects of CDK4/6 inhibition combined with radiation therapy in GSCs in vitro. Further investigation is ongoing to evaluate this combination therapy.

Citation Format: Christopher Nguyen, Yuji Piao, Juan Emmanuel Martinez-Ledesma, Jianwen Dong, Soon Yeung Park, Roel Verhaak, Erik Sulman, John F. De Groot. Antitumor activity of CDK4/6 inhibition in combination with radiation therapy on glioblastoma stem cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2815.

Mesenchymal Stem Cells Isolated From Human Gliomas Increase Proliferation and Maintain Stemness of Glioma Stem Cells Through the IL-6/gp130/STAT3 Pathway

Although mesenchymal stem cells (MSCs) have been implicated as stromal components of several cancers, their ultimate contribution to tumorigenesis and their potential to drive cancer stem cells, particularly in the unique microenvironment of human brain tumors, remain largely undefined. Consequently, using established criteria, we isolated glioma-associated-human MSCs (GA-hMSCs) from fresh human glioma surgical specimens for the first time. We show that these GA-hMSCs are nontumorigenic stromal cells that are phenotypically similar to prototypical bone marrow-MSCs. Low-passage genomic sequencing analyses comparing GA-hMSCs with matched tumor-initiating glioma stem cells (GSCs) suggest that most GA-hMSCs (60%) are normal cells recruited to the tumor (group 1 GA-hMSCs), although, rarely (10%), GA-hMSCs may differentiate directly from GSCs (group 2 GA-hMSCs) or display genetic patterns intermediate between these groups (group 3 GA-hMSCs). Importantly, GA-hMSCs increase proliferation and self-renewal of GSCs in vitro and enhance GSC tumorigenicity and mesenchymal features in vivo, confirming their functional significance within the GSC niche. These effects are mediated by GA-hMSC-secreted interleukin-6, which activates STAT3 in GSCs. Our results establish GA-hMSCs as a potentially new stromal component of gliomas that drives the aggressiveness of GSCs, and point to GA-hMSCs as a novel therapeutic target within gliomas.

Abstract 3744: High-throughput in vitro screening of glioma stem cell lines: Evaluation of over 350 tyrosine kinase inhibitors

Despite the availability of hundreds of drugs, there is little data on the efficacy of these agents in the extremely heterogeneous populations of tumor cells observed in glioblastoma. A high-throughput compound-screening assay was used to identify drug sensitivities in a panel of glioma stem cell (GSC) lines to 350 tyrosine kinase inhibitors (GSK PKIS1) with varying cellular targets and mechanisms of kinase inhibition. Twelve glioma stem cell lines, which are representative of the classic TCGA molecular subtypes, were screened. Cell lines were screened in 384-well plates at a density of 1000 cells/well with drug concentrations of either 5 or 0.5 µM. Cell viability measurements were taken using Cell-Titer Glo five days after drug treatment and compared to control wells to calculate percentage inhibition. Compounds were defined as highly active (>90 % inhibition at 5µM; > 50% inhibition at 0.5µM), moderately active (>70% inhibition at 5µM; >30% inhibition at 0.5µM), or weakly active (>50% inhibition at 5µM; >15% inhibition at 0.5µM.) We identified three compounds that were highly active against eleven cell lines, three more compounds that were highly effective against at least seven cell lines, and seven additional compounds that were highly effective against at least four cell lines. The compounds in the screen were further analyzed by testing their inhibition efficacy against 220 kinases. A separate set of compounds containing molecularly targeted agents to TGF-beta, STAT3, PI3K and Notch were used for comparison of drug efficacy. Ongoing experiments are being performed to fully characterize the molecular phenotypes of the different GSC's by analyzing RNAseq, miRNA, the whole exome, the proteome, DNA methylation, and copy number variation. Integrating this information with the kinase and growth inhibition data will allow us to have a complete picture of the underlying mechanisms which drive resistance/sensitivity in GSC's. After determining which kinases are the most effective targets for the treatment of glioblastoma, promising compounds will be validated in intracranial in vivo xenograft models.

Citation Format: Craig Thomas, Ji Liang, Yuji Piao, Nghi Nguyen, Erik Sulman, Clifford Stephan, Alfred Yung, John F. de Groot. High-throughput in vitro screening of glioma stem cell lines: Evaluation of over 350 tyrosine kinase inhibitors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3744. doi:10.1158/1538-7445.AM2014-3744