Leanne C. Sayles

Wilms tumor 1 (WT1) regulates KRAS-driven oncogenesis and senescence in mouse and human models

KRAS is one of the most frequently mutated human oncogenes. In some settings, oncogenic KRAS can trigger cellular senescence, whereas in others it produces hyperproliferation. Elucidating the mechanisms regulating these 2 drastically distinct outcomes would help identify novel therapeutic approaches in RAS-driven cancers. Using a combination of functional genomics and mouse genetics, we identified a role for the transcription factor Wilms tumor 1 (WT1) as a critical regulator of senescence and proliferation downstream of oncogenic KRAS signaling. Deletion or suppression of Wt1 led to senescence of mouse primary cells expressing physiological levels of oncogenic Kras but had no effect on wild-type cells, and Wt1 loss decreased tumor burden in a mouse model of Kras-driven lung cancer. In human lung cancer cell lines dependent on oncogenic KRAS, WT1 loss decreased proliferation and induced senescence. Furthermore, WT1 inactivation defined a gene expression signature that was prognostic of survival only in lung cancer patients exhibiting evidence of oncogenic KRAS activation. These findings reveal an unexpected role for WT1 as a key regulator of the genetic network of oncogenic KRAS and provide important insight into the mechanisms that regulate proliferation or senescence in response to oncogenic signals.

A Rare Population of CD24+ITGB4+Notchhi Cells Drives Tumor Propagation in NSCLC and Requires Notch3 for Self-Renewal

Sustained tumor progression has been attributed to a distinct population of tumor-propagating cells (TPCs). To identify TPCs relevant to lung cancer pathogenesis, we investigated functional heterogeneity in tumor cells isolated from Kras-driven mouse models of non-small-cell lung cancer (NSCLC). CD24(+)ITGB4(+)Notch(hi) cells are capable of propagating tumor growth in both a clonogenic and an orthotopic serial transplantation assay. While all four Notch receptors mark TPCs, Notch3 plays a nonredundant role in tumor cell propagation in two mouse models and in human NSCLC. The TPC population is enriched after chemotherapy, and the gene signature of mouse TPCs correlates with poor prognosis in human NSCLC. The role of Notch3 in tumor propagation may provide a therapeutic target for NSCLC.

Hypoxia in Models of Lung Cancer: Implications for Targeted Therapeutics

Purpose: To efficiently translate experimental methods from bench to bedside, it is imperative that laboratory models of cancer mimic human disease as closely as possible. In this study, we sought to compare patterns of hypoxia in several standard and emerging mouse models of lung cancer to establish the appropriateness of each for evaluating the role of oxygen in lung cancer progression and therapeutic response. Experimental Design: Subcutaneous and orthotopic human A549 lung carcinomas growing in nude mice as well as spontaneous K-ras or Myc-induced lung tumors grown in situ or subcutaneously were studied using fluorodeoxyglucose and fluoroazomycin arabinoside positron emission tomography, and postmortem by immunohistochemical observation of the hypoxia marker pimonidazole. The response of these models to the hypoxia-activated cytotoxin PR-104 was also quantified by the formation of γH2AX foci in vitro and in vivo. Finally, our findings were compared with oxygen electrode measurements of human lung cancers. Results: Minimal fluoroazomycin arabinoside and pimonidazole accumulation was seen in tumors growing within the lungs, whereas subcutaneous tumors showed substantial trapping of both hypoxia probes. These observations correlated with the response of these tumors to PR-104, and with the reduced incidence of hypoxia in human lung cancers relative to other solid tumor types. Conclusions: These findings suggest that in situ models of lung cancer in mice may be more reflective of the human disease, and encourage judicious selection of preclinical tumor models for the study of hypoxia imaging and antihypoxic cell therapies. Clin Cancer Res; 16(19); 4843–52. ©2010 AACR.

Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis

Lung cancer is the leading cause of cancer deaths worldwide, with the majority of mortality resulting from metastatic spread. However, the molecular mechanism by which cancer cells acquire the ability to disseminate from primary tumors, seed distant organs, and grow into tissue-destructive metastases remains incompletely understood. We combined tumor barcoding in a mouse model of human lung adenocarcinoma with unbiased genomic approaches to identify a transcriptional program that confers metastatic ability and predicts patient survival. Small-scale in vivo screening identified several genes, including Cd109, that encode novel pro-metastatic factors. We uncovered signaling mediated by Janus kinases (Jaks) and the transcription factor Stat3 as a critical, pharmacologically targetable effector of CD109-driven lung cancer metastasis. In summary, by coupling the systematic genomic analysis of purified cancer cells in distinct malignant states from mouse models with extensive human validation, we uncovered several key regulators of metastatic ability, including an actionable pro-metastatic CD109–Jak–Stat3 axis.

An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer

KRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report the identification of a common transcriptional signature across mutant KRAS cancers of distinct tissue origin that includes the transcription factor FOSL1. High FOSL1 expression identifies mutant KRAS lung and pancreatic cancer patients with the worst survival outcome. Furthermore, FOSL1 genetic inhibition is detrimental to both KRAS-driven tumour types. Mechanistically, FOSL1 links the KRAS oncogene to components of the mitotic machinery, a pathway previously postulated to function orthogonally to oncogenic KRAS. FOSL1 targets include AURKA, whose inhibition impairs viability of mutant KRAS cells. Lastly, combination of AURKA and MEK inhibitors induces a deleterious effect on mutant KRAS cells. Our findings unveil KRAS downstream effectors that provide opportunities to treat KRAS-driven cancers.

Abstract 07: Using copy number alterations to identify targeted therapies in a preclinical model of osteosarcoma

Osteosarcoma (OS) is an aggressive bone malignancy affecting approximately 400 pediatric patients in the United States annually. Compared with other pediatric cancers, OS has a low 5-year overall survival rate. There are few treatment options for patients that progress on standard therapy, making it important to identify new therapeutic targets for these high-risk patients. At the genomic level, OS is characterized by significant genomic instability, resulting in numerous copy number alterations (CNA) and structural variations (SV). Unfortunately, many of the CNAs and SV events are non-recurrent, making each disease highly patient-specific. We hypothesized that CNAs may be drivers of OS and that we could use patient-specific CNA profiles to identify actionable targets in OS. In order to test this in a preclinical setting, we have developed a robust program for generating and maintaining patient-derived xenografts (PDX) from patients with OS. In a pilot study of 3 patients, we used a combination of tumor/normal whole-genome sequencing (WGS) and commercial gene panel testing to identify potentially druggable targets using CNA. For samples tested with WGS, gene-level CNA was assessed for a number of clinically actionable genes. For each gene, CNA was determined using the normalized ratio of sequencing reads mapped to the gene in the tumor versus the normal sample. The degree of CNA was used to help prioritize potential targets. For the commercially tested samples, genes were either reported as amplified or not. Using these results to inform target selection, we treated each PDX with a drug matched to its corresponding CNA predicted target. In each sample, we saw a significant reduction in the growth rate of the PDX compared to vehicle or a non-matched drug. This suggests that using the patient-specific CNAs to identify drug targets may be an effective strategy in the treatment of OS. Citation Format: Marcus R. Breese, Leanne C. Sayles, Alejandro Sweet-Cordero. Using copy number alterations to identify targeted therapies in a preclinical model of osteosarcoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 07.

Abstract B28: Genomic analysis of osteosarcoma for identification of targeted therapies

Osteosarcoma (OS) is an aggressive pediatric bone malignancy that affects 400 children per year in the United States. OS is characterized by genomic instability and numerous copy number alterations (CNA). We hypothesized that CNA may be drivers of OS and that targeting cancer genes with CNAs may be a novel approach for treatment of OS. We have established a robust approach for generation of patient-derived xenografts (PDX) from patients with OS. To date, 15 PDX have been established from OS patients. Using whole-genome sequencing (WGS), we have identified possible target CNAs for individual patients and are currently testing them in their corresponding PDX. In two patients, an amplification in c-myc suggested possible susceptibility to the BRD4 inhibitor JQ1 or the CDK9 inhibitor AT7519. In a third patient sample, amplification of Cyclin D and Cyclin E in the setting of wild-type Rb suggested responsiveness to a CDK inhibitor. A fourth patient had a FOXM1 amplification which suggests a vulnerability to Palbociclib, a CDK4/6 specific inhibitor. This patient sample also had an Aurora kinase B amplification, suggesting susceptibility to inhibition of this kinase as a therapeutic approach. We treated the corresponding PDX with the drug predicted to target the patient sample based on CNA. In all cases, treatment of the PDX with the drugs predicted show a significant reduction in tumor growth compared to vehicle alone or to the drugs predicted for the other patient CNAs. As a follow up we are currently submitting several more patient samples and paired PDX for WGS as well as RNAseq to determine other potential targeted therapeutics based on CNA. In summary, our work suggests that WGS can be used to identify potential novel therapies for patients with OS. Further work will be needed to determine whether response in PDX models correlates with clinical response in patients. Citation Format: Leanne Sayles, Marcus Breese, E. Alejandro Sweet-Cordero. Genomic analysis of osteosarcoma for identification of targeted therapies. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B28.

Abstract A35: Characterization of the genomic landscape of osteosarcoma metastasis

Early metastasis to the lungs is a cardinal feature of osteosarcoma (OS), and complications from metastatic disease remain the most common cause of cancer-related death. Despite the prevalence of metastasis in OS, the pathogenesis is poorly understood. We have established a collection of 16 patient-derived xenografts (PDX) from human OS tumors, both from the primary site as well as metastasis. Our collection includes 9 diagnostic biopsies from primary site tumors, 2 primary tumor resections, 3 lung metastases, and 1 ascites fluid metastasis. Gene expression analysis of an initial set of 5 PDX models (3 metastases, 2 primaries) has been completed. A more extensive analysis of all 16 models by RNAseq and WGS is currently underway. Preliminary gene expression analysis identified a significant number of genes differentially expressed between metastatic samples and non-metastatic samples. This list included genes associated with cell adhesion and motility such as MEGF10, genes associated with endochondral ossification and bone remodeling such as RANKL, and genes associated with deposition of extracellular matrix (ECM) such as COL21A. Another candidate gene, ENPP1, is responsible for mineralization of the ECM and has been implicated in breast cancer metastasis to bone. We have validated differential expression of a number of these genes in independent samples of metastatic OS. We are currently using small hairpin RNA (shRNA), CRISPR, and overexpression vectors to knockdown, silence, and overexpress ENPP1 and other candidate genes in OS cell lines. Using in vitro migration and invasion assays as well as intravenous injection and orthotopic mouse models, we are characterizing the contribution of candidate genes to the metastatic propensity of OS. Citation Format: Amanda L. Koehne, Leanne C. Sayles, Marcus R. Breese, Dedeepya Vaka, Alejandro Sweet-Cordero. Characterization of the genomic landscape of osteosarcoma metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A35.

Abstract 502: Copy number alterations identify targeted therapies in preclinical models of osteosarcoma

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA Osteosarcoma (OS) is an aggressive pediatric bone malignancy that affects 400 children per year in the United States. It has one of the lowest 5 yr. survival rates of any pediatric cancer. OS is characterized by genomic instability and numerous copy number alterations (CNA). We hypothesized that CNA may be drivers of OS and that targeting cancer genes with CNAs may be a novel approach for treatment of OS. We have established a robust approach for generation of patient-derived xenografts (PDX) from patients with OS. To date, 12 PDX have been established from OS patients. Using whole-genome sequencing (WGS), we have identified possible target CNAs for individual patients and are currently testing them in their corresponding PDX. In one patient, an amplification in c-myc suggested possible susceptibility to the bromodomain inhibitor JQ1. In a second patient sample, amplification of Cyclin D1 in the setting of p16 loss and wild-type Rb suggested responsiveness to a CDK4/6 specific inhibitor. This patient sample also has an Aurora kinase B amplification, suggesting susceptibility to inhibition of this kinase as a therapeutic approach. We treated the corresponding PDX with the drug predicted to target the patient sample based on CNA. In one case, JQ1 treatment inhibited tumor growth in the PDX generated from the patient sample with c-myc amplification. In the second case, Aurora kinase B inhibition arrested tumor growth in the PDX harboring the Aurora kinase B amplification. We are currently testing whether CDK4/6 inhibition is sufficient to inhibit tumor growth as predicted by WGS. As a follow up we are currently submitting several more patient samples and paired PDX for WGS as well as RNAseq to determine other potential targeted therapeutics based on CNA. In summary, our work suggests that WGS can be used to identify potential novel therapies for patients with OS. Further work will be needed to determine whether response in PDX models correlates with clinical response in patients. Citation Format: Leanne C. Sayles, Marcus Breese, Alejandro Sweet-Cordero. Copy number alterations identify targeted therapies in preclinical models of osteosarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 502. doi:10.1158/1538-7445.AM2015-502

Abstract A78: Using primary osteosarcoma samples to study tumor heterogeneity

Osteosarcoma (OS) is an aggressive pediatric bone malignancy that affects 400 children per year in the United States. It has one of the lowest 5 yr. survival rates of any pediatric cancer. In order to gain a better understanding of the pathogenesis of OS, we have established a panel of patient derived xenografts (PDX). Through a three institution collaboration, we have obtained 52 OS patient samples, 38 pre-chemotherapy biopsies and 16 post induction chemotherapy resections. These samples were implanted into immunocompromised mice either subrenal or intradermal and allowed to expand. We were able to generate 20 PDX samples (38% take rate) and have characterized 7 of them. This includes one pre and post-chemo pair from the same patient. The PDX samples had similar histology to the original patient biopsy including formation of osteoid, which is a hallmark of OS. Tumor propagating cells (TPCs) are a rare subset of cells with in the tumor that are thought to contain the properties necessary to propagate and give rise to all cells found in the original tumor. TPCs are also thought to be resistant to chemotherapy and thus, it is important to identify and study these cells to gain a better understand the biology that underlies the TPCs ability to propagate the tumor. To identify the TPCs in OS, we selected a panel of cell surface markers that have been associated with TPCs in other cancer types and assessed for their expression across multiple OS PDX samples. CD49f, CD146 and CD90 were expressed heterogeneously in most PDX samples. There was also a high degree of overlap in the expression of these three markers in a subset of OS cells. To determine if the heterogenenous staining observed has a biological significance, we sorted CD49f positive and negative cells and implanted them in serial dilutions into immunocompromized mice. Although no difference in tumor instance was observed, CD49f + tumor cells formed significantly larger tumors than those arising from CD49f- tumor cells. Thus, CD49f expression may mark a more proliferative subset of cells within the bulk tumor. Further studies are currently ongoing to define the functional relevance of CD146 and CD90 expression and their role in tumor propagation and tumor morphology using OS PDX samples. To further characterize these OS PDX samples, we have employed RNA sequencing technology. To date we have obtained RNAseq on 4 pre-chemotherapy and 3 post-chemotherapy patient samples. Analysis of this dataset is ongoing and may provide insight into mechanisms of chemoresistance. Citation Format: Leanne C. Sayles, Justin Vincent-Tompkins, Charles Chan, Irving Weissman, E. Alejandro Sweet-Cordero. Using primary osteosarcoma samples to study tumor heterogeneity. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A78.