Natalie K. Wolf

Forward genetic screen for malignant peripheral nerve sheath tumor formation identifies new genes and pathways driving tumorigenesis

Malignant peripheral nerve sheath tumors (MPNSTs) are sarcomas of Schwann cell lineage origin that occur sporadically or in association with the inherited syndrome neurofibromatosis type 1. To identify genetic drivers of MPNST development, we used the Sleeping Beauty (SB) transposon-based somatic mutagenesis system in mice with somatic loss of transformation-related protein p53 (Trp53) function and/or overexpression of human epidermal growth factor receptor (EGFR). Common insertion site (CIS) analysis of 269 neurofibromas and 106 MPNSTs identified 695 and 87 sites with a statistically significant number of recurrent transposon insertions, respectively. Comparison to human data sets identified new and known driver genes for MPNST formation at these sites. Pairwise co-occurrence analysis of CIS-associated genes identified many cooperating mutations that are enriched in Wnt/β-catenin, PI3K-AKT-mTOR and growth factor receptor signaling pathways. Lastly, we identified several new proto-oncogenes, including Foxr2 (encoding forkhead box R2), which we functionally validated as a proto-oncogene involved in MPNST maintenance.

A Sleeping Beauty forward genetic screen identifies new genes and pathways driving osteosarcoma development and metastasis

Osteosarcomas are sarcomas of the bone, derived from osteoblasts or their precursors, with a high propensity to metastasize. Osteosarcoma is associated with massive genomic instability, making it problematic to identify driver genes using human tumors or prototypical mouse models, many of which involve loss of Trp53 function. To identify the genes driving osteosarcoma development and metastasis, we performed a Sleeping Beauty (SB) transposon-based forward genetic screen in mice with and without somatic loss of Trp53. Common insertion site (CIS) analysis of 119 primary tumors and 134 metastatic nodules identified 232 sites associated with osteosarcoma development and 43 sites associated with metastasis, respectively. Analysis of CIS-associated genes identified numerous known and new osteosarcoma-associated genes enriched in the ErbB, PI3K-AKT-mTOR and MAPK signaling pathways. Lastly, we identified several oncogenes involved in axon guidance, including Sema4d and Sema6d, which we functionally validated as oncogenes in human osteosarcoma.

A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma

UNLABELLED Metastasis is the leading cause of death in patients with osteosarcoma, the most common pediatric bone malignancy. We conducted a multistage genome-wide association study of osteosarcoma metastasis at diagnosis in 935 osteosarcoma patients to determine whether germline genetic variation contributes to risk of metastasis. We identified an SNP, rs7034162, in NFIB significantly associated with metastasis in European osteosarcoma cases, as well as in cases of African and Brazilian ancestry (meta-analysis of all cases: P = 1.2 × 10(-9); OR, 2.43; 95% confidence interval, 1.83-3.24). The risk allele was significantly associated with lowered NFIB expression, which led to increased osteosarcoma cell migration, proliferation, and colony formation. In addition, a transposon screen in mice identified a significant proportion of osteosarcomas harboring inactivating insertions in Nfib and with lowered NFIB expression. These data suggest that germline genetic variation at rs7034162 is important in osteosarcoma metastasis and that NFIB is an osteosarcoma metastasis susceptibility gene. SIGNIFICANCE Metastasis at diagnosis in osteosarcoma is the leading cause of death in these patients. Here we show data that are supportive for the NFIB locus as associated with metastatic potential in osteosarcoma.

RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens

Forward genetic screens using Sleeping Beauty (SB)-mobilized T2/Onc transposons have been used to identify common insertion sites (CISs) associated with tumor formation. Recurrent sites of transposon insertion are commonly identified using ligation-mediated PCR (LM-PCR). Here, we use RNA sequencing (RNA-seq) data to directly identify transcriptional events mediated by T2/Onc. Surprisingly, the majority (∼80%) of LM-PCR identified junction fragments do not lead to observable changes in RNA transcripts. However, in CIS regions, direct transcriptional effects of transposon insertions are observed. We developed an automated method to systematically identify T2/Onc-genome RNA fusion sequences in RNA-seq data. RNA fusion-based CISs were identified corresponding to both DNA-based CISs (Cdkn2a, Mycl1, Nf2, Pten, Sema6d, and Rere) and additional regions strongly associated with cancer that were not observed by LM-PCR (Myc, Akt1, Pth, Csf1r, Fgfr2, Wisp1, Map3k5, and Map4k3). In addition to calculating recurrent CISs, we also present complementary methods to identify potential driver events via determination of strongly supported fusions and fusions with large transcript level changes in the absence of multitumor recurrence. These methods independently identify CIS regions and also point to cancer-associated genes like Braf. We anticipate RNA-seq analyses of tumors from forward genetic screens will become an efficient tool to identify causal events.

Modular assembly of transposon integratable multigene vectors using RecWay assembly

Studying complex biological processes such as cancer development, stem cell induction and transdifferentiation requires the modulation of multiple genes or pathways at one time in a single cell. Herein, we describe straightforward methods for rapid and efficient assembly of bacterial marker free multigene cassettes containing up to six complementary DNAs/short hairpin RNAs. We have termed this method RecWay assembly, as it makes use of both Cre recombinase and the commercially available Gateway cloning system. Further, because RecWay assembly uses truly modular components, it allows for the generation of randomly assembled multigene vector libraries. These multigene vectors are integratable, and later excisable, using the highly efficient piggyBac (PB) DNA transposon system. Moreover, we have dramatically improved the expression of stably integrated multigene vectors by incorporation of insulator elements to prevent promoter interference seen with multigene vectors. We demonstrate that insulated multigene PB transposons can stably integrate and faithfully express up to five fluorescent proteins and the puromycin-thymidine kinase resistance gene in vitro, with up to 70-fold higher gene expression compared with analogous uninsulated vectors. RecWay assembly of multigene transposon vectors allows for widely applicable modelling of highly complex biological processes and can be easily performed by other research laboratories.

Comparative transcriptome analysis quantifies immune cell transcript levels, metastatic progression and survival in osteosarcoma

Overall survival of patients with osteosarcoma (OS) has improved little in the past three decades, and better models for study are needed. OS is common in large dog breeds and is genetically inducible in mice, making the disease ideal for comparative genomic analyses across species. Understanding the level of conservation of intertumor transcriptional variation across species and how it is associated with progression to metastasis will enable us to more efficiently develop effective strategies to manage OS and to improve therapy. In this study, transcriptional profiles of OS tumors and cell lines derived from humans (n = 49), mice (n = 103), and dogs (n = 34) were generated using RNA sequencing. Conserved intertumor transcriptional variation was present in tumor sets from all three species and comprised gene clusters associated with cell cycle and mitosis and with the presence or absence of immune cells. Further, we developed a novel gene cluster expression summary score (GCESS) to quantify intertumor transcriptional variation and demonstrated that these GCESS values associated with patient outcome. Human OS tumors with GCESS values suggesting decreased immune cell presence were associated with metastasis and poor survival. We validated these results in an independent human OS tumor cohort and in 15 different tumor data sets obtained from The Cancer Genome Atlas. Our results suggest that quantification of immune cell absence and tumor cell proliferation may better inform therapeutic decisions and improve overall survival for OS patients.Significance: This study offers new tools to quantify tumor heterogeneity in osteosarcoma, identifying potentially useful prognostic biomarkers for metastatic progression and survival in patients. Cancer Res; 78(2); 326-37. ©2017 AACR.

Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays

The CRISPR/Cas9 system is an RNA guided nuclease system that evolved as a mechanism of adaptive immunity in bacteria. This system has been adopted for numerous genome engineering applications in research and recently, therapeutics. The CRISPR/Cas9 system has been largely implemented by delivery of Cas9 as protein, RNA, or plasmid along with a chimeric crRNA-tracrRNA guide RNA (gRNA) under the expression of a pol III promoter, such as U6. Using this approach, multiplex genome engineering has been achieved by delivering several U6-gRNA plasmids targeting multiple loci. However, this approach is limited due to the efficiently of delivering multiple plasmids to a single cell at one time. To augment the capability and accessibility of multiplexed genome engineering, we developed an efficient golden gate based method to assemble gRNAs linked by optimal Csy4 ribonuclease sequences to deliver up to 10 gRNAs as a single gRNA array transcript. Here we report the optimal expression of our guide RNA array under a strong pol II promoter. This system can be implemented alongside the myriad of CRISPR applications, allowing users to model complex biological processes requiring numerous gRNAs.

Abstract A36: Validation of candidate cancer genes using the CRISPR system

We have used Sleeping Beauty (SB) transposon mutagenesis to study the development of several types of sarcomas including osteosarcoma (OS) and malignant peripheral nerve sheath tumors (MPNST). This work has revealed the power of SB mutagenesis to identify critical genes and genetic pathways that, when altered, can cooperate to cause these tumors. We have discovered specific novel oncogenes, such as FOXR2 in MPNST and SEMA4D in OS, recurrent alterations in certain pathways, such as the Wnt/β−catenin pathway in MPNST, and information about what genetic alterations can cooperate in sarcomagenesis, such as loss of NF1 and PTEN in MPNST. We have functionally validated these genetic alterations in several ways, including the use of genetically engineered mouse (GEM) models and TAL effector nucleases (TALEN) or CRISPR RNA-guided Cas9 nuclease modified human cell lines. However, these studies typically analyzed only single candidates of great interest due to the alteration observed in comparative genomics analyses or novelty in the cancer field. In an attempt to further study our candidate cancer genes (CCGs) we have implemented the CRISPR nuclease system to perform a medium throughput screen of all candidate tumor suppressor genes (TSGs). To this end, we are generating and validating CRISPR gRNAs to target all TSGs identified in our MPNST and OS SB screens (~300 genes). Using immortalized human cell lines we have targeted these candidate TSGs and screened for their ability to increase colony formation in soft agar, migration, and xenograft tumor formation. We have identified numerous genes that when mutated by CRISPR resulted in increased tumorigenic properties. These genes are currently being tested for their ability to induce xenograft formation in immunocompromised mice. This CRISPR screen for MPNST and OS CCGs is ongoing and new results will be reported. Citation Format: Natalie Wolf, Branden Smeester, Madison Weg, David A. Largaespada, Branden Scott Moriarity. Validation of candidate cancer genes using the CRISPR system. [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 A36.

Abstract 64: Identification and validation of novel therapeutic targets of osteosarcoma using cutting edge technologies

Osteosarcomas are sarcomas of the bone, derived from osteoblasts or their precursors, with a high propensity to metastasize. The current treatment options have not changed over the last four decades and rely on tumor resection and nonspecific combination chemotherapy, resulting in a 5-year survival rate of 0-29% if clinically apparent metastases are present. Although these tumors are rare in humans, with ∼900 cases annually, they are highly prevalent in canines, with over 50,000 cases annually, and have seemingly similar genetics. Osteosarcoma is associated with massive genomic instability, making it problematic to identify driver genes using human tumors or prototypical mouse models, many of which involve loss of Trp53 function. To identify the genes driving osteosarcoma development and metastasis, we performed a Sleeping Beauty (SB) transposon-based forward genetic screen in mice with and without somatic loss of Trp53. Common insertion site (CIS) analysis of 119 primary tumors and 134 metastatic nodules identified 232 sites associated with osteosarcoma development and 43 sites associated with metastasis, respectively. Analysis of CIS- associated genes identified numerous known and new osteosarcoma-associated genes enriched in the ErbB, PI3K-AKT-mTOR, MAPK, and ERK5 signaling pathways. We identified several oncogenes involved in axon guidance, including Sema4d and Sema6d, which we functionally validated as oncogenes in human osteosarcoma. We have now begun pre-clinical testing of inhibitors of our top actionable targets to treat osteosarcoma, namely SEMA4D and CSF1R. Further, we have begun to validate top candidate metastasis genes using the CRISPR nuclease system in immortalized osteoblasts and osteosarcoma cell lines. Preliminarily we have found that loss of candidate osteosarcoma metastasis genes ANAPC1 or TOAK1 increases the migration capacity of immortalized osteoblasts, while loss of EXOC1 or GRLF increases their ability for anchorage independent growth in soft agar assay. Results of these ongoing studies will be presented. Citation Format: Branden Smeester, Natalie Wolf, Branden S. Moriarity. Identification and validation of novel therapeutic targets of osteosarcoma using cutting edge technologies. [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 64.

Coping with cancer genes altered by copy number.

Cancer is a genetically heterogeneous disease in which many, many genes or gene products have altered expression or activity due to a variety of genetic and epigenetic mechanisms. These alterations result in activation of oncogenic processes that do not occur in normal somatic cell counterparts. With advances in high-throughput sequencing and other technologies over the past decade, genomic analysis of various cancers has led to new insights of these oncogenic processes. It was recently discovered in a meta-analysis of many human tumor types, that they are characterized as having either a large number of somatic mutations (M class) or copy number of alterations (C class), but usually not both [1]. Many common and lethal human cancers, such as glioblastoma multiforme and acute myeloid leukemia, have been identified as M class tumors. Whole genome sequencing technologies (WGS) have identified many of the genes that drive these cancers when mutated, some of which are good targets for therapy. However, C class tumors present a challenge for the identification of drivers that would make good targets for therapy. This is because the gene copy number alterations often affect large regions of the genome, containing many genes, in any one case. Moreover, we know from recent chromosome engineering studies in mice, and other studies, that even low-level gene copy number alterations can contribute to the formation of cancer [2]. Being able to determine elusive C class driver genes could aid in our understanding of the oncogenic processes in these misunderstood tumors, and suggest new ways to treat these forms of cancer.