Functional genomics of human clear cell sarcoma: genomic, transcriptomic and chemical biology landscape for clear cell sarcoma

BACKGROUND

Systemic therapy for metastatic clear cell sarcoma (CCS) bearing EWSR1-CREB1/ATF1 fusions remains an unmet clinical need in children, adolescents, and young adults.

METHODS

To identify key signaling pathway vulnerabilities in CCS, a multi-pronged approach was taken: (i) genomic and transcriptomic landscape analysis, (ii) integrated chemical biology interrogations, (iii) development of CREB1/ATF1 inhibitors, and (iv) antibody-drug conjugate testing (ADC). The first approach encompassed DNA exome and RNA deep sequencing of the largest human CCS cohort yet reported consisting of 47 patient tumor samples and 8 cell lines.

RESULTS

Sequencing revealed recurrent mutations in cell cycle checkpoint, DNA double-strand break repair or DNA mismatch repair genes, with a correspondingly low to intermediate tumor mutational burden. DNA multi-copy gains with corresponding high RNA expression were observed in CCS tumor subsets. CCS cell lines responded to the HER3 ADC patritumab deruxtecan in a dose-dependent manner in vitro, with impaired long term cell viability.

CONCLUSION

These studies of the genomic, transcriptomic and chemical biology landscape represent a resource 'atlas' for the field of CCS investigation and drug development. CHK inhibitors are identified as having potential relevance, CREB1 inhibitors non-dependence of CCS on CREB1 activity was established, and the potential utility of HER3 ADC being used in CCS is found.

Abstract B027: The development of a multiscale transcriptional atlas of sarcoma

Objectives: Sarcomas are mesodermal cancers of bone and soft tissue of which there are >60 malignant varieties, many of which can be difficult to diagnose or subtype using traditional histopathology. A universal molecular definition of sarcoma types would therefore be an invaluable tool to the diagnostic pathologist. RNA has the potential to offer a complimentary perspective to cytogenetic- and methylation-based diagnostics, as it represents the active state of the disease at sampling and better reveals its phenotype. Recognizing the potential for RNA-based classification, we set out to create a first-generation transcriptional atlas of sarcoma. Methods: To develop transcriptional definitions of cancers with the potential to further subclassify tumor types, we designed a self-optimizing and scale-adaptive unsupervised method (RACCOON), which groups samples into hierarchically organized clusters. We used this approach on the UCSC Treehouse Childhood Cancer Compendium, a set of 2,178 pediatric and 9,400 adult tumors, 1,130 of which are sarcomas, as well as 1,735 non-neoplastic samples. We then trained an ensemble of convolutional neural networks to classify tumors to these transcriptional clusters. We have now added 624 more sarcoma samples from Toronto centers and international collaborators to better represent the breadth of sarcoma. We are actively sequencing 500 additional samples in partnership with the Gabriella Miller Kids First Research Program to yield an expanded cohort of >2,200 uniformly processed and analyzed sarcomas. Results: Sarcomas organize into two clusters at the highest hierarchical level: one characterized by entities which occur primarily in adults and resemble mature tissue, the other by primarily pediatric entities which exhibit high stemness and resemble embryonic tissue. Several included entities are not bona fide sarcomas but originate from the mesoderm (e.g., Wilms Tumor) signifying a common transcriptional identity for mesodermal neoplasms. Additionally, we demonstrate the first transcriptional subtypes of central osteosarcoma reflecting its major histotypes and representing divergent clinical courses. We also determine Ewing Sarcoma (ES) to be a distinct entity which clusters separately from all other cancers, raising questions of its origin and affinity to sarcoma. When classifying ongoing patients to the atlas, we correctly classified >85% of tumors and corrected the diagnosis of 7%. We find 14% of ES in our dataset were likely misdiagnosed CIC- or BCOR-driven sarcomas. Critically, assigned subtypes are consistent between primary and relapse pairs. Conclusion: RNA-seq is a promising tool for both subtype discovery and classifying sarcoma in ongoing patients. We have already included this tool in tumor boards to help inform patient care. Our method reveals the overarching organization of sarcoma for the first time and specifies its underlying biology. This atlas is ever-growing and is open to the community to contribute.

Citation Format: Joshua O. Nash, Federico Comitani, Rose Chami, Sarah Cohen-Gogo, Astra Chang-Schwertschkow, Yael Babichev, Jodi Lees, Noa Alon, Nalan Gokgoz, Stephen Man Yu, Kyoko Yuki, Miranda Lorenti, Zhanqin Liu, Alaina McGoey, Famida Spatare, Bernarld Castro, Kim Tsoi, Hagit Peretz Soroka, Jack Brzezinski, Anita Villani, Albiruni Razak, Abha Gupta, Elizabeth Demicco, Gino Somers, Brendan C. Dickson, Jay S. Wunder, Irene L. Andrulis, David Malkin, Rebecca A. Gladdy, Adam Shlien. The development of a multiscale transcriptional atlas of sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B027.

Abstract 5112: Investigating the use of circulating tumor DNA for sarcoma management

Circulating tumor DNA (ctDNA) has the potential to detect sarcoma recurrence and metastasis but requires highly sensitive methods to detect and quantify genetic variants present in very low quantities. Plasma was isolated from 20mL peripheral blood samples collected from over 400 pre-operative sarcoma patients, and matched tumor samples from surgical resection were frozen and stored. Cell-free DNA (cfDNA) extracted from plasma was quantified using qPCR, and the quality was assessed using capillary electrophoresis. A subset of these cases were selected for whole exome sequencing (WES). WES of bulk tumor and whole blood samples identified tumor-specific genetic alterations, which then serve as personalized biomarkers of tumor DNA in patient plasma. We previously showed that droplet digital PCR (ddPCR) can detect and quantify ctDNA, by targeting patient-specific variants. However, ddPCR is limited in that it can only investigate one tumor variant sequence at a time. The purpose of the present study is to investigate methods of targeting multiple tumor variants simultaneously, increasing the chances of detecting ctDNA in patient blood. To this end, four cases were selected for multiplex PCR (mPCR) followed by targeted amplicon sequencing. For each case, six to eight of the tumor variants identified by WES were selected as targets, and primers were designed to amplify these sequences concurrently by mPCR. The amplicons will then be sequenced to detect the tumor variants. Additionally, two of the four cases have plasma collected at two different time points. To assess the viability of this method as a way to monitor disease surveillance, these cfDNA samples will be compared to determine how the abundance and nature of ctDNA changes over time. To date, cfDNA has been extracted from over 100 cases, the majority of which were positive for cfDNA. For each of the cases whole exome sequenced, a variety of tumor-specific variations were identified. The variants chosen as targets were selected based on having the highest variant allele frequency (VAF), with priority being given to mutations that alter the protein coding sequence. Thus far, mPCR primers have been designed and optimized for four separate cases. Across all cases analyzed by amplicon sequencing, the variant sequences could be detected in the amplicons generated by mPCR of tumor DNA. Furthermore, amplicon sequencing was able to recapitulate the variant allele frequency observed in WES. This indicates that the mPCR successfully amplified the sequences of interest in the tumor DNA, and that the sequencing results are accurate. Furthermore, no tumor variants were detected in the amplicons generated from blood DNA, which is to be expected. The cfDNA amplicons for these cases will be sequenced in this manner to investigate the presence of ctDNA. If successful, the ability to detect ctDNA in plasma will be an important first step in developing a testing protocol for clinical use.

Citation Format: Paige Darville-O'Quinn, Nalan Gokgoz, Kim M. Tsoi, Jay S. Wunder, Irene L. Andrulis. Investigating the use of circulating tumor DNA for sarcoma management [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5112.

Abstract 5400: Detection of satellite tumor cells in peritumoral edema in myxofibrosarcoma and undifferentiated pleomorphic sarcoma using targeted gene sequencing

Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcomas (UPS) are soft tissue sarcomas with high local recurrence rates following resection. Common with these cancers is peritumoral edema, termed tumor tails, which our group has found could contain satellite tumor cells. A precise and accurate method of determining the presence of satellite tumor cells in this region is required to improve surgical planning, as the standard morphology-based technique is prone to misclassification. An emerging technology is targeted gene sequencing (t-NGS), a combination of whole genome or exome sequencing (WGS/WXS) comparing primary tumor and patient-matched blood, and digital droplet PCR (ddPCR). The objective of this study was to determine the viability of t-NGS in the detection of satellite tumor cells in the areas of edema surrounding MFS and UPS. A cohort of patients diagnosed with extremity MFS and UPS at Mount Sinai Hospital (Toronto, Canada) who underwent resection were retrospectively studied. Cases with available WGS/WXS data were used (n=8) to identify case-specific tumor-specific variants (TSV) to detect with the QX200 ddPCR platform. (n=4-5/case). Cases with a major TSV-positive droplet population in the tumor tails tissue indicated the presence of satellite tumor cells. Our quality analysis showed DNA above the ddPCR threshold of detection was extracted from the tumor tails of 6 of 8 cases. The ddPCR assay showed that a TSV-positive droplet population was detected within the tumor tails in 5 of 6 cases, while 1 of 6 cases showed no such population in the tumor tails. Overall, our results indicates that t-NGS has potential for TSV detection within tumor tails. A prospective study is underway to further test its validity and compare it with standard histology. The project aims to improve surgical planning by ensuring removal of satellite tumor cells while lowering the risk of wound complications.

Targeted gene-sequencing results of all cases within this study Case # Histology Pre-op Radiation DNA Extraction Successful TSV Probes (n) TSV+ Tumor TSV+ Tails TSV+ Normal 1 MFS N Y 5 4 4 0 2 MFS N Y 3 2 2 0 3 MFS Y Y* (normal insufficient) 3 3 0 N/A 4 UPS Y Y 3 2 0 1 5 MFS N Y 4 4 1 0 6 UPS N Y 3 3 3 1 7 MFS Y N N/A N/A N/A N/A 8 MFS Y N N/A N/A N/A N/A

Citation Format: Miguel Alfonso V. Principe, Nalan Gokgoz, Patrick Prochazka, Peter C. Ferguson, Simin Dewji, Jay S. Wunder, Irene A. Andrulis, Brendan C. Dickson, Kim M. Tsoi. Detection of satellite tumor cells in peritumoral edema in myxofibrosarcoma and undifferentiated pleomorphic sarcoma using targeted gene sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5400.

Abstract 5609: Investigating the undifferentiated pleomorphic sarcoma microenvironment through cytokine profiles of primary tumor and immune infiltrates

Sarcoma is a heterogeneous group of connective tissue cancers with over 60 subtypes. Curative treatment relies on surgical resection combined with radiation. In the event of metastasis, chemotherapy is used but generally only with palliative intent. Given the heterogeneity of sarcomas, targeted therapies are limited, which has contributed to the relatively stagnant survival rates seen in the past decades.

Objective: Personalized treatments, such as adoptive cell therapy (ACT), may be promising for select sarcoma patients, specifically those with Undifferentiated Pleomorphic Sarcoma (UPS). To better understand ACT’s feasibility for UPS, we aim to investigate the intersection of tumor-infiltrating lymphocytes (TILs) and tumor cells by examining their cytokine output, whose role remains largely unstudied.

Methods: Tissue samples from untreated sarcoma patients have been collected and viably preserved by our group. The samples were processed for in vitro expansion of tumor or TIL cell lines. Tumor cultures were validated with Whole Exome Sequencing (WES) to ensure tumor-specific variations were retained. TILs were isolated with tumor fragment (TF) processing and magnetic bead coated anti-CD3/CD28 Rapid Expansion Protocol (REP). After validating tumor cultures, both tumor and TIL-secreted cytokines were evaluated using Luminex assays.

Results: Of the 11 primary UPS samples cultured, 10 generated viable cell cultures as defined by the presentation of stable growth beyond passage 5. A total of 3 cell lines were selected for further validation, and through WES, retained tumor specific variations beyond passage 5. On the other hand, the sarcoma-optimized TF and REP protocols expanded TILs from 7 of 8 UPS cases and yielded up to 6 x 10^7 cells. Although IL-2 is commonly used to facilitate TIL growth, it can also cause activation-induced cell death which is problematic for therapy. We demonstrated that an alternative γ-chain interleukin, IL-15, can support UPS TIL growth comparable to IL-2. Unbiased cytokine screening detected anti-tumoral CXCL9/IFN-γ and pro-tumoral IL-10/TGF-Beta as highly secreted by TIL cultures while some tumor cultures secreted relatively high concentrations of IL-6 and CCL2.

Conclusion: We developed a robust in vitro pipeline to expand sarcoma tumor cultures and TILs for downstream characterization. Functional assays aimed at dissecting the consequences of tumor-mediated IL-6 secretion are underway. These include siRNA-induced knock downs of genes hypothesized to augment the cytokine profile of tumor cells. Future evaluation of TILs will identify their clinical efficacy via flow cytometry and intracellular cytokine staining. Understanding cytokine secretion from both the tumor and immune components of sarcoma will aid in elucidating interactions within the microenvironment that may be therapeutically relevant.

Citation Format: Victoria Coward, Jacky Chen, Nalan Gokgoz, Kim Tsoi, Jay S. Wunder, Irene L. Andrulis. Investigating the undifferentiated pleomorphic sarcoma microenvironment through cytokine profiles of primary tumor and immune infiltrates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5609.

Investigating the Potential of Isolating and Expanding Tumour-Infiltrating Lymphocytes from Adult Sarcoma

Simple Summary

Sarcomas are rare cancers that arise from connective tissue. There are more than 50 subtypes, many of which are associated with a high risk of metastasis and poor prognosis. Subtype-specific treatment is limited and conventional treatment for advanced disease has varying effects across individuals and tumour subtypes. Adoptive cell therapy shows potential to provide more personalized treatment; this study aims to explore the potential of using tumour-infiltrating lymphocytes (TIL) to treat sarcoma. We optimized a sarcoma-specific expansion protocol and successfully expanded TILs from 54 of 92 sarcoma specimens. We characterized primarily CD4⁺ and CD8⁺ T-cells in the expanded TIL cultures and demonstrated their reactivity to general stimuli. Although sarcomas in general do not have abundant lymphocytic infiltration, our expansion protocol allowed for successful expansions of viable and reactive lymphocytes, thus showing the prospects of adopting TIL therapy in sarcoma.

Abstract

Sarcomas are a heterogeneous group of mesenchymal neoplasms, many of which are associated with a high risk of metastasis and poor prognosis. Conventional chemotherapy and targeted therapies have varying effects across individuals and tumour subtypes. The current therapies frequently provide limited clinical benefit; hence, more effective treatments are urgently needed. Recent advances in immunotherapy, such as checkpoint inhibition or adoptive cell therapy (ACT), show potential in increasing efficacy by providing a more personalized treatment. Therapy with tumour-infiltrating lymphocytes (TILs) is an emerging field in immunotherapy. Here, we collected 190 sarcoma tumour specimens from patients without pre-operative adjuvant treatment in order to isolate TILs. We compared different methods of TIL expansion and optimized a protocol specifically for efficacy in culturing TILs from sarcoma. The expanded TIL populations were characterized by flow cytometry analysis using CD3, CD4, CD8, CD14, CD19 and CD56 markers. The TIL populations were non-specifically stimulated to establish TIL reactivity. Through an optimized expansion protocol, TILs were isolated and cultured from 54 of 92 primary sarcoma specimens. The isolated TILs varied in CD4⁺ and CD8⁺ T-cell compositions and retained their ability to release IFNγ upon stimulation. Our results suggest that certain sarcoma subtypes have the potential to yield a sufficient number of TILs for TIL therapy.

168 Expanding and characterizing tumor infiltrating lymphocytes from myxofibrosarcoma and undifferentiated pleomorphic sarcoma

Background

Sarcoma is a group of rare bone and soft tissue tumors with over 50 distinct subtypes. Survival rate ranges widely due to the lack of efficacious treatments. Immunotherapy, such as adoptive cell therapy (ACT), has drawn significant interest due to its minimal toxicity. In ACT, tumor infiltrating lymphocytes (TILs) are isolated from patients, expanded, and autologously infused back. We recently observed TILs’ presence in Undifferentiated Pleomorphic Sarcoma (UPS) and Myxofibrosarcoma (MFS) tumors and found that tumor’s PD-L1 overexpression is correlated with better clinical outcome in UPS but not MFS.1 The Th1 anti-tumoral inflammatory pathway was highly activated in the former cohort, which may explain the favorable outcome. We hypothesize that there are phenotypic and functional differences between TILs of UPS with differential PD-L1 expression, which may be related to clinical outcomes. However, sarcoma TILs are rare and challenging to culture, which significantly impedes their studies. We first aim to robustly expand sarcoma TILs to sufficient numbers.

Methods

Tumors’ PD-L1 expression was determined by RT-qPCR (table 1). To initiate the tumor-fragment (TF) method of TIL culturing, primary tumors were fragmented and cultured in IMDM, IL-2, and 10% HSA. We further optimized the TF protocol to expand rare sarcoma TILs. Rapid expansion protocol (REP) with anti-CD3/anti-CD28 co-stimulating beads was employed for additional expansion. During REP, TILs were co-treated with gamma-chain cytokines (IL-2, 7, 15, 21).

Results

Of the 15 MFS TIL populations expanded, only 40% achieved sufficient growth (1x106) for analysis (figure 1A). Our optimized TF protocol expanded TILs from 8 UPS cases with a 62.5% success rate (figure 1B). UPS TILs were further stimulated with REP and various gamma-chain cytokine treatments. In ACT, prolonged culturing with IL-2 is known to cause activation-induced cell death, problematic in clinical treatments. We demonstrated that treatments with a Trio-cocktail (IL-7, 15, and 21) or IL-15 alone can achieve TIL proliferation comparable to that of IL-2 (figure 2).

Abstract 168 Figure 1

Initial TIL Culturing with Tumor Fragment Method. Figure A.. The traditional tumor fragment protocol was used to expand TILs of four MFS cases. TILs were cultured and expanded from primary tumor fragments in IL-2 (6000IU/mL) supplemented complete media (CM) over four weeks in duration. Fifteen TIL populations were derived from the four MFS cases. Populations were categorized based on their growth rates and labeled as ‘1’ or ‘2’ representing ‘fast’ or ‘slow’ growing TILs, respectively. Additional populations ‘A’ and ‘B’ represent biological replicates. Population TIL164 ‘2’ had no replicates. At Week 4, populations’ cell counts were determined via hemocytometer. As shown, only 6 out of 15 populations achieved > 1x10^6 cells (40% success rate). Figure B. An optimized tumor fragment protocol was used to expand TILs of eight UPS cases. Optimization includes shortening the culturing duration from four weeks to two weeks, reducing frequency of cell culture disruption, and adjusting cell culture environments. TILs were expanded from primary tumor fragments in CM over two weeks in duration. At Week 2, populations’ cell counts were determined via hemocytometer. As shown, 5 out of 8 cases achieved >1x10^6 cells (62.5% success rate).

Abstract 168 Figure 2

Gamma-chain cytokine treatments of UPS TILs. Gamma-chain cytokine treatments of UPS TILs with CD3/CD28 stimulation. Magnetic Dynabeads coated with CD3 and CD28 monoclonal antibodies were used to stimulate cells at a bead to cell ratio of 1:3. In ACT, IL-2 is a gold-standard cytokine that facilitates potent T-cell growth. However, it is known to cause activation-induced cell death. Resulting TIL population also possesses an exhausted-effector phenotype with low durability. UPS TIL Case 52 and Case 166 were treated with various interleukins during two weeks of REP, including gamma-chain IL-7, 15, 21 and inflammatory IL-12. IL-7, IL-12, and IL-21 individually did not elicit significant T-cell growth. IL-15 alone and in combination with IL-7 and IL-21 yield growth comparable to IL-2. IL-2 was obtained from Novartis (50ng/mL). All other cytokines were obtained from PeproTech (25ng/mL).

Abstract 168 Table 1

Tumor PD-L1 RNA Expression. Four MFS and eight UPS cases were processed. Tumors’ PD-L1 RNA expression was determined via RT-qPCR and evaluated as a ratio with the housekeeping gene STAM2. TIL359’s PD-L1 status has yet to be evaluated.

Conclusions

Sarcoma infiltrates are difficult to culture, and their roles remain largely unstudied. By optimizing the TF protocol in conjunction with anti-CD3/CD28 treatments, we developed a robust in vitro pipeline to expand rare sarcoma TILs, enabling downstream characterization. We also demonstrated the potential for alternate gamma-chain cytokines to favorably replace IL-2 during TIL expansion. Future phenotypic and functional evaluation of UPS TILs would elucidate the impact of tumors’ differential PD-L1 expression on UPS patients‘ prognoses. These findings would inform the implementation of ACT in sarcoma treatments.

References

Wunder J, Lee M, Nam J, Lau B, Dickson B, Pinnaduwage D, Bull S, Ferguson P, Seto A, Gokgoz N, Andrulis I. Osteosarcoma and soft-tissue sarcomas with an immune infiltrate express PD-L1: relation to clinical outcome and Th1 pathway activation. Onco Immunology 2020;9: e1737385-1- e1737385-13.

Ethics Approval

Patients provided signed consent before study entry, as approved by Mount Sinai Hospital’s Ethics Board (REB#01-0138-U).

Detection and utility of cell-free and circulating tumour DNA in bone and soft-tissue sarcomas

Aims

Cell-free DNA (cfDNA) and circulating tumour DNA (ctDNA) are used for prognostication and monitoring in patients with carcinomas, but their utility is unclear in sarcomas. The objectives of this pilot study were to explore the prognostic significance of cfDNA and investigate whether tumour-specific alterations can be detected in the circulation of sarcoma patients.

Methods

Matched tumour and blood were collected from 64 sarcoma patients (n = 70 samples) prior to resection of the primary tumour (n = 57) or disease recurrence (n = 7). DNA was isolated from plasma, quantified, and analyzed for cfDNA. A subset of cases (n = 6) underwent whole exome sequencing to identify tumour-specific alterations used to detect ctDNA using digital droplet polymerase chain reaction (ddPCR).

Results

Cell-free was present in 69 of 70 samples above 0.5 ng/ml. Improved disease-free survival was found for patients with lower cfDNA levels (90% vs 48% at one-year for ≤ 6 ng/ml and > 6 ng/ml, respectively; p = 0.005). Digital droplet PCR was performed as a pilot study and mutant alleles were detectable at 0.5% to 2.5% of the wild type genome, and at a level of 0.25 ng tumour DNA. Tumour-specific alterations (ctDNA) were found in five of six cases.

Conclusion

This work demonstrates the feasibility and potential utility of cfDNA and ctDNA as biomarkers for bone and soft-tissue sarcomas, despite the lack of recurrent genomic alterations. A larger study is required to validate these findings.

Cite this article: Bone Joint Res 2021;10(9):602–610.

Inhibition of P53-mediated cell cycle control as the determinant in dedifferentiated liposarcomas development

Liposarcomas are a heterogeneous group of sarcomas, including well-differentiated and dedifferentiated liposarcoma, myxoid/round cell liposarcoma, and pleomorphic liposarcoma. Complete surgical resection is the key of treatment. Radiotherapy, based on the tumor grade and the vicinity of critical structures with the tumor, can be used to prevent local recurrence. The group of dedifferentiated liposarcomas (DDLS) is poorly sensitive to adjuvant chemotherapy. Improved understanding of the genetic aberrations that lead to liposarcoma initiation is necessary for the development of targeted therapies to improve tumor control and survival. DDLS share genetic abnormalities with other groups, exhibiting high-level amplifications of chromosome 12, including the MDM2 and CDK4 genes, and harbor additional amplifications of chromosomes 6 and 1. Novel therapies targeted at the gene products of chromosome 12 are currently considered in clinical trials. Our work consisted in a genomic characterization of DDLS to draw up a complete picture of alterations, including genomic signatures, tumor mutation burden, gene mutations, copy number variations, translocations, gene fusions and methylation modifications. Analysis of translocations helped to understand the mechanisms underlying the amplification processes. Combination of mutations and loss of heterozygosity or homozygous deletions were detected and led to inactivate tumor suppressor genes (TSG). In contrast, methylation anomalies seemed not linked to any particular genomic profile. All identified anomalies, whether amplifications and/or TSG inactivation, involve genes playing a role in p53 regulation, that appears to be the epicenter of the initiation process in DDLS tumorigenesis, as is also known to be responsible for Li-Fraumeni syndrome, a family cancer syndrome highly predisposing to sarcomas.

RNA expression profiling reveals PRAME, a potential immunotherapy target, is frequently expressed in solitary fibrous tumors

Solitary fibrous tumors are a type of translocation-associated sarcoma with up to 30% rates of metastasis and poor response to conventional chemotherapy. Other translocation-associated sarcomas have been shown to display elevated expression of various cancer-testis antigens which may render them susceptible to immunotherapy strategies such as cancer vaccines and adoptive T-cell therapy. After an RNA sequencing assay brought the cancer-testis antigen Preferentially Expressed Antigen In Melanoma (PRAME) to our attention as possibly being upregulated in aggressive TERT promoter-mutated solitary fibrous tumors, we used tissue microarrays to asses PRAME expression in a large series of previously characterized solitary fibrous tumors, with correlation to various clinicopathologic features, as well as with tumor-infiltrating macrophages and the associated signal regulatory protein α (SIRPα)-CD47 regulatory checkpoint. We found that PRAME was expressed in 165/180 solitary fibrous tumors, with high expression seen in 58%, irrespective of TERT promoter status. Elevated PRAME expression was more frequent in primary intrathoracic solitary fibrous tumors and correlated with older age at primary diagnosis. Elevated PRAME was also associated with features suggestive of immune evasion, including lower numbers of antigen-presenting CD163+ and CD68+ macrophages, and expression of the "don't eat me" receptor CD47 on tumor cells. Taken together, these features suggest that strategies targeting PRAME with or without concomitant SIRPα-CD47 axis inhibition may represent a potential future therapeutic option in aggressive solitary fibrous tumor.

Abstract LB-307: Translational and mechanistic implications of osteosarcoma genomics: A TARGET report

Osteosarcoma (OS) is the most common malignant bone tumor of children and young adults. Although the optimization of combination chemotherapy has led to significantly improved prognosis, survival remains poor for patients with recurrent tumor or metastatic disease at diagnosis. The international TARGET (Therapeutically Applicable Research to Generate Effective Therapy) OS project team collected 285 clinically annotated samples (age <40 years) for integrative genomics analyses. Eighty-nine cases, the discovery set, were characterized with paired tumor and normal DNA sequencing as well as profiling of transcriptomes, DNA methylation, and miRNA. An additional 196 validation cases were used for copy number analysis and targeted DNA sequencing guided by results from the discovery set. The most frequent recurrent somatic mutations cause loss of function in the tumor suppressors TP53, RB1, CDKN2A, PTEN, and NF1 as well as the chromatin remodeler ATRX. Structural rearrangements are an important mechanism of inactivation for all of these genes. In the discovery set, every case carried at least one mutation of a cell cycle regulator, with TP53 somatically altered in 87/89 cases. Analysis of TP53 mutations suggests that these are often truncal. OS genomes are strikingly complex and contain copy number aberrations (CNA) arising from aneuploidy and extensive structural rearrangements. Transcriptome analysis revealed profound remodeling of gene expression with statistically significant correlation of CNA and gene expression of 3340 genes (FDR<0.001). Regions of high copy number amplification include known therapeutically relevant cancer drivers (e.g. PDGFRA, MYC, CDK4, MDM2, IGF1R, and CCNE1). In contrast, activating mutations of signal transduction genes were rare. With few exceptions (e.g. MYC amplification), mutations or CNA of individual genes were not predictive of outcome. The pattern of significant co-occurrence or mutual exclusion of frequent mutations and amplifications allowed partitioning of 240 cases into four distinct genomic groups. One of these, characterized by relatively simple genomes lacking high copy number amplification, had a more favorable outcome. Unsupervised transcriptome analysis by NMF separated the discovery set into two groups with significantly different outcomes. A pathway-based approach identified a high-risk bone differentiation signature comprised of genes highly correlated with the expression of the osteogenic transcription factors. NMF analysis of DNA methylation and miRNA data also partitioned the discovery set into two groups with the methylation groups significantly correlated with clinical outcome. Our results provide a detailed picture of the genomic complexity and heterogeneity of these tumors that suggests a model wherein most OS are initiated by TP53 loss in a proliferative cell of the osteoblast lineage. TP53 deficiency leads directly to impairment of cell cycle control, DNA repair, and terminal differentiation, a state permissive for the development of secondary CNA and epigenetic changes. The TARGET OS data are publicly available (phs000218) and of immediate relevance to future investigations of the molecular mechanisms driving osteosarcoma. Findings suggest a path forward to improved assessment of risk for individual patients and support a precision medicine approach to future clinical trial development.

Citation Format: Paul S. Meltzer, Sean Davis, Jack Zhu, Yonghong Wang, Sven Bilke, Joshua Waterfall, Robert Walker, Marbin Pineda, Yuan Jiang, Sharon Savage, Lisa Mirabello, Tsz-Kwong Man, Aaron Taylor, Monika J. Sun, Jay Wunder, Irene Andrulis, Nalan Gokgoz, Shintaro Iwata, Miki Ohira, Mark Krailo, Don Barkauskas, Lisa Teot, Timothy Triche, Silvia de Toledo, Antonio S. Petrilli, Jaime M. Guidry Auvil, Richard Gorlick, Malcolm A. Smith, Daniela Gerhard, Ching C. Lau. Translational and mechanistic implications of osteosarcoma genomics: A TARGET report [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-307.

Abstract 1984: Investigating circulating tumor DNA as a biomarker of cancer progression and recurrence in sarcoma

Objective: Circulating tumour DNA (ctDNA) is an active area of research in many types of cancer due to its value as a non-invasive diagnostic tool. Despite making up a small fraction of total cell-free DNA (cfDNA), detection of ctDNA has been made possible given advances in next generation sequencing and Digital Droplet PCR (ddPCR). CtDNA testing has some key advantages compared to tissue biopsy; ease of repetition provides a means of real-time monitoring of treatment response and signs of recurrence in cancer. This has specific relevance in sarcoma, where early detection of recurrence may provide an opportunity for faster intervention and can potentially lead to better prognostic outcomes. The purpose of this study is to determine if ctDNA is detectable in plasma samples collected from sarcoma patients and to validate our pre-analytical procedures and to identify opportunities to optimize our protocols for future use.

Methods: 20 ml of blood samples were collected from 270 soft tissue sarcoma and osteosarcoma patients with or without pre-operative adjuvant treatment and processed to separate the plasma. Cf DNA was isolated from 2ml of plasma and the quantity and quality assessment was performed by qRT-PCR and capillary electrophoresis, respectively. Whole exome sequencing (WES) was performed on 6 matched tumor-blood DNA samples to identify tumour specific single nucleotide alterations. Sequence variants identified from WES analysis were used to design primers and probes to detect the tumor specific alterations in the corresponding ctDNA in those 6 cases using ddPCR.

Results: Of the 60 patient samples analysed to date, the majority were positive for cfDNA. Quality assessment of 41cfDNA by capillary electrophoresis showed peaks approximately 170 bp in size, characteristic of cfDNA. WES of 6 patients' matched tumor-blood samples identified many tumor specific variants. Six of those sequence variants on SMAD4, COL19A1, DDX3X, ADGRG4, HECW1 and FOXR2 genes (Table 1) were used to design primers and probes to detect the tumour specific alterations in the corresponding ctDNA using dd PCR. We observed the presence tumour specific mutations in all corresponding ctDNAs tested in this study.

Table 1:Identification of tumour specific variants by WESCaseGeneSNVSarcoma SubtypeVariant Allele Frequency1SMAD4T1584CMyxofibrosarcoma86%2COL19A1G1252AUndifferentiated pleomorphic sarcoma50%3DDX3XA1038COsteosarcoma54%4ADGRG4T6361CLiposarcoma65%5HECW1C1874AMyxofibrosarcoma25%6FOXR2C130GMyxofibrosarcoma24%

Conclusions: Our ongoing study to evaluate the use of ctDNA as a biomarker in sarcoma monitoring shows promise related to the efficiency of our protocols and assays. Further testing is ongoing to assess the clinical value in sarcoma.

Citation Format: Nalan Gokgoz, Paige Darville-O'Quinn, Ainaz Malekoltojari, Patrick Prochazka, Peter C. Ferguson, Jay S. Wunder, Irene L. Andrulis. Investigating circulating tumor DNA as a biomarker of cancer progression and recurrence in sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1984.

Abstract 3875: Investigating tumor-immune interactions in adult sarcomas of the extremities

Introduction: Sarcoma is a heterogeneous group of connective tissue cancers with over 60 different subtypes. Curative treatment relies on surgical resection combined with radiation. In the event of metastasis, chemotherapy is commonly used but generally only with palliative intent. Given the heterogeneity of sarcomas, targeted therapies are limited and this has contributed to the relatively stagnant survival rates seen in the past decades.

Objective: With poorly defined cancer antigens and genetic mutations, more personalized treatments, such as immunotherapy, and in particular adoptive cell transfer therapy (ACT), may be a more viable and promising option for select sarcoma patients than currently available palliative chemotherapy. As such, our study aims to create patient specific models to investigate the interactions between tumor-infiltrating lymphocytes (TILs) and autologous tumor cells.

Methods: Over 250 tissue and blood samples from untreated sarcoma patients have been collected. The tissue samples are dissected and used for in vitro expansion of TILs or tumor cells. TIL cultures are characterized via flow cytometry and TIL responses are quantified using an IFNy ELISA. Tumor cultures are validated with RT-qPCR and dd-PCR to ensure tumor-specific mutations are retained. After characterizing and validating the cultures, autologous tumor cells and TILs are co-cultured to examine tumor-immune interactions. Outcomes of immune activity in the presence of tumor cells and tumorigenicity are evaluated to better understand the mechanisms that may be implicated in sarcoma immunotherapy.

Results: At the end of a 3-week expansion period, of the 93 primary tumor samples cultured for TILs, only 7 did not yield any TIL growth; however, the final TIL yield varied between different patient samples, ranging from 0.005 - 83M cells. Both TIL cultures expanded from different samples of the same tumor and from tumors of different patients demonstrated variable cell proportions of CD4+ and CD8+ TILs. Some cultures also contained a proportion of CD56+ cells. ELISA documented TIL responses to stimulation in all collected cultures, indicating a viable and functional population. Of the 24 primary tumor samples cultured, 17 (8 of 10 undifferentiated pleomorphic sarcomas; 7 of 10 myxofibrosarcomas; 2 of 4 osteosarcomas) generated viable tumor cell cultures as defined by the presentation of stable growth beyond passage 5.

Conclusion: Tumor cells and functional TILs can be isolated and expanded from most sarcomas; however, the methods must be optimized for each case. Further tumor culture validation by whole exome sequencing in combination with ddPCR is ongoing. A benchmark of an effective and clinically significant TIL yield will need to be better defined going forward. TILs are active in vitro and vary in population composition. Future experiments will focus on evaluating the killing capacity and tumor specificity of TILs.

Citation Format: Alice Ko, Victoria Coward, Minji Lee, Kayley Xu, Nalan Gokgoz, Brendan Dickson, Jay Wunder, Irene L. Andrulis. Investigating tumor-immune interactions in adult sarcomas of the extremities [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3875.

The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways

Soft-tissue sarcomas (STS) are rare malignancies showing lineage differentiation toward diverse mesenchymal tissues. Half of all high-grade STSs develop lung metastasis with a median survival of 15 months. Here, we used a genetically engineered mouse model that mimics undifferentiated pleomorphic sarcoma (UPS) to study the molecular mechanisms driving metastasis. High-grade sarcomas were generated with Cre recombinase technology using mice with conditional mutations in Kras and Trp53 (KP) genes. After amputation of the limb bearing the primary tumor, mice were followed for the development of lung metastasis. Using RNA-sequencing of matched primary KP tumors and lung metastases, we found that the long noncoding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (Neat1) is significantly upregulated in lung metastases. Furthermore, NEAT1 RNA ISH of human UPS showed that NEAT1 is upregulated within a subset of lung metastases compared with paired primary UPS. Remarkably, CRISPR/Cas9-mediated knockout of Neat1 suppressed the ability of KP tumor cells to colonize the lungs. To gain insight into the underlying mechanisms by which the lncRNA Neat1 promotes sarcoma metastasis, we pulled down Neat1 RNA and used mass spectrometry to identify interacting proteins. Interestingly, most Neat1 interacting proteins are involved in RNA splicing regulation. In particular, KH-Type Splicing Regulatory Protein (KHSRP) interacts with Neat1 and is associated with poor prognosis of human STS. Moreover, depletion of KHSRP suppressed the ability of KP tumor cells to colonize the lungs. Collectively, these results suggest that Neat1 and its interacting proteins, which regulate RNA splicing, are involved in mediating sarcoma metastasis. IMPLICATIONS: Understanding that lncRNA NEAT1 promotes sarcoma metastasis, at least in part, through interacting with the RNA splicing regulator KHSRP may translate into new therapeutic approaches for sarcoma.

Osteosarcoma and soft-tissue sarcomas with an immune infiltrate express PD-L1: relation to clinical outcome and Th1 pathway activation

Immune checkpoint proteins, such as PD-L1 and PD-1, are important in several cancers; however, their role in osteosarcoma (OSA) and soft tissue sarcoma (STS) remains unclear. Our aims were to determine whether subsets of OSA/STS harbor tumor-infiltrating lymphocytes (TILs) and express PD-L1, and how PD-L1 expression is related to clinical outcome. Tissue sections of 25 cases each of untreated undifferentiated pleomorphic sarcoma (UPS), myxofibrosarcoma (MFS), liposarcoma (LPS) and 24 of leiomyosarcoma (LMS) were subjected to immunohistochemistry (IHC) for immune cells, PD-L1 and PD-1. RT-qPCR was utilized to quantify levels of PD-L1 mRNA from 33 UPS, 57 MFS and 79 OSA primary-untreated specimens. PD-L1 mRNA levels were tested for their correlation with overall survival in patients presenting without metastases. Transcriptome analysis evaluated biological pathway differences between high and low PD-L1 expressers. A subset of UPS and MFS contained TILs and expressed PD-L1 and PD-1; LMS and LPS did not. PD-L1 levels by IHC and RT-qPCR were positively correlated. PD-L1 over-expression was associated with better survival for UPS and OSA, but not MFS. The Th1 pathway was significantly activated in UPS with high levels of PD-L1 and improved survival. Some sarcoma subtypes harbor TILs and express PD-L1. Patients with UPS and OSA with high levels of PD-L1 had better overall survival than those with low expression levels. Important biological pathways distinguish PD-L1 high and low groups. The stratification of patients with OSA/STS with respect to potential immune therapies may be improved through investigation of the expression of immune cells and checkpoint proteins.

Abstract LB-306: Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways

Soft tissue sarcomas (STS) are malignant tumors from diverse mesenchymal tissues. About 40% STS patients develop fatal lung metastasis with a median survival of 15 months. The mechanisms driving the development of lung metastasis in sarcoma patients are poorly understood. Therefore, our lab has developed a genetically engineered mouse model (GEMM) of high-grade primary STS with conditional mutations in Kras and Trp53 (KP) where 40% of mice tumors develop lung metastasis. This KP model recapitulates human patients with Undifferentiated Pleomorphic Sarcoma (UPS), one of the most common subtypes of STS diagnosed in adults. RNA sequencing (RNA-Seq) was performed on paired primary and lung metastases in KP mouse sarcomas and determined that the expression of the long non-coding RNA (lncRNA) Neat1 is increased in lung metastases compared to paired primary tumors. Real time PCR (qPCR) in 22 paired KP mouse primary sarcomas and lung metastases further confirmed that Neat1 is significantly upregulated in some lung metastases. In addition, RNA-Seq and qPCR data from 10 pairs of human primary sarcomas and matched lung metastases also showed that NEAT1 levels are increased in lung metastases. Furthermore, NEAT1 RNA in situ hybridization (ISH) on tissue microarrays (TMAs) of human primary UPS and lung metastases determined that the expression of NEAT1 is upregulated in lung metastases. Next, CRISPR/Cas9 technology was applied to delete Neat1 in primary mouse sarcoma cells and loss of expression of Neat1 was confirmed by qPCR and northern blot in knockout (KO) clones. In addition, loss of Neat1 significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Furthermore, RNA pull down assay with mass spectrometry analysis determined Neat1 interacting proteins, such as Khsrp, were mainly involved in RNA splicing pathways which was also shown to be dysregulated in lung metastases and Neat1 KO cells. Finally, CRISPR/Cas9 mediated knockout of Khsrp significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Overall, these results suggest that upregulation of Neat1 promotes lung metastasis of soft tissue sarcoma through regulating RNA splicing pathways and NEAT1 is a potential target to prevent or treat lung metastasis in sarcoma patients.

Citation Format: Jianguo Huang, Eric Xu, Mohit Sachdeva, Timothy Robinson, Xiaodi Qin, Dadong Zhang, Kouros Owzar, Nalan Gokgoz, Andrew Seto, Irene Andrulis, Jay Wunder, Tomoyo Okada, Simuel Singer, Alexander Lazar, Brian Rubin, David G. Kirsch. Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-306.

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors

Sarcomas are cancers of the bone and soft tissue often defined by gene fusions. Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors. We explored how and when EWSR1-ETS fusions arise by studying the whole genomes of Ewing sarcomas. In 52 of 124 (42%) of tumors, the fusion gene arises by a sudden burst of complex, loop-like rearrangements, a process called chromoplexy, rather than by simple reciprocal translocations. These loops always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions. Similar loops forming canonical fusions were found in three other sarcoma types. Chromoplexy-generated fusions appear to be associated with an aggressive form of Ewing sarcoma. These loops arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Abstract 516: Long noncoding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma

Soft tissue sarcomas (STS) are malignant tumors from diverse mesenchymal tissues. About 40% STS patients develop fatal lung metastasis with a median survival of 15 months. The mechanisms driving the development of lung metastasis in sarcoma patients are poorly understood. Therefore, our lab has developed a genetically engineered mouse model (GEMM) of high-grade primary STS with conditional mutations in Kras and Trp53 (KP) where 40% of mice tumors develop lung metastasis. This KP model recapitulates human patients with Undifferentiated Pleomorphic Sarcoma (UPS), one of the most common subtypes of STS diagnosed in adults. RNA sequencing (RNA-Seq) was performed on paired primary and lung metastases in KP mouse sarcomas and determined that the expression of the long non-coding RNA (lncRNA) Neat1 is increased in lung metastases compared to paired primary tumors. Real time PCR (qPCR) in 22 paired KP mouse primary sarcomas and lung metastases further confirmed that Neat1 is significantly upregulated in lung metastases. In addition, RNA-Seq data from 5 pairs of human primary sarcomas and matched lung metastases also showed that NEAT1 levels are increased in lung metastases. Furthermore, NEAT1 RNA in situ hybridization (ISH) on tissue microarrays (TMAs) of human primary UPS and lung metastases determined that the expression of NEAT1 is upregulated in lung metastases. Next, CRISPR/Cas9 technology was applied to delete Neat1 in primary mouse sarcoma cells and loss of expression of Neat1 was confirmed by qPCR and northern blot in knockout (KO) clones. In addition, loss of Neat1 significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. To further test that loss of Neat1 reduces lung metastasis in primary sarcoma mouse model, primary tumors with Neat1 deletion are generated in GEMMs using in vivo CRISPR/Cas9 technology and KrasLSL-G12D/+; Trp53Flox/Flox; Neat1-/- (KPN) mouse model. Finally, RNA-Seq and capture hybridization analysis of RNA targets (CHART) are performed to determine mechanisms by which Neat1 regulates lung metastasis. Overall, these results suggest that upregulation of Neat1 promotes lung metastasis of soft tissue sarcoma and NEAT1 is a potential target to prevent or treat lung metastasis in sarcoma patients.

Citation Format: Jianguo Huang, Eric Xu, Mohit Sachdeva, Timothy Robinson, Xiaodi Qin, Dadong Zhang, Kouros Owzar, Nalan Gokgoz, Andrew Seto, Irene Andrulis, Jay Wunder, Tomoyo Okada, Samuel Singer, Alexander Lazar, Brian Rubin, David G. Kirsch. Long noncoding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 516.

Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients

Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. We conducted a multi-institutional genome-wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma, including 523 patients of European ancestry and 109 from Brazil. We conducted a time-to-event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease. The results were combined across the European and Brazilian case sets using a random-effects meta-analysis. The strongest association after meta-analysis was for rs3765555 at 9p24.1, which was inversely associated with overall survival (HR = 1.76; 95% CI 1.41-2.18, p = 4.84 × 10-7 ). After imputation across this region, the combined analysis identified two SNPs that reached genome-wide significance. The strongest single association was with rs55933544 (HR = 1.9; 95% CI 1.5-2.4; p = 1.3 × 10-8 ), which localizes to the GLDC gene, adjacent to the IL33 gene and was consistent across both the European and Brazilian case sets. Using publicly available data, the risk allele was associated with lower expression of IL33 and low expression of IL33 was associated with poor survival in an independent set of patients with osteosarcoma. In conclusion, we have identified the GLDC/IL33 locus on chromosome 9p24.1 as associated with overall survival in patients with osteosarcoma. Further studies are needed to confirm this association and shed light on the biological underpinnings of this susceptibility locus.

Abstract B39: Investigation of the effects of alterations in the glutamate receptor, GRIK2, on osteosarcoma tumorigenesis

Osteosarcoma is a primary, malignant bone tumor that mainly occurs in young adults and survival rates (60-70% over five years) have remained steady and novel treatment targets are needed. Osteosarcoma tumors exhibit chromosomal instability and are heterogeneous. In this study we identified recurrent copy number alterations in 44 flash-frozen osteosarcoma tumors obtained at biopsy with 25 blood-matched samples. Copy number losses were observed in 14% of tumors in the 6q16.3 region, specifically in the 5 intergenic space and first intron of the GRIK2 gene. GRIK2 encodes an ionotropic glutamate receptor that has been identified as a tumor-suppressor gene in gastric cancer, but the relationship between alterations in this region and osteosarcoma are still to be determined. We found that the focal deletions do not overlap with any coding sequence of GRIK2; however, there is a region of interest that contains a SETDB1 histone methyltransferase binding site that is shared by several deletions. The 5 intergenic space is enriched with H3K9Me3 histone marks which is indicative of transcriptional repression. SETDB1 is responsible for adding H3K9Me3 histone marks and deletion of this site may alter the expression of GRIK2. The goal of this study is to determine the relationship between noncoding deletions in 6q16.3 and GRIK2 by examining the effects of the deletions on the expression, function, and regulation on osteosarcoma cells in vitro.

Gene expression levels of GRIK2 were quantified with RT-qPCR in both osteosarcoma tumors and cell lines. The functional role of GRIK2 was characterized in both U2-OS and SaOS-2 osteosarcoma cells through gain-of-function experiments. Cell viability was measured by the XTT assay and cell migration was quantified with a wound-healing assay. Apoptosis levels were assessed with an annexin V experiment. The effect of noncoding deletions of the SETDB1 binding site was examined using CRISPR/cas9 gene editing. Following transfection of a CRISPR/cas9 vector, U2-OS cells were sorted by fluorescence-activated cell sorting, grown for 7-10 days, and GRIK2 gene expression levels were measured.

The expression levels of GRIK2 varied in tumors and were low in cell lines. Several tumors with focal deletions were among a subset of tumors with increased transcript levels relative to cell lines. Due to this observation, GRIK2 was overexpressed in U2-OS and SaOS-2 cells and found to result in decreased cell proliferation, migration, and increased apoptosis levels. Gene editing of the SETDB1 binding site was confirmed following DNA extraction and PCR of the deleted region. Following cell sorting and growth, GRIK2 transcript levels were increased in edited cells relative to untreated cells.

Noncoding deletions in the 6q16.3 region were associated with increased expression levels of GRIK2 and overexpression of GRIK2 in vitro may result in a less aggressive phenotype. Gene editing of the SETDB1 binding site with CRISPR/cas9 demonstrated that focal deletions of the region may be involved in epigenetic regulation of GRIK2. Noncoding deletions of GRIK2 are linked to expression and functional changes in GRIK2 and further studies will examine GRIK2 as a potential target for therapeutic intervention.

Citation Format: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis. Investigation of the effects of alterations in the glutamate receptor, GRIK2, on osteosarcoma tumorigenesis [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B39.

Abstract A04: Molecular characterization of undifferentiated pleomorphic sarcomas

Objective: Undifferentiated pleomorphic sarcomas (UPS) are high-grade soft-tissue sarcomas (STS) with no apparent line of differentiation. Despite overall gains in the management of STS, progress in therapies based on molecular targets and understanding the unknown genetic diversity is needed, especially in UPS where response to therapy is limited. Using integrated multi-omic analysis, we aim to characterize UPS for recurrent genetic mutations, altered pathways, and the mutational spectrum. These insights into UPS may enable robust classification, identify prognostic markers, and lead to novel treatment approaches.

Methods: Clinically well-annotated cases of UPS with matched blood specimens were retrieved from the Sarcoma Tumor Bank at Mount Sinai Hospital, Toronto. Using current World Health Organization histopathologic classification, reevaluated cases were subjected to whole-genome (WGS) or whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Cell lines and/or mouse xenografts were established from some of the UPS tumors. The goal of this study was to integrate annotated somatic mutations, expressed transcripts, mRNA fusions, structural rearrangements, and copy number aberrations to detect recurrent molecular features in UPS.

Results: At present, 43 UPS tumor, 8 matched metastatic samples, 6 mouse xenografts, and 4 cell lines have been sequenced by WGS or WES and RNA-seq. Among the 34 cases analyzed by WES, known cancer genes TP53, LRP1B, ATRX, and RB1 are found to recurrently contain somatic variants. Among these genes, nonsilent somatic variants were found in 18/34 tumors. The somatic variant burden among the WES tumors is approximately 5 muts/Mb. Two UPS cases were hypermutated with a somatic variant burden >10 muts/Mb. In examining the base changes in the hypermutated cases, the two display a C>A bias, in which the 5' and 3' bases flanking the C>A alterations in the hypermutated cases have a distinct pattern (TpCpN, CpCpA) that differ from the other samples. These somatic C>A biases in their trinucleotide context were not detected in >10K tumor cases across 33 cancer types sequenced by TCGA. An RB1 and ATXN10 fusion transcript that lacks the RB1 tumor-suppressing domain was confirmed in one case, while the derived cell line also expressed the RB1-ATXN10 fusion. The cell lines and xenograft models retained 8-71% of their matched tumors' somatic variants. The metastatic samples contained between 13-63% of the somatic variants also identified in their matched primary tumors, among the 4 WES metastatic samples analyzed thus far.

Conclusion: Initial analyzes of UPS tumors has identified recurrently mutated cancer-related genes and a unique pattern of C>A bias not previously seen. Ongoing multi-omic analysis, integrating the RNA-seq with the somatic alterations, of UPS tumors may reveal further genomic events that may aid in stratification of UPS, understand the drivers of the disease, identify actionable targets, and realize novel therapeutics.

Citation Format: Andrew Seto, Nalan Gokgoz, Qingxia Wei, Yael Babichev, Brendan C. Dickson, Benjamin Alman, Rebecca A. Gladdy, Adam Shlien, Jay Wunder, Irene L. Andrulis. Molecular characterization of undifferentiated pleomorphic sarcomas [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A04.

Identifying actionable variants using next generation sequencing in patients with a historical diagnosis of undifferentiated pleomorphic sarcoma

There are limited data regarding the molecular characterization of undifferentiated pleomorphic sarcomas (UPS; formerly malignant fibrous histiocytoma). This study aimed to investigate the utility of next generation sequencing (NGS) in UPS to identify subsets of patients who harbour actionable mutations. Patients diagnosed with UPS underwent pathological re-evaluation by a pathologist specializing in sarcoma. Tumor DNA was isolated from archived fresh frozen tissue samples and genotyped using NGS with the Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons). In total, 95 patients initially classified with UPS were identified. Following pathology re-review the histological subtypes were reclassified to include: Myxofibrosarcoma (MFS, N = 44); UPS(N = 18); and Others (N = 27; including undifferentiated spindle cell sarcoma (N = 15) and dedifferentiated liposarcoma (N = 6)). Seven cases were excluded from further analysis for other reasons. Baseline demographics of the finalized cohort (N = 88) showed a median age of 66 years (32-95), primarily with stage I-III disease (92%) and high-grade (86%) lesions. Somatic mutations were identified in 31 cases (35%)(Total mutations = 36: solitary mutation(n = 27); two mutations( =n = 3); three mutations(n = 1)). The most commonly identified mutations were in TP53 (n = 24), ATM (n = 3) and PIK3CA (n = 2). Three of 43 patients with MFS and one of 18 patients with UPS had clinically relevant mutations, mainly related to biomarkers of prediction of response; however few had targetable driver mutations. Somatic mutation status did not influence disease free or overall survival. Based on the small number of clinically relevant mutations, these data do not support the routine use of targeted NGS panels outside of research protocols in UPS.

Abstract 5507: Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis

Osteosarcoma is a primary, malignant bone tumour mainly affecting young adults with a five-year survival rate of 60-70% depending on presentation of metastasis at diagnosis. Tumours are marked by genetic instability and heterogeneity and for this reason, molecular subtypes have yet to be characterized. Survival rates have remained consistent over the past few decades and novel molecular targets for treatment are needed. Current genomic strategies have identified recurrent copy number alterations. In a study of 44 flash frozen osteosarcoma tumours which were obtained at the time of biopsy and 25 blood-matched samples we identified recurrent copy number losses including a region at 6q16.3 in 14% of tumours. Focal deletions were observed in the 5’ intergenic space and first intron of the GRIK2 gene and do not overlap with any coding sequence. The relationship between alterations in this region and osteosarcoma tumourigenesis has yet to be explored in depth. GRIK2 encodes an ionotropic glutamate receptor that has been implicated as a tumour suppressor in gastric cancer. An interesting feature of the tumours was the overlap of focal deletions with a SETDB1 histone methyltransferase binding site indicating a potential connection with epigenetic regulation of GRIK2. The goal of this study is to examine the effects of non-coding, focal deletions on GRIK2 gene expression, function and regulation in osteosarcoma cells. GRIK2 transcript levels were measured in osteosarcoma tumours and cell lines using qRT-PCR. Functional assays were performed to characterize the role of GRIK2 in osteosarcoma cell proliferation, migration and apoptosis in vitro. Gene editing with CRISPR/cas9 was performed to examine the link between non-coding deletions and GRIK2 expression. GRIK2 transcript levels varied in tumours; several tumours with focal deletions had increased transcript levels relative to cell lines which demonstrated low expression levels. Due to the observation of low transcript levels, a gain of function approach was employed to examine GRIK2 function in vitro. Overexpression of GRIK2 decreased proliferation, migration and increased apoptosis in osteosarcoma cells. Gene editing of the SETDB1 binding site resulted in increased GRIK2 transcript levels relative to untreated cells. This study suggests that non-coding focal deletions are linked to high expression levels of GRIK2 which may confer a less aggressive phenotype and are involved in epigenetic regulation of the gene.

Citation Format: Justin G. Mayers, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis. Investigation of the effects of alterations in the glutamate receptor, GRIK2 on osteosarcoma tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5507. doi:10.1158/1538-7445.AM2017-5507

Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for Thirteen Cancer Types

BACKGROUND

Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.

METHODS

Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.

RESULTS

GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl (2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.

CONCLUSION

Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.

The genomic landscape of epithelioid sarcoma cell lines and tumours

We carried out whole genome and transcriptome sequencing on four tumour/normal pairs of epithelioid sarcoma. These index cases were supplemented with whole transcriptome sequencing of three additional tumours and three cell lines. Unlike rhabdoid tumour (the other major group of SMARCB1-negative cancers), epithelioid sarcoma shows a complex genome with a higher mutational rate, comparable to that of ovarian carcinoma. Despite this mutational burden, SMARCB1 mutations remain the most frequently recurring event and are probably critical drivers of tumour formation. Several cases show heterozygous SMARCB1 mutations without inactivation of the second allele, and we explore this further in vitro. Finding CDKN2A deletions in our discovery cohort, we evaluated CDKN2A protein expression in a tissue microarray. Six out of 16 cases had lost CDKN2A in greater than or equal to 90% of cells, while the remaining cases had retained the protein. Expression analysis of epithelioid sarcoma cell lines by transcriptome sequencing shows a unique profile that does not cluster with any particular tissue type or with other SWI/SNF-aberrant lines. Evaluation of the levels of members of the SWI/SNF complex other than SMARCB1 revealed that these proteins are expressed as part of a residual complex, similarly to previously studied rhabdoid tumour lines. This residual SWI/SNF is susceptible to synthetic lethality and may therefore indicate a therapeutic opportunity.

Abstract 5574: High prevalence of germline TP53 mutations in young osteosarcoma cases

Osteosarcoma, the most common primary bone malignancy, has a bimodal age distribution, with a primary peak in adolescence and a smaller peak in the elderly. The etiologic contribution of germline genetic variation to osteosarcoma is not well-understood. It occurs at higher than expected frequencies in individuals with the Li-Fraumeni syndrome (LFS) cancer predisposition syndrome. Approximately 70% of classic LFS families have germline TP53 mutations. Two previous studies reported that 3% of young osteosarcoma cases (<20 years old, N = 235) and 7% of all aged cases (N = 95) had germline TP53 mutations.

We determined the prevalence of germline TP53 mutations in 765 unselected osteosarcoma cases. DNA was extracted from blood and TP53 sequenced using custom Ampliseq panels. Variants were validated with Sanger sequencing. The IARC germline TP53 database was used to identify TP53 mutations reported in families with LFS (LFS-associated mutations). Variants were considered “likely LFS-associated mutations” if absent from publically available databases (ESP and 1,000 Genomes Project) and predicted non-functional or deleterious using in silico algorithms. Variants were considered “rare exonic variants” if their minor allele frequency (MAF) was <2% in public databases and they had uncertain clinical significance.

There were 32 LFS-associated or rare TP53 variants in 62 osteosarcoma cases. The frequency of cases with an LFS or likely LFS-associated mutation and/or rare exonic variant was 8.1%. Notably, all 32 TP53 variants were present in cases <30 years of age (“young cases”, N = 505), 9.5% of young cases, compared with none in older cases (N = 51; P<0.001). TP53 variants did not have an even distribution within the first three age decades in young cases. LFS or likely LFS-associated mutations, which confer significant cancer risk, had the highest frequency in patients aged 0-9 years (4.8% of all cases, and 6.1% of European cases), and rare exonic variants were most frequent in patients aged 10-19 years (6.1% of all cases, and 5.6% of European cases).

A logistic regression case-case analysis identified a novel significant association between a rare TP53 variant, rs1800372 (p.R213R), and metastasis at diagnosis in cases of European ancestry (odds ratio [OR] 4.27, 95% CI 1.2-15.5, P = 0.026). We additionally confirmed that a common exonic variant, rs1042522 (p.P72R), was significantly associated with osteosarcoma risk (OR 1.22, 95% CI 1.1-1.4, P = 0.0098) and poorer survival (HR 1.35, 95% CI 1.00-1.83, P = 0.048).

Our data suggest that genetic susceptibility to young onset osteosarcoma is distinct from adult onset osteosarcoma. The high TP53 mutation prevalence we identified in osteosarcoma cases aged <20 years of 9.7% is significantly greater than the previously reported prevalence of 3% in unselected cases (P = 0.002). Based on these findings, genetic counseling and TP53-mutation testing of all young patients with osteosarcoma should be considered.

Citation Format: Lisa J. Mirabello, Meredith Yeager, Phuong L. Mai, Julie Gastier-Foster, Richard Gorlick, Chand Khanna, Ana Patiño-Garcia, Luis Sierrasesúmaga, Fernando Lecanda, Irene L. Andrulis, Jay S. Wunder, Nalan Gokgoz, Donald A. Barkauskas, Xijun Zhang, Aurelie Vogt, Kristine Jones, Joseph F. Boland, Stephen J. Chanock, Sharon A. Savage. High prevalence of germline TP53 mutations in young osteosarcoma cases. [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 5574. doi:10.1158/1538-7445.AM2015-5574

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

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.

Germline TP53 variants and susceptibility to osteosarcoma

The etiologic contribution of germline genetic variation to sporadic osteosarcoma is not well understood. Osteosarcoma is a sentinel cancer of Li-Fraumeni syndrome (LFS), in which approximately 70% of families meeting the classic criteria have germline TP53 mutations. We sequenced TP53 exons in 765 osteosarcoma cases. Data were analyzed with χ(2) tests, logistic regression, and Cox proportional hazards regression models. We observed a high frequency of young osteosarcoma cases (age <30 years) carrying a known LFS- or likely LFS-associated mutation (3.8%) or rare exonic variant (5.7%) with an overall frequency of 9.5%, compared with none in case patients age 30 years and older (P < .001). This high TP53 mutation prevalence in young osteosarcoma cases is statistically significantly greater than the previously reported prevalence of 3% (P = .0024). We identified a novel association between a TP53 rare variant and metastasis at diagnosis of osteosarcoma (rs1800372, odds ratio = 4.27, 95% confidence interval = 1.2 to 15.5, P = .026). Genetic susceptibility to young onset osteosarcoma is distinct from older adult onset osteosarcoma, with a high frequency of LFS-associated and rare exonic TP53 variants.

Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.

Abstract 1447: Investigating susceptibility to sporadic osteosarcoma by genome-wide copy number analysis

Constitutional copy-number variants (CNVs) frequently overlap genomic regions that contain genes associated with cancer. In addition, copy number alterations (CNAs) in tumors often coincide with sites of CNVs and may arise through progression of CNVs. Osteosarcoma (OS), the most common human bone malignancy, can arise in familial or sporadic forms. While germline mutations of tumor suppressor genes have been implicated in a minority of OS cases, little is known about genetic changes that contribute to the etiology of sporadic OS. Using high-resolution SNP/CNV arrays, we observed a higher global germline CNV frequency in patients with sporadic OS compared to healthy controls. Given the early age of onset and the extensive constitutional CNVs, we hypothesize that these genomic alterations are linked to susceptibility to OS. Here we investigate whether specific constitutional CNVs are related to susceptibility to sporadic OS and whether OS tumor CNAs arise via progression of constitutional CNVs in these patients. Blood derived DNA samples from patients with sporadic OS with wild-type germline p53 sequence and gene dosage were selected for analysis on Affymetrix GW6.0 arrays with paired pre-therapy tumor biopsies. Initial results from a discovery set of samples (n=43 pairs) reveal a copy number loss at 1q43, in a region that overlaps several genes that have a role in bone formation, microtubules and cytoskeletal organization. This loss was present in 43% of the blood-derived DNA samples and 44% of the tumor-derived samples, whereas this variant was noted in only 1.2% of controls. Furthermore, the germline 1q43 deletion correlates with poor survival of the OS patients (p=0.04, Long Rank). Analysis of an independent validation set (n=32 pairs) is currently underway to confirm the initial finding and further characterize specific constitutional CNVs among sporadic OS patients. The findings of this study will open new avenues for the discovery of novel loci implicated in susceptibility to OS with potential for improved diagnostic and prognostic options as well as further insight into disease pathogenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1447. doi:1538-7445.AM2012-1447

Abstract 4917: PRKCE and other genetic networks in osteosarcoma metastasis

Osteosarcoma (OS) is the most common malignant bone cancer with approximately 1, 000 new cases reported annually in North America. Unfortunately OS has a poor 5-year survival rate (∼60%), and this is attributable largely to its propensity towards pulmonary metastasis: roughly a fifth (20%) of newly diagnosed cases are accompanied by macroscopic pulmonary metastases, and it is estimated that four fifths (80%) of all cases have undetectable microscopic metastases at diagnosis. The aim of the present study was to identify and characterize genetic networks that contribute to the metastasis of OS.

Gene-expression profiling was performed on a cohort of 63 primary OS tumor samples: 46 with undetectable metastasis at diagnosis (‘localized’), and 17 that had detectable pulmonary metastasis at time of diagnosis (‘metastatic’). The relative abundance of transcripts from approximately 9, 000 genes was measured. This information was overlain on the Pathway Commons human interactome, and two independent methods of supervised network analysis were performed. Those networks with significantly differential gene expression, or ‘activity’ (Chuang et al. Mol. Sys. Biol. 2007), and those networks with significantly differential internal gene correlation, or ‘organization’ (Taylor et al. Nature Biotech. 2009) were discovered. Networks were assigned to biological processes using Gene Ontology Slim Generic. Real-time PCR was performed in vitro and in vivo to corroborate and validate the initial findings.

The supervised network analysis has elucidated the 43 most significantly differentially activated, and 11 most significantly differentially organized networks in metastatic OS. One candidate differentially activated network, comprising RASGRP3, PRKCE and GNB2, was selected for follow-up. In vitro analysis in a panel of paired OS cell lines has corroborated the findings of the profiling screen: RASGRP3 was found to be under-expressed in some highly metastatic sub-lines, and PRKCE was found to be over-expressed in some highly metastatic sub-lines. Independent validation of PRKCE expression in the original tumor cohort has confirmed the increased expression in metastatic samples. A less stringent inspection of the network results reveals global trends in network aberrations: differentially activated networks are commonly found in transport, translation and protein modification processes, while dis-organized networks are commonly found in metabolism, signaling, transcription and organization processes. The study here described has revealed significant network aberrations in metastatic OS primary tumours. Additionally, several high-confidence networks have been identified for detailed follow-up. Subsequent in vitro and in vivo expression analysis has confirmed that one network is differentially expressed in metastatic OS. Knockdown assays are ongoing to demonstrate the impact of this network on OS metastatic progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4917. doi:10.1158/1538-7445.AM2011-4917

Characterization of the 12q15 MDM2 and 12q13-14 CDK4 amplicons and clinical correlations in osteosarcoma

The chromosomal region 12q13-15 is recurrently amplified in osteosarcoma (OS), but its importance in bone tumor development remains unknown. Although there are two major candidate genes (MDM2, a TP53 downregulator, and CDK4, involved in cell cycle progression) considered to be the driving genes in this region, the size of the amplicon and number of genes involved have not been determined. In this study, we used 130 classical OS and 15 parosteal OS to determine MDM2 and CDK4 amplification frequency in OS. Tumors in which these genes were amplified were used to map the 12q13-15 amplified region and to determine its correlation with clinical prognosis. The 12q13-15 amplification was more prevalent in parosteal OS (67% of cases) than in high-grade classical OS (12%). Quantitative real-time PCR of MDM2, CDK4, and 25 other genes showed that this region contains two different amplicons: one at 12q15 centered on MDM2 and one at 12q13-14 centered on CDK4. Both regions were frequently co-amplified in both types of OS, and MDM2 and CDK4 amplification was correlated with higher expression levels for both genes. Univariate and multivariate analyses of clinical data indicated that classical OS patients whose tumors exhibited MDM2 amplification were more likely to be older at diagnosis (median age 32.6 vs. 17.8 years) and female (66.7 vs. 33.3%) than those without gene amplification. There was no association with other clinical parameters. In conclusion, co-amplification of MDM2 and CDK4 in two separate amplicons occurs frequently in parosteal OS and less so in classical high-grade OS.

COPS3 amplification and clinical outcome in osteosarcoma

BACKGROUND

Amplification of several genes that map to a region of chromosome 17p11.2, including COPS3, was observed in high-grade osteosarcoma. These genes were also shown to be overexpressed and may be involved in osteosarcoma tumorigenesis. COPS3 encodes a subunit of the COP9 signalosome implicated in the ubiquitination and ultimately degradation of the P53 tumor suppressor. To determine the relation between COPS3 amplification, P53 mutation, and patient outcome in osteosarcoma, tumors from a large cohort of patients with high-grade osteosarcoma and long-term clinical follow-up were examined.

METHODS

Quantitative real-time polymerase chain reaction (PCR) was performed to detect copy number changes for COPS3, as well as additional genes (NCOR1, TOM1L2, and PMP22) from the 17p11.2 amplicon, in 155 osteosarcomas from a prospective collection of tumors with corresponding clinical data. Univariate and multivariate analyses were performed to assess differences in survival between groups.

RESULTS

Amplification of COPS3, detected in 31% of the osteosarcomas, was strongly associated with large tumor size (P=.0009), but was not associated with age at diagnosis, site, sex, and tumor necrosis. COPS3 amplification was significantly correlated with a shorter time to metastasis with an estimated hazard ratio (HR) of 1.61 (95% confidence interval [CI], 1.02-2.55) in univariate analysis (log-rank test, P=.042). However, in an a priori multivariate Cox model including the other clinical parameters, the HR for COPS3 amplification decreased to 1.32 (95% CI, 0.82-2.13, P=.25), mainly due to the strong correlation with tumor size. COPS3 amplification and P53 mutation frequently occurred in the same tumors, suggesting that these are not mutually exclusive events in osteosarcoma. Although not statistically significant, patients whose tumors exhibited both molecular alterations tended to be more likely to develop metastasis compared with patients with either COPS3 amplification or P53 mutation alone.

CONCLUSIONS

COPS3 is the likely target of the 17p11.2 amplicon. COPS3 may function as an oncogene in osteosarcoma, and an increased copy number may lead to an unfavorable prognosis.

hCDC4 variation in osteosarcoma

The hCDC4 gene (also known as Fbw7 or Archipelago) encodes an F-box protein that is responsible for targeting cyclin E for Skp1-cullin-F box protein (SCF) ubiquitination and proteosomal degradation. Disruption of this pathway has been associated with chromosomal instability and aneuploidy in several cancer cell lines and primary tumors. This study aimed to examine whether hCDC4 mutations contribute to aneuploidy in osteosarcoma. We analyzed 147 primary high-grade osteosarcoma specimens and 6 osteosarcoma cell lines. The protein truncation test (PTT) and single-strand conformation polymorphism (SSCP) analysis with subsequent sequencing were performed to detect alterations of the hCDC4 gene. All specimens exhibited the same PTT pattern of normal bands with less intense common bands. Two shifts were detected by SSCP, and subsequent DNA analysis identified one in-frame three-base GAG (424-426) deletion and one silent nucleotide substitution (C1261T). We conclude that somatic hCDC4 mutations are infrequent in osteosarcoma, and are unlikely to play an important role in aneuploidy of this tumor.

Application of reliability coefficients in cDNA microarray data analysis

Gene expression microarray technology has been widely used in areas such as human cancer research to identify molecular characteristics of sample specimens. The microarray study, however, is a very complicated procedure which involves numerous sources of variability that may be either systematic or random. Systematic variation is often eliminated by applying normalization procedures, but at present there are no standard criteria available to evaluate the performance of a particular normalization approach. In this paper, we propose a reliability-type coefficient as a criterion to assess the effectiveness of normalization procedures in eliminating systematic variation. Simulation studies show that this criterion performs reasonably well in a range of settings. The proposed method is illustrated using a subset of an ongoing microarray study of soft-tissue sarcoma.

Functional characterization of novel presenilin-2 variants identified in human breast cancers

We identified in breast cancer cases two germline alterations, R62H and R71W, in presenilin-2 (PS-2), a gene involved in familial Alzheimer's disease (FAD). The role of these alleles in FAD is unclear, but neither allele affected Abeta(42)/Abeta(40) ratio. However, both R62H and R71W alterations compromised PS-2 function in Notch signaling in Caenorhabditis elegans and cell growth inhibition in mouse embryonic fibroblasts, and these effects were dependent on gene dosage. We found that both alterations enhanced the degradation of the PS-2 full-length protein, indicating that they may have a loss-of function effect. The effect of the R71W alteration was noticeably stronger, and we observed an almost threefold higher frequency of this allele in breast cancer cases versus controls, but this difference did not reach statistical significance. Nonetheless, these results collectively suggest that the novel PS-2 alleles described here, especially R71W, affect PS-2 function and may potentially confer a moderate risk of susceptibility to breast cancer.

Constitutive hedgehog signaling in chondrosarcoma up-regulates tumor cell proliferation

Chondrosarcoma is a malignant cartilage tumor that may arise from benign precursor lesions, such as enchondromas. Some cases of multiple enchondromas are caused by a mutation that results in constitutive activation of Hedgehog-mediated signaling. We found that chondrosarcomas expressed high levels of the Hedgehog target genes PTCH1 and GLI1. Treatment with parathyroid hormone-related protein down-regulated Indian Hedgehog (IHH) expression in normal growth plates but not in chondrosarcoma or enchondroma organ cultures. Treatment of the chondrosarcoma organ cultures with Hedgehog protein increased cell proliferation rate, whereas addition of chemical inhibitors of Hedgehog signaling decreased the proliferation rate. Chondrosarcoma xenografts from 12 different human tumors were established in NOD-SCID mice. Treatment with triparanol, an inhibitor of Hedgehog signaling, resulted in a 60% decrease in tumor volume, a 30% decrease in cellularity, and a 20% reduction in proliferation rate. These results show that Hedgehog signaling is active in chondrosarcoma and benign cartilage tumors and regulates tumor cell proliferation. Our data raise the intriguing possibility that Hedgehog blockade could serve as an effective treatment for chondrosarcoma, a tumor for which there are currently no universally effective nonsurgical management options.

LAF-4 is aberrantly expressed in human breast cancer

LAF-4, which encodes a nuclear protein with transactivation potential, is fused to the MLL gene in acute lymphoblastic leukemia (ALL). We identified LAF-4 as a gene that is transcriptionally deregulated in breast tumors and thus may have a pathological role in mammary tumorigenesis. In line with the previous finding that LAF-4 expression is tissue specific, we did not detect any LAF-4 mRNA in normal mammary epithelial cell lines. However, 2 of 5 breast cancer cell lines were found to express LAF-4 at both the RNA and protein levels. In 2 of 9 primary tumor-normal pairs, the expression of LAF-4 was clearly elevated in the tumor tissue. Using RNA in situ hybridization, we demonstrated that LAF-4 is expressed in mammary tumor cells but not in normal acini. In a group of 64 primary human breast tumors, we found that LAF-4 was overexpressed in approximately 20% of the cases. Although epigenetic changes may be involved in altered expression of some genes, differences in LAF-4 expression were not associated with DNA methylation of the predicted promoter region. Our results suggest that LAF-4 may be a proto-oncogene that is transcriptionally activated in some cases of breast cancer.

TP53 mutations and outcome in osteosarcoma: a prospective, multicenter study

PURPOSE

Mutations of the TP53 gene have been associated with resistance to chemotherapy as well as poor prognosis in many different malignancies. This is the first prospective study of the prognostic value of somatic TP53 mutations in patients with newly diagnosed extremity osteosarcoma.

PATIENTS AND METHODS

One hundred ninety-six patients with high-grade, nonmetastatic osteosarcoma of the extremities were enrolled from seven tertiary care institutions and observed prospectively for tumor recurrence (median follow-up duration, 44 months). All patients received neoadjuvant or adjuvant chemotherapy and surgery. Tumors were analyzed for the presence of TP53 mutations by polymerase chain reaction single-strand conformation polymorphism analysis and direct DNA sequencing. The association of the status of the TP53 gene with the risk of systemic recurrence was examined using survival analyses with traditional and histologic markers as prognostic factors.

RESULTS

Patient age was the only factor that varied with TP53 gene status (P = .05). No relationship was identified between TP53 status and systemic relapse (relative risk, 1.24; P = .41). Analyses based on missense or nonsense mutations gave similar results (P > .10). In multivariate analysis, large (> 9 cm) tumor size (relative risk, 1.9; P = .006) and poor histologic response (< or = 90% necrosis) to chemotherapy (relative risk, 2.14; P = .02) were the only significant independent predictors of systemic outcome.

CONCLUSION

We found no evidence that TP53 mutations predict for development of metastases in patients with high-grade osteosarcoma. Identification of other genes that influence chemotherapy response and clinical outcome in osteosarcoma is needed to facilitate further improvements in patient outcomes.

Epigenetic and genetic loss of Hic1 function accentuates the role of p53 in tumorigenesis

The gene hypermethylated in cancer 1 (HIC1) is epigenetically inactivated, but not mutated, in cancer. Here we show that cooperative loss of Hic1 with p53, but not INK4a, yields distinct tumor phenotypes in mice. Germline deletion of one allele of each gene on the opposite chromosome yields breast and ovarian carcinomas and metastatic osteosarcomas with epigenetic inactivation of the wild-type Hic1 allele. Germline deletion of the two genes on the same chromosome results in earlier appearance and increased prevalence and aggressiveness of osteosarcomas with genetic deletion of both wild-type genes. In human osteosarcomas, hypermethylation of HIC1 is frequent only in tumors with p53 mutations. Our results indicate the importance of genes altered only through epigenetic mechanisms in cancer progression in conjunction with genetically modified tumor suppressor genes.

Cloning and mutation analysis of ZFP276 as a candidate tumor suppressor in breast cancer

Loss of heterozygosity (LOH) involving chromosome 16q23.4 occurs frequently in breast tumors, which suggests that this region may contain a tumor suppressor gene. Since ZFP276 is located in this region, we have therefore cloned and performed mutation analysis of its coding region in 70 breast tumors. One silent polymorphism and two alterations predicted to result in amino acid changes were detected. Absence of the wild-type allele in tumors carrying the E530D variant suggests a possible role for this change in tumorigenesis.

A mutant PTH/PTHrP type I receptor in enchondromatosis

Enchondromas are common benign cartilage tumors of bone. They can occur as solitary lesions or as multiple lesions in enchondromatosis (Ollier and Maffucci diseases). Clinical problems caused by enchondromas include skeletal deformity and the potential for malignant change to chondrosarcoma. The extent of skeletal involvement is variable in enchondromatosis and may include dysplasia that is not directly attributable to enchondromas. Enchondromatosis is rare, obvious inheritance of the condition is unusual and no candidate loci have been identified. Enchondromas are usually in close proximity to, or in continuity with, growth-plate cartilage. Consequently, they may result from abnormal regulation of proliferation and terminal differentiation of chondrocytes in the adjoining growth plate. In normal growth plates, differentiation of proliferative chondrocytes to post-mitotic hypertrophic chondrocytes is regulated in part by a tightly coupled signaling relay involving parathyroid hormone related protein (PTHrP) and Indian hedgehog (IHH). PTHrP delays the hypertrophic differentiation of proliferating chondrocytes, whereas IHH promotes chondrocyte proliferation. We identified a mutant PTH/PTHrP type I receptor (PTHR1) in human enchondromatosis that signals abnormally in vitro and causes enchondroma-like lesions in transgenic mice. The mutant receptor constitutively activates Hedgehog signaling, and excessive Hedgehog signaling is sufficient to cause formation of enchondroma-like lesions.

Comparison of p53 mutations in patients with localized osteosarcoma and metastatic osteosarcoma

BACKGROUND

In some malignancies, p53 mutations are associated with tumor progression. To address the role of p53 mutations in the development and progression of osteosarcoma, the authors analyzed specimens from 247 patients with primary localized osteosarcomas and 25 patients with osteosarcomas that were metastatic at the time of diagnosis. The group included 27 matched biopsy-resection specimens and 21 biopsy-metastasis paired specimens.

METHODS

The authors examined the nature and location of p53 mutations (exons 4-10) by polymerase chain reaction-single-strand conformation polymorphism and confirmed mutations by direct DNA sequencing.

RESULTS

The overall frequency of p53 mutations was 22% (60 of 272 specimens), with 13 of 60 mutations located in exons 4 or 10. A similar proportion of localized osteosarcomas had alterations of the p53 gene (55 of 247 specimens; 22.3%) compared with tumors from patients who had metastases at the time of diagnosis (5 of 25 specimens; 20%; P = 0.96). Patients who had p53 missense mutations were older compared with patients who had nonsense alterations or a wild type gene (P = 0.01). Examination of paired biopsy-resection and biopsy-metastasis specimens revealed that the p53 status was concordant between the biopsy and later tumor specimens in all patients.

CONCLUSIONS

The p53 mutation status did not differentiate between patients who presented with a localized osteosarcoma and those who presented with metastases at the time of diagnosis. The current data indicate that p53 mutations are not late events in osteosarcoma tumor progression, because they are evident before the development of metastases. The inclusion of exons 4 and 10 increased the sensitivity of the analysis.

p53 missense but not truncation mutations are associated with low levels of p21(CIP1/WAF1) mRNA expression in primary human sarcomas

Many growth-suppressing signals converge to control the levels of the CDK inhibitor p21(CIP1/WAF1). Some human cancers exhibit low levels of expression of p21(CIP1/WAF1) and mutations in p53 have been implicated in this down-regulation. To evaluate whether the presence of p53 mutations was related to the in vivo expression of p21(CIP1/WAF1) mRNA in sarcomas we measured the p21(CIP1/WAF1) mRNA levels for a group of 71 primary bone and soft tissue tumours with known p53 status. As expected, most tumours with p53 mutations expressed low levels of p21(CIP1/WAF1)mRNA. However, we identified a group of tumours with p53 gene mutations that exhibited normal or higher levels of p21(CIP1/WAF1) mRNA. The p53 mutations in the latter group were not the common missense mutations in exons 4-9, but were predominantly nonsense mutations predicted to result in truncation of the p53 protein. The results of this study suggest that different types of p53 mutations can have different effects on the expression of downstream genes such as p21(CIP1/WAF1) in human sarcomas.

Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients

Identification of mutations causing cystic fibrosis (CF) in the Turkish population is essential for assessment of the molecular basis of CF in Turkey and the development of strategies for prenatal diagnosis and genetic counseling. Here, we present an updated report of mutations found in the Turkish CF population from an extensive screening study of the entire coding region, including exon-intron boundaries and the promoter region. Cases for which mutations could not be identified were also screened for previously defined large alterations and (TG)mTn-M470V loci. This study revealed a total of 27 different mutations accounting for almost 60% of disease genes in the Turkish population. In this study, we also identified the haplotypes associated with 17 mutations and those associated with unknown mutations. The mutation spectrum of CF in Turkey and its associated haplotypes indicated the presence of a major Mediterranean component in the contemporary Turkish population.

Screening of deletions in SMN, NAIP and BTF2p44 genes in Turkish spinal muscular atrophy patients

Deletions of the spinal muscular atrophy (SMA)-determining gene, SMN1, NAIP, and a third multicopy gene, BTF2p44tel were investigated in 60 unrelated Turkish SMA patients. SMN1 was deleted for at least exons 7 and 8 in 85% of the Turkish SMA patients. The NAIP gene was deleted in 75 and 33% of type I and type II SMA patients, respectively. Analysis of the 5'end of the BTF2p44tel gene indicated the extension of deletion in 13.3% of the cases, mainly in type I patients. Deletions of the NAIP and BTF2p44tel genes were detected in 1.3 and 3.9% of carrriers, respectively, in Turkish SMA families. Two patients were detected to harbor the hybrid SMN gene, one type II with deletion of the NAIP gene, and one type III without deletion of the NAIP gene.

Familial posterior fossa brain tumors of infancy secondary to germline mutation of the hSNF5 gene

We have identified a family afflicted over multiple generations with posterior fossa tumors of infancy, including central nervous system (CNS) malignant rhabdoid tumor (a subset of primitive neuroectodermal tumors, or PNET) and choroid plexus carcinoma. Various hereditary tumor syndromes, including Li-Fraumeni syndrome, Gorlin syndrome, and Turcot syndrome, have been linked to increased risk of developing CNS PNETs and choroid plexus tumors. Malignant rhabdoid tumors of the CNS and kidney show loss of heterozygosity at chromosome 22q11. The hSNF5 gene on chromosome 22q11 has recently been identified as a candidate tumor-suppressor gene in sporadic CNS and renal malignant rhabdoid tumors. We describe a family in which both affected and some unaffected family members were found to have a germline splice-site mutation of the hSNF5 gene, leading to exclusion of exon 7 from the mature cDNA and a subsequent frameshift. Tumor tissue shows loss of the wild-type hSNF5 allele, in keeping with a tumor-suppressor gene. These findings suggest that germline mutations in hSNF5 are associated with a novel autosomal dominant syndrome with incomplete penetrance that predisposes to malignant posterior fossa brain tumors in infancy.

Expression of osteocalcin and its transcriptional regulators core-binding factor alpha 1 and MSX2 in osteoid-forming tumours

Osteosarcoma, fibrous dysplasia, and myositis ossificans contain osteoid-producing cells that are not necessarily morphologically typical osteoblasts. Nevertheless, these pathologic cells may share differentiation steps with osteoblasts at the molecular level. Osteocalcin, a bone-specific extracellular matrix protein, is a marker of mature osteoblasts. Osteocalcin is upregulated by the transcription factor core-binding factor alpha 1, which is responsible for commitment to the osteoblastic lineage, and is downregulated by MSX2, a homeobox-containing transcription factor expressed during the early proliferative phase of osteoblast differentiation. Semiquantitative reverse transcription-polymerase chain reaction was used to compare expression levels of osteocalcin, core-binding factor alpha 1, and MSX2 in 34 osteosarcoma, five fibrous dysplasia, and five myositis ossificans specimens, as well as in seven normal cortical bone samples. Despite normal or elevated levels of core-binding factor alpha-1 expression in most specimens, osteocalcin expression was low or undetectable in most cases of osteosarcoma (25 of 34) and myositis ossificans (4 of 5). Single-strand conformation polymorphism and sequencing did not identify any mutations in the DNA-binding domain of core-binding factor alpha 1. However, a high level of MSX2 expression was demonstrated in these lesions, which may inhibit osteocalcin transcription. The presence of moderate levels of osteocalcin in fibrous dysplasia may contribute to the characteristic disconnected appearance of trabeculae in that entity because osteocalcin is a negative regulator of bone formation.

Co-amplification and overexpression of CDK4, SAS and MDM2 occurs frequently in human parosteal osteosarcomas

Amplification of genes in the 12q13-15 region occurs frequently in several malignancies including osteosarcoma. The products of these amplified genes are thought to provide cancer cells with a selective growth advantage; however, the specific gene(s) driving this amplicon is unknown. We have previously shown that the SAS gene is amplified in most parosteal osteosarcomas. In this study we analysed additional putative growth regulatory genes in this chromosomal region in 24 primary osteosarcoma specimens. CDK4 and SAS were coamplified in 6/6 parosteal tumors, and MDM2 was also amplified in 4/5 parosteal cases. In comparison, amplification occurred in only 2/16 classical intramedullary osteosarcomas and involved the SAS gene. Each amplified gene had a correspondingly elevated mRNA level. Four high grade intramedullary tumors had elevated mRNA expression of SAS, but did not exhibit gene amplification. Gene amplification/overexpression was not associated with metastatic disease and did not change markedly with tumor progression, as evidenced by analysis of sequential tumor specimens from eight patients. Three other genes in the 12q13-15 region (CDK2, WNT1 and WNT10b) were not amplified in any of the tumors. The different patterns of gene amplification and overexpression of CDK4, SAS and MDM2 in parosteal and intramedullary osteosarcomas may help explain the disparity in the biological behaviour of these two types of osteosarcoma.