Optical Genome Mapping for Comprehensive Cytogenetic Analysis of Soft-Tissue and Bone Tumors for Diagnostic Purposes

Soft-tissue and bone tumors represent a heterogeneous group of tumors encompassing more than 100 histologic subtypes today. Identifying genetic aberrations increasingly is important in these tumors for accurate diagnosis. Although gene mutations typically are detected by second-generation sequencing, the identification of structural variants (SVs) and copy number alterations (CNAs) remains challenging and requires various cytogenetic techniques including karyotyping, fluorescence in situ hybridization, and arrays, each with important limitations. Optical Genome Mapping (OGM), a non-sequencing-based technique for high-resolution detection of SVs and CNAs, was applied in a retrospective series of diagnostic soft-tissue and bone tumor samples. Sample preparation was successful in 38 of 53 cases, with the highest success rate in nonadipocytic soft-tissue tumors (24 of 27 cases; 89%). In 32 of 35 cases carrying a diagnostic SV or CNA, OGM identified the aberration (91%), including a POU2AF3::EWSR1 fusion in a round cell sarcoma and a translocation t(1;5)(p22;p15) in a myxoinflammatory fibroblastic sarcoma. Interestingly, OGM shed light on the genomic complexity underlying the various aberrations. In five samples, OGM showed that chains of rearrangements generated the diagnostic fusion, three of which involved chromoplexy. In addition, in nine samples, chromothripsis was causal to the formation of giant marker/ring/double-minute chromosomes. Finally, compared with standard-of-care cytogenetics, OGM revealed additional aberrations, requiring further investigation of their potential clinical relevance.

Case report: Cardiac intimal sarcoma in a young child

Undifferentiated mesenchymal tumors from the intimal layer (intimal sarcomas) are rare within the ventricles and exceptional in children. A rare case of an intimal sarcoma located in the right ventricle in a young child is presented with need for urgent surgical resection due to mechanical flow obstruction. Tumor cells showed amplification of MDM2 gene and a homozygous loss of CDKN2A on 9p21. A review of the literature regarding primary cardiac malignancies and intimal sarcoma in children is provided.

Abstract 3100: XenoSarc: patient-derived xenograft (PDX) models of soft tissue sarcoma (STS) and their histopathological and molecular characterization

STS constitutes a family of rare mesenchymal tumors with more than 70 subtypes described. The limited treatment options available for advanced STS patients underline the need for reliable preclinical models to test new therapeutic approaches. We established a panel of PDX models (XenoSarc) by subcutaneous implantation of fresh tumor specimens in athymic mice (nu/nu NRMI). Once tumor growth was observed, pieces of tumor were re-transplanted to next generations of animals. At each passage tumor fragments were collected for histopathological and molecular characterization. In an ongoing effort 493 STS samples from 414 consenting patients treated at the University Hospitals, Leuven (Belgium) have been transplanted. A total of 67 PDX models from 20 STS subtypes have been established, meaning they have stable morphological, immunohistochemical and genetic characteristics over at least 2 passages. The PDX platform includes more common STS subtypes such as myxofibrosarcoma (n=12 models), gastrointestinal stromal tumors (9), dedifferentiated liposarcoma (10), and leiomyosarcoma (8), as well as models from ultra-rare subtypes, e.g. pulmonary intimal sarcoma, extraskeletal osteosarcoma, mesenchymal chondrosarcoma, myxoinflammatory fibroblastic sarcoma and others. All relevant details about the donor patient and tumor characteristics, including sensitivity to the standard treatments, are known for every model. The models are well-characterized, with availability of molecular information on genomic profile (by low-coverage whole genome sequencing), and expression profile (by RNA sequencing). Xenografts are accompanied by ready to use tissue microarrays (TMA) from the models, which can be exploited for target identification and model selection for preclinical studies. Ex-mouse material can also be used to establish primary cell cultures and 3D organoids for in vitro screening purposes. The XenoSarc platform offers opportunities for studying the biology of various sarcoma subtypes including ultra-rare entities and was found to be a very reliable tool for early drug screening in STS in preparation of clinical testing of novel compounds. The platform is available for collaborative preclinical projects with academic and industrial partners.

Citation Format: Agnieszka Wozniak, Luna De Sutter, Lore De Cock, Britt Van Renterghem, Che-Jui Lee, Yannick Wang, Ulla Vanleeuw, Kimberly Verbeeck, Daphne Hompes, Friedl Sinnaeve, Hazem Wafa, Baki Topal, Joris Jaekers, Dirk Van Raemdonck, Maria Debiec-Rychter, Raf Sciot, Patrick Schöffski. XenoSarc: patient-derived xenograft (PDX) models of soft tissue sarcoma (STS) and their histopathological and molecular characterization [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 3100.

Correlation of Immunological and Molecular Profiles with Response to Crizotinib in Alveolar Soft Part Sarcoma: An Exploratory Study Related to the EORTC 90101 "CREATE" Trial

Alveolar soft part sarcoma (ASPS) is a rare subtype of soft tissue sarcoma characterized by an unbalanced translocation, resulting in ASPSCR1-TFE3 fusion that transcriptionally upregulates MET expression. The European Organization for Research and Treatment of Cancer (EORTC) 90101 “CREATE” phase II trial evaluated the MET inhibitor crizotinib in ASPS patients, achieving only limited antitumor activity. We performed a comprehensive molecular analysis of ASPS tissue samples collected in this trial to identify potential biomarkers correlating with treatment outcome. A tissue microarray containing 47 ASPS cases was used for the characterization of the tumor microenvironment using multiplex immunofluorescence. DNA isolated from 34 available tumor samples was analyzed to detect recurrent gene copy number alterations (CNAs) and mutations by low-coverage whole-genome sequencing and whole-exome sequencing. Pathway enrichment analysis was used to identify diseased-associated pathways in ASPS sarcomagenesis. Kaplan–Meier estimates, Cox regression, and the Fisher’s exact test were used to correlate histopathological and molecular findings with clinical data related to crizotinib treatment, aiming to identify potential factors associated with patient outcome. Tumor microenvironment characterization showed the presence of PD-L1 and CTLA-4 in 10 and 2 tumors, respectively, and the absence of PD-1 in all specimens. Apart from CD68, other immunological markers were rarely expressed, suggesting a low level of tumor-infiltrating lymphocytes in ASPS. By CNA analysis, we detected a number of broad and focal alterations. The most common alteration was the loss of chromosomal region 1p36.32 in 44% of cases. The loss of chromosomal regions 1p36.32, 1p33, 1p22.2, and 8p was associated with shorter progression-free survival. Using whole-exome sequencing, 13 cancer-associated genes were found to be mutated in at least three cases. Pathway enrichment analysis identified genetic alterations in NOTCH signaling, chromatin organization, and SUMOylation pathways. NOTCH4 intracellular domain dysregulation was associated with poor outcome, while inactivation of the beta-catenin/TCF complex correlated with improved outcome in patients receiving crizotinib. ASPS is characterized by molecular heterogeneity. We identify genetic aberrations potentially predictive of treatment outcome during crizotinib therapy and provide additional insights into the biology of ASPS, paving the way to improve treatment approaches for this extremely rare malignancy.

Detection of MDM2 amplification by shallow whole genome sequencing of cell-free DNA of patients with dedifferentiated liposarcoma

High-level amplification of MDM2 and other genes in the 12q13–15 locus is a hallmark genetic feature of well-differentiated and dedifferentiated liposarcomas (WDLPS and DDLPS, respectively). Detection of this genomic aberration in plasma cell-free DNA may be a clinically useful assay for non-invasive distinction between these liposarcomas and other retroperitoneal tumors in differential diagnosis, and might be useful for the early detection of disease recurrence. In this study, we performed shallow whole genome sequencing of cell-free DNA extracted from 10 plasma samples from 3 patients with DDLPS and 1 patient with WDLPS. In addition, we studied 31 plasma samples from 11 patients with other types of soft tissue tumors. We detected MDM2 amplification in cell-free DNA of 2 of 3 patients with DDLPS. By applying a genome-wide approach to the analysis of cell-free DNA, we also detected amplification of other genes that are known to be recurrently affected in DDLPS. Based on the analysis of one patient with DDLPS with longitudinal plasma samples available, we show that tracking MDM2 amplification in cell-free DNA may be potentially useful for evaluation of response to treatment. The patient with WDLPS and patients with other soft tissue tumors in differential diagnosis were negative for the MDM2 amplification in cell-free DNA. In summary, we demonstrate the feasibility of detecting amplification of MDM2 and other DDLPS-associated genes in plasma cell-free DNA using technology that is already routinely applied for other clinical indications. Our results may have clinical implications for improved diagnosis and surveillance of patients with retroperitoneal tumors.

Histopathological and Molecular Profiling of Clear Cell Sarcoma and Correlation with Response to Crizotinib: An Exploratory Study Related to EORTC 90101 "CREATE" Trial

Simple Summary

Clear cell sarcoma (CCSA) is a rare subtype of soft tissue sarcoma characterized by EWSR1 rearrangement and subsequent MET upregulation. The European Organisation for Research and Treatment of Cancer 90101 phase II trial evaluated the MET inhibitor crizotinib in CCSA but resulted in only sporadic responses. The aim of this exploratory study was to identify the molecular alterations potentially relevant for the treatment outcome by using archival CCSA samples and trial-related clinical data. We characterized MET signaling and revealed an infrequent activation of MET, which may explain the lack of response to crizotinib in the disease cohort. Based on sequencing analyses, we discovered copy number alterations, mutations and dysregulated pathways with potentially predictive or prognostic values for patients’ outcomes. This work describes the molecular heterogeneity in CCSA and provides deep insight into the biology of this ultra-rare malignancy, which may potentially lead to better therapeutic approaches.

Abstract

Clear cell sarcoma (CCSA) is characterized by a chromosomal translocation leading to EWSR1 rearrangement, resulting in aberrant transcription of multiple genes, including MET. The EORTC 90101 phase II trial evaluated the MET inhibitor crizotinib in CCSA but resulted in only sporadic responses. We performed an in-depth histopathological and molecular analysis of archival CCSA samples to identify alterations potentially relevant for the treatment outcome. Immunohistochemical characterization of MET signaling was performed using a tissue microarray constructed from 32 CCSA cases. The DNA from 24 available tumor specimens was analyzed by low-coverage whole-genome sequencing and whole-exome sequencing for the detection of recurrent copy number alterations (CNAs) and mutations. A pathway enrichment analysis was performed to identify the pathways relevant for CCSA tumorigenesis. Kaplan–Meier estimates and Fisher’s exact test were used to correlate the molecular findings with the clinical features related to crizotinib treatment, aiming to assess a potential association with the outcomes. The histopathological analysis showed the absence of a MET ligand and MET activation, with the presence of MET itself in most of cases. However, the expression/activation of MET downstream molecules was frequently observed, suggesting the role of other receptors in CCSA signal transduction. Using sequencing, we detected a number of CNAs at the chromosomal arm and region levels. The most common alteration was a gain of 8q24.21, observed in 83% of the cases. The loss of chromosomes 9q and 12q24 was associated with shorter survival. Based on exome sequencing, 40 cancer-associated genes were found to be mutated in more than one sample, with SRGAP3 and KMT2D as the most common alterations (each in four cases). The mutated genes encoded proteins were mainly involved in receptor tyrosine kinase signaling, polymerase-II transcription, DNA damage repair, SUMOylation and chromatin organization. Disruption in chromatin organization was correlated with longer progression-free survival in patients receiving crizotinib. Conclusions: The infrequent activation of MET may explain the lack of response to crizotinib observed in the majority of cases in the clinical trial. Our work describes the molecular heterogeneity in CCSA and provides further insight into the biology of this ultra-rare malignancy, which may potentially lead to better therapeutic approaches for CCSA.

Comprehensive Molecular Analysis of Inflammatory Myofibroblastic Tumors Reveals Diverse Genomic Landscape and Potential Predictive Markers for Response to Crizotinib

PURPOSE

The European Organization for Research and Treatment of Cancer (EORTC) clinical phase II trial 90101 "CREATE" showed high antitumor activity of crizotinib, an inhibitor of anaplastic lymphoma kinase (ALK)/ROS1, in patients with advanced inflammatory myofibroblastic tumor (IMFT). However, recent findings suggested that other molecular targets in addition to ALK/ROS1 might also contribute to the sensitivity of this kinase inhibitor. We therefore performed an in-depth molecular characterization of archival IMFT tissue, collected from patients enrolled in this trial, with the aim to identify other molecular alterations that could play a role in the response to crizotinib.

EXPERIMENTAL DESIGN

Twenty-four archival IMFT samples were used for histopathological assessment and DNA/RNA evaluation to identify gene fusions, copy-number alterations (CNA), and mutations in the tumor tissue. Results were correlated with clinical parameters to assess a potential association between molecular findings and clinical outcomes.

RESULTS

We found 12 ALK fusions with 11 different partners in ALK-positive IMFT cases by Archer analysis whereas we did not identify any ROS1-rearranged tumor. One ALK-negative patient responding to crizotinib was found to have an ETV6-NTRK fusion in the tumor specimen. The CNA profile and mutational landscape of IMFT revealed extensive molecular heterogeneity. Loss of chromosome 19 (25% of cases) and PIK3CA mutations (9% of cases) were associated with shorter progression-free survival in patients receiving crizotinib.

CONCLUSIONS

We identified multiple genetic alterations in archival IMFT material and provide further insight into the molecular profile of this ultra-rare, heterogeneous malignancy, which may potentially translate into novel treatment approaches for this orphan disease.

Long-term efficacy update of crizotinib in patients with advanced, inoperable inflammatory myofibroblastic tumour from EORTC trial 90101 CREATE

PURPOSE

European Organisation for Research and Treatment of Cancer (EORTC) 90101 (CREATE) was a prospective, multicentric, non-randomised, open-label phase II basket trial to assess the efficacy and safety of crizotinib in patients with different types of cancers, including advanced inflammatory myofibroblastic tumour (IMT) with or without anaplastic lymphoma kinase (ALK) rearrangements. Here, we report updated results with long-term follow-up.

PATIENTS/METHODS

After central reference pathology, eligible ALK-positive and ALK-negative patients with advanced/metastatic IMT deemed incurable with surgery, radiotherapy or systemic therapy received oral crizotinib 250 mg twice daily. The ALK status was assessed centrally using immunohistochemistry and fluorescence in situ hybridisation. The primary end-point was the proportion of patients who achieved an objective response (i.e. complete or partial response). If ≥6 ALK-positive patients achieved a confirmed response, the trial would be deemed successful.

RESULTS

At data cut-off on 28th January 2021, we performed the final analysis of this trial. Of the 20 eligible and treated patients (19 of whom were evaluable for efficacy), with a median follow-up of 50 months, five were still on crizotinib treatment (4/12 ALK-positive and 1/8 ALK-negative patients). The updated objective response rate (ORR) was 66.7% (95% confidence interval [CI] 34.9-90.1%) in ALK-positive patients and 14.3% (95% CI 0.0-57.9%) in ALK-negative patients. In the ALK-positive and ALK-negative patients, the median progression-free survival was 18.0 months (95% CI 4.0-NE) and 14.3 months (95% CI 1.2-31.1), respectively; 3-year overall survival rates were 83.3% (95% CI 48.2-95.6) and 34.3% (95% CI 4.8-68.5). Safety results were consistent with previously reported data.

CONCLUSION

These updated results confirm previous findings that crizotinib is effective, with durable responses, in patients with locally advanced or metastatic ALK-positive IMT. With further follow-up after the original primary analysis, the ORR increased, as patients derived long-term benefit and some responses converted from stable disease to partial responses.

CLINICAL TRIAL NUMBER

EORTC 90101, NCT01524926.

Management of Synovial Sarcoma in a Tertiary Referral Center: A Retrospective Analysis of 134 Patients

BACKGROUND

Synovial sarcomas (SS) are malignant mesenchymal neoplasms that account for about 10% of all sarcomas. Complete surgical excision is the mainstay of primary treatment for localized disease, but SS have a high tendency for local relapse and metastases. Metastatic disease is commonly treated with systemic chemotherapy.

METHODS

We designed a retrospective analysis to describe the clinical presentation, course of treatment, outcome, and prognosis of patients with SS. Univariate and multivariate analyses were performed for potential prognostic factors.

RESULTS

We identified 134 patients treated between 1987 and 2018, with a cutoff date of December 2018. Demographics, disease characteristics, treatment, and survival rates were collected and analyzed. The median overall survival (mOS) from the date of diagnosis was 96.7 months. The median progression-free survival was 6.37 months. Disease-free survival was 26 months. Age over 65 years was found to be a prognostic factor with statistically significant value in the univariate analysis regarding mOS (p = 0.015) and mOS after local relapse (p = 0.0228).

CONCLUSIONS

Even though our study is limited by the retrospective nature of the analysis, it adds an important amount of clinical data regarding the treatment and outcome of SS.

Loss of 9p21 Regulatory Hub Promotes Kidney Cancer Progression by Upregulating HOXB13

Loss of chromosome 9p21 is observed in one-thirds of clear-cell renal cell carcinoma (ccRCC) and is associated with poorer patient survival. Unexpectedly, 9p21 LOH does not lead to decreased expression of the 9p21 tumor suppressor genes, CDKN2A and CDKN2B, suggesting alternative mechanisms of 9p-mediated tumorigenesis. Concordantly, CRISPR-mediated 9p21 deletion promotes growth of immortalized human embryonic kidney epithelial cells independently of the CDKN2A/B pathway inactivation. The 9p21 locus has a highly accessible chromatin structure, suggesting that 9p21 loss might contribute to kidney cancer progression by dysregulating genes distal to the 9p21 locus. We identified several 9p21 regulatory hubs by assessing which of the 9p21-interacting genes are dysregulated in 9p21-deleted kidney cells and ccRCCs. By focusing on the analysis of the homeobox gene 13 (HOXB13) locus, we found that 9p21 loss relieves the HOXB13 locus, decreasing HOXB13 methylation and promoting its expression. Upregulation of HOXB13 facilitates cell growth and is associated with poorer survival of patients with ccRCC. IMPLICATIONS: The results of our study propose a novel tumor suppressive mechanism on the basis of coordinated expression of physically associated genes, providing a better understanding of the role of chromosomal deletions in cancer.

Comprehensive targeted next-generation sequencing approach in the molecular diagnosis of gastrointestinal stromal tumor

Mutational analysis guides therapeutic decision making in patients with advanced-stage gastrointestinal stromal tumors (GISTs). We evaluated three targeted next-generation sequencing (NGS) assays, consecutively used over 4 years in our laboratory for mutational analysis of 162 primary GISTs: Agilent GIST MASTR, Illumina TruSight 26 and an in-house developed 96 gene panels. In addition, we investigated the feasibility of a more comprehensive approach by adding targeted RNA sequencing (Archer FusionPlex, 11 genes) in an attempt to reduce the number of Wild Type GISTs. We found KIT or PDGFRA mutations in 149 out of 162 GISTs (92.0%). Challenging KIT exon 11 alterations were initially missed by different assays in seven GISTs and typically represented deletions at the KIT intron 10-exon 11 boundary or large insertions/deletions (>24 base pairs). Comprehensive analysis led to the additional identification of driver alterations in 8/162 GISTs (4.9%): apart from BRAF and SDHA mutations (one case each), we found five GISTs harboring somatic neurofibromatosis type 1 (NF1) alterations (3.1%) and one case with an in-frame TRIM4-BRAF fusion not reported in GIST before. Eventually, no driver alteration was found in two out of 162 GISTs (1.2%) and three samples (1.9%) failed analysis. Our study shows that a comprehensive targeted NGS approach is feasible for routine mutational analysis of GIST, thereby substantially reducing the number of Wild Type GISTs, and highlights the need to optimize assays for challenging KIT exon 11 alterations.

Abstract 1676: Plocabulin, a novel tubulin inhibitor, has antitumor activity in various patient-derived xenograft models of soft tissue sarcoma

Objective: Soft tissue sarcomas (STS) constitute a heterogeneous group of rare, malignant tumors arising in mesenchymal tissue. Doxorubicin (DOX)-based chemotherapy has been the standard of care for patients with advanced and metastatic STS, despite providing low response rates and poor disease control in this disease. Even for patients who respond to treatment, the outcome of advanced and metastatic STS is poor. In light of this, there is a clear need for more effective and novel therapeutic compounds for STS. In the current study, we explored the activity of plocabulin (PLO; PM060184, PharmaMar), a novel cytotoxic tubulin-dynamics modifier, in patient-derived xenograft (PDX) models of some common and some rare histologic subtypes of STS.

Methods: Female NMRI nu/nu mice (n=80) were transplanted bilaterally with human STS xenografts: UZLX-STS134CRS (CIC-rearranged sarcoma), UZLX-STS124DDLPS (dedifferentiated liposarcoma), UZLX-STS22_2FLMS (leiomyosarcoma) and UZLX-STS122FIS (intimal sarcoma). Xenografted animals were randomly assigned to three treatment groups: 1) vehicle (20% hydroxypropyl β-cyclodextrin) 6.4 ml/kg intravenously (i.v.) once weekly (QW), 2) DOX 3.0 mg/kg i.v. QW, or 3) PLO 16 mg/kg i.v. QW. All treatments lasted 22 days. Antitumor activity was assessed by tumor volume analysis, histopathology and Western blotting. Mitotic count, phospho-histone H3 and Ki-67 were analyzed for proliferative activity. Apoptotic count, and cleaved poly-(ADP-ribose)-polymerase were analyzed for apoptotic activity. CD31 immunostains were used to evaluate the tumor vasculature. The Kruskal-Wallis test with Dunn's multiple comparisons (DMC) test was used to compare non-parametric variables between groups. Statistical significance was defined as p <0.05.

Results: PLO treatment resulted in tumor shrinkage in UZLX-STS134CRS (to 40% of baseline volume) and UZLX-STS22_2FLMS (to 27%), and tumor volume stabilization in UZLX-STS124DDLPS and UZLX-STS122FIS. Vehicle-treated tumors of UZLX-STS134CRS, UZLX-STS22_2FLMS and UZLX-STS124DDLPS reached 363%, 287% and 261% of baseline volume, respectively. DOX did not affect tumor volume. All DOX-treated mice of UZLX-STS122FIS were lost before the end of the experiment: one mouse was sacrificed on day 16 due to body weight loss, the remaining five were found dead on day 19. Despite this, relative tumor volumes already differed significantly between the vehicle-PLO and DOX-PLO groups on day 16 for this model (p<0.001 and p=0.002, respectively, DMC). PLO-treated tumors of UZLX-STS134CRS and UZLX-STS22_2FLMS were necrotic and degenerated to such an extent that histological analysis could not be performed in full. In the PLO-treated tumors of UZLX-STS122FIS, we demonstrated a significant decrease in the total vascular area, consistent with the drug's vascular disrupting capacity. No effects on proliferation or apoptosis were observed. The experimental drug was well tolerated throughout the experiment at the administered dose.

Conclusion: PLO is a novel anti-tubulin agent showing potent antitumor activity in a variety of PDX modes of STS. The drug induces cytotoxicity mainly through necrosis and is more active than DOX. This study provides strong arguments to study PLO further in STS and to explore the compound in clinical trials involving mesenchymal malignancies.

Citation Format: Yannick Wang, Agnieszka Wozniak, Jasmien Cornillie, Che-Jui Lee, María José Guillén, Pablo Avilés, Maria Debiec-Rychter, Raf Sciot, Patrick Schöffski. Plocabulin, a novel tubulin inhibitor, has antitumor activity in various patient-derived xenograft models of soft tissue 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 1676.

Abstract 794: Molecular analysis of archival inflammatory myofibroblastic tumor tissue samples from EORTC 90101 “CREATE” and correlation with response to crizotinib

About 50% of inflammatory myofibroblastic tumors (IMFTs) harbor rearrangements of anaplastic lymphoma kinase (ALK), the most common driver in this rare tumor. EORTC 90101 “CREATE” is so far the only prospective, disease-specific phase II clinical trial performed in IMFT. It showed high antitumor activity of crizotinib, an ALK/ROS1/MET-inhibitor. This activity was mainly seen in ALK-rearranged IMFT, but the trial results suggested that other molecular events may also contribute to crizotinib sensitivity. Here we present results of an in-depth molecular analysis of archival IMFTs collected from patients within the CREATE trial with the aim to identify other molecular alterations, which could be responsible for response to crizotinib. DNA from archival IMFTs (primary tumor or metastatic lesion) was used for low-coverage whole genome sequencing to identify genomic regions of gains or losses. Whole exome sequencing (WES) was used to assess the mutational landscape, and mutations affecting cancer consensus genes (CCGs) were analyzed in more detail. Correlative and statistical analysis were used to assess the association between molecular findings and clinical outcomes of IMFT patients. In 24 IMFTs analyzed, the recurrent whole-arm copy number losses were: 22q (58% of cases), 16p (33%), 16q (29%), 13q (29%), 19q (29%), 19p (25%), 6p (25%), 6q (21%) and 18q (21%). Loss of chromosome 19 was found to be associated with shorter progression-free survival in patients receiving crizotinib (p = 0.008). Moreover, 2p21 (including EPAS1, SIX2, EML4 from the CCG set) was frequently amplified (54% of cases), while recurrent losses were observed at 22q12.3 (71%, ISX), 7q36.3 (54%, MNX1), 10q26.3 (54%, MGMT, DUX4), 1p36.32 (50%, RPL22, SKI, TNFRSF14, CAMTA1, PRDM16), 8p23.3 (50%, ARHGEF10), 12q24.33 (46%, POLE), and 11q13.4 (33%, CCND1). No significant correlations were found between focal copy number alterations and crizotinib response. A complex genetic rearrangement involving chromosome 2, identified in 2 ALK-rearranged cases, was likely consistent with chromothripsis, a form of genomic instability related to cancer development. WES was performed in 22 cases with an average of 392 alterations per sample. When considering non-synonymous mutations in CCG, a total of 178 mutations were identified, affecting 143 genes with an average of 7 per case. Mutations in 30 CCGs, identified in ≥ 2 cases, were mainly related to DNA damage/repair mechanism, WNT, RB1-TP53, and RTK-RAS-PI3K signaling. In a case with no ALK rearrangement and ALK immunopositivity, a single base substitution in ALK (p.N571K) was identified. In conclusion, we identified multiple molecular alterations in archival IMFTs and provided further insight in the molecular profile of this ultra-rare malignancy, which may potentially lead to the identification of novel therapeutic targets for IMFT patients.

Citation Format: Che-Jui Lee, Patrick Schöffski, Elodie Modave, Bram Boeckx, Diether Lambrechts, Maria Debiec-Rychter, Raf Sciot, Jozef Sufliarsky, Hans Gelderblom, Jean-Yves Blay, Agnieszka Wozniak. Molecular analysis of archival inflammatory myofibroblastic tumor tissue samples from EORTC 90101 “CREATE” and correlation with response to crizotinib [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 794.

Abstract 1117: XenoSarc: Patient-derived xenograft (PDX) models of soft tissue sarcoma (STS) and their histopathological and molecular characterization

Background: STS constitutes a rare family of mesenchymal tumors with more than 70 subtypes classified by WHO (2013). The limited treatment options available for advanced STS underline the need for reliable preclinical models, especially from ultra-rare subtypes, to test novel therapeutic strategies.

Methods: A panel of PDX models was established by subcutaneous implantation of fresh tumor specimens in immunodeficient, athymic nude NMRI mice. Once tumor growth was observed, pieces of tumor were re-transplanted to next generations of mice. At each passage tumor fragments were collected for histopathological and molecular characterization. A model was considered “established” after observing stable histological and molecular features for at least two passages. Furthermore, ex-mouse tumor tissue samples were stored, further characterized by immunocytology and flow cytometry and cultured to be used for in vitro drug testing.

Results: Between September 2011 and November 2019, 375 STS samples from 325 consenting patients treated at the University Hospitals, Leuven, Belgium have been transplanted. A total of 56 PDX models were established, maintaining the histopathological and molecular features of the original tumor. Detailed clinical information about the donor patient and tumor characteristics (including sensitivity to standard and experimental agents), is known for every model.

At present the XenoSarc platform includes ready to use models of dedifferentiated liposarcoma (11 models), gastrointestinal stromal tumor (8), myxofibrosarcoma (8), leiomyosarcoma (7), malignant peripheral nerve sheath tumor (3), synovial sarcoma (2), pulmonary artery intimal sarcoma (2), epithelioid hemangioendothelioma (1), mesenchymal chondrosarcoma (1), pleomorphic rhabdomyosarcoma (1), CIC-rearranged round cell sarcoma (1), myxoinflammatory fibroblastic sarcoma (1), rhabdomyosarcoma not otherwise specified (NOS) (1), telangiectatic extraskeletal osteosarcoma (1), extraskeletal osteosarcoma (1) and high-grade undifferentiated pleomorphic sarcoma (7). These models are well-characterized, including molecular information on copy number changes (by low-coverage whole genome sequencing), gene expression profile (by RNA-Seq) and targeted sequencing to detect mutations in genes involved in tumorigenesis. In addition, we have constructed tissue microarrays (TMA) from the xenografts which are used for target identification and model selection for preclinical studies. We are using the xenografts for in vivo testing of novel agents, including targeted and cytotoxic (pro-)drugs, and results already served as rationale for a number of prospective clinical trials. A total of 27 other xenografts are still in early stages of engraftment, not yet fulfilling our criteria of an “established” model.

Conclusion: The XenoSarc platform offers a lot of opportunities for studying the biology of a variety of important sarcoma subtypes including ultra-rare entities, and has proven efficiency for early drug screening in STS in preparation of clinical testing of novel compounds. The platform is well maintained and continuously expanded, and available to collaborators from academia and industry.

Citation Format: Agnieszka Wozniak, Britt Van Renterghem, Jasmien Cornillie, Yannick Wang, Che-Jui Lee, Jasmien Wellens, Ulla Vanleeuw, Madita Nysen, Daphne Hompes, Friedl Sinnaeve, Hazem Wafa, Baki Topal, Tom Verbelen, Maria Debiec-Rychter, Raf Sciot, Patrick Schöffski. XenoSarc: Patient-derived xenograft (PDX) models of soft tissue sarcoma (STS) and their histopathological and molecular characterization [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 1117.

Plocabulin, a novel tubulin inhibitor, has potent antitumor activity in patient-derived xenograft models of gastrointestinal stromal tumors

The majority of patients with gastrointestinal stromal tumors (GIST) eventually become resistant with time due to secondary mutations in the driver receptor tyrosine kinase. Novel treatments that do not target these receptors may therefore be preferable. For the first time, we evaluated a tubulin inhibitor, plocabulin, in patient-derived xenograft (PDX) models of GIST, a disease generally considered to be resistant to cytotoxic agents. Three PDX models of GIST with different KIT genotype were generated by implanting tumor fragments from patients directly into nude mice. We then used these well characterized models with distinct sensitivity to imatinib to evaluate the efficacy of the novel tubulin inhibitor. The efficacy of the drug was assessed by volumetric analysis of the tumors, histopathology, immunohistochemistry and Western blotting. Plocabulin treatment led to extensive necrosis in all three models and significant tumor shrinkage in two models. This histological response can be explained by the drug's vascular-disruptive properties, which resulted in a shutdown of tumor vasculature, reflected by a decreased total vascular area in the tumor tissue. Our results demonstrated the in vivo efficacy of the novel tubulin inhibitor plocabulin in PDX models of GIST and challenge the established view that GIST are resistant to cytotoxic agents in general and to tubulin inhibitors in particular. Our findings provide a convincing rationale for early clinical exploration of plocabulin in GIST and warrant further exploration of this class of drugs in the management of this common sarcoma subtype.

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First study evaluating a tubulin inhibitor in patient-derived xenograft models of gastro-intestinal stromal tumors

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Plocabulin, a novel tubulin inhibitor, has efficacy independant of KIT genotype

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Plocabulin induced extensive, central tumor necrosis, mainly through its antiangiogenic properties.

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Our results challenge the established view that gastro-intestinal stromal tumors are resistant to cytotoxic agents.

Differential antitumor activity of compounds targeting the ubiquitin-proteasome machinery in gastrointestinal stromal tumor (GIST) cells

The majority of gastrointestinal stromal tumors (GISTs) are driven by oncogenic KIT signaling and can therefore be effectively treated with the tyrosine kinase inhibitor (TKI) imatinib mesylate. However, most GISTs develop imatinib resistance through secondary KIT mutations. The type of resistance mutation determines sensitivity to approved second-/third-line TKIs but shows high inter- and intratumoral heterogeneity. Therefore, therapeutic strategies that target KIT independently of the mutational status are intriguing. Inhibiting the ubiquitin-proteasome machinery with bortezomib is effective in GIST cells through a dual mechanism of KIT transcriptional downregulation and upregulation of the pro-apoptotic histone H2AX but clinically problematic due to the drug’s adverse effects. We therefore tested second-generation inhibitors of the 20S proteasome (delanzomib, carfilzomib and ixazomib) with better pharmacologic profiles as well as compounds targeting regulators of ubiquitination (b-AP15, MLN4924) for their effectiveness and mechanism of action in GIST. All three 20S proteasome inhibitors were highly effective in vitro and in vivo, including in imatinib-resistant models. In contrast, b-AP15 and MLN4924 were only effective at high concentrations or had mostly cytostatic effects, respectively. Our results confirm 20S proteasome inhibitors as promising strategy to overcome TKI resistance in GIST, while highlighting the complexity of the ubiquitin-proteasome machinery as a therapeutic target.

Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas

PURPOSE

The preoperative distinction between uterine leiomyoma (LM) and leiomyosarcoma (LMS) is difficult, which may result in dissemination of an unexpected malignancy during surgery for a presumed benign lesion. An assay based on circulating tumor DNA (ctDNA) could help in the preoperative distinction between LM and LMS. This study addresses the feasibility of applying the two most frequently used approaches for detection of ctDNA: profiling of copy number alterations (CNAs) and point mutations in the plasma of patients with LM.

PATIENTS AND METHODS

By shallow whole-genome sequencing, we prospectively examined whether LM-derived ctDNA could be detected in plasma specimens of 12 patients. Plasma levels of lactate dehydrogenase, a marker suggested for the distinction between LM and LMS by prior studies, were also determined. We also profiled 36 LM tumor specimens by exome sequencing to develop a panel for targeted detection of point mutations in ctDNA of patients with LM.

RESULTS

We identified tumor-derived CNAs in the plasma DNA of 50% (six of 12) of patients with LM. The lactate dehydrogenase levels did not allow for an accurate distinction between patients with LM and patients with LMS. We identified only two recurrently mutated genes in LM tumors (MED12 and ACLY).

CONCLUSION

Our results show that LMs do shed DNA into the circulation, which provides an opportunity for the development of ctDNA-based testing to distinguish LM from LMS. Although we could not design an LM-specific panel for ctDNA profiling, we propose that the detection of CNAs or point mutations in selected tumor suppressor genes in ctDNA may favor a diagnosis of LMS, since these genes are not affected in LM.

XenoSarc: A comprehensive platform of patient-derived xenograft (PDX) models of soft tissue sarcoma (STS) for early drug testing

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Background: STS is a family of rare, heterogeneous tumors with > 70 subtypes. There is an urgent need for reliable preclinical models, especially for orphan subtypes of STS, given the limited treatment options. Methods: A panel of PDX models was established by s.c. implantation of fresh tumor specimens in athymic NMRI mice. Growing pieces of tumor were re-transplanted to next generations of mice. At each passage fragments were collected for histological/molecular characterization. A model was considered “established” after observing stable features for at least 2 passages. Ex-mouse tissue samples were stored, characterized by immunohistochemistry/flow cytometry and used for in vitro drug testing. Results: Between 2011-2019, 329 samples from 301 consenting patients were transplanted; 56 models are established, 16 additional models are in early passaging. Clinical information about donor and tumor (including sensitivity to standard and experimental agents) is available. The platform includes models of dedifferentiated lipo- (10 models), myxofibro- (8), leiomyo- (7), synovial (2), intimal (2), CIC-positive round cell (1), mesenchymal chondro- (1), extraskeletal osteo- (1), myxoid lipo- (1), myxoinflammatory fibroblastic (1), rhabdomyo- (2) and high-grade undifferentiated pleomorphic sarcoma (7), as well as GIST (8), MPNST (4) and epithelioid hemangioendothelioma (1). Models are well-characterized, with molecular information on copy number changes (low-coverage whole genome sequencing) and gene expression profile (RNA-Seq) available. We also constructed tissue microarrays from the xenografts which are used for target identification and model selection for preclinical studies. Xenografts are available for in vivo testing of novel agents, and results already served as a rationale for a number of prospective clinical trials. Conclusions: XenoSarc offers opportunities for studying the biology of a variety of sarcoma subtypes including ultra-rare entities and is a valuable tool for early drug screening in preparation of clinical STS trials. The platform is well maintained and continuously expanded, and available to collaborators from academia and industry.

Assessment of the platelet-derived growth factor receptor alpha antibody olaratumab in a panel of patient-derived soft tissue sarcoma xenografts

Background

Soft tissue sarcoma (STS) comprises a family of rare, heterogeneous tumors of mesenchymal origin. Single-agent doxorubicin remains the first-line standard-of-care treatment for advanced and inoperable STS, but response rates are only around 15%. In 2016, phase Ib/II clinical trial results reported an overall survival benefit of 11.8 months when combining doxorubicin and the platelet-derived growth factor receptor alpha (PDGFRA)-directed antibody olaratumab compared to doxorubicin alone, without providing a scientific rationale for such unprecedented therapeutic effect. We decided to evaluate the efficacy of olaratumab in a panel of STS patient-derived xenografts (PDX).

Methods

NMRI nu/nu mice were bilaterally transplanted with tumor tissue of patient-derived xenograft models expressing PDGFRA, including models of leiomyosarcoma (UZLX-STS22), malignant peripheral nerve sheath tumor (UZLX-STS39), myxofibrosarcoma (UZLX-STS59) and undifferentiated pleomorphic sarcoma (UZLX-STS84). Mice were randomly divided into four different treatment groups: (1) control, (2) doxorubicin (3 mg/kg once weekly), (3) anti-PDGFRA [olaratumab (60 mg/kg twice weekly) + mouse anti-PDGFRA antibody 1E10 (20 mg/kg twice weekly)] and (4) the combination of doxorubicin and anti-PDGFRA (same dose/schedule as in the single treatment arms). Tumor volume, histopathology and Western blotting were used to assess treatment efficacy.

Results

Anti-PDGFRA treatment as a single agent did not reduce tumor growth and did not result in significant anti-proliferative or pro-apoptotic activity. Combining doxorubicin and anti-PDGFRA did not reduce tumor burden, though a mild inhibition of proliferation was observed in UZLX-STS39 and -STS59. A pro-apoptotic effect was observed in all models except UZLX-STS22. Antitumor effects on histology were not significantly different comparing doxorubicin and the combination treatment. Moreover, anti-PDGFRA treatment, both as a single agent as well as combined with doxorubicin, did not result in inhibition of the downstream MAPK and PI3K/AKT signaling pathways.

Conclusions

We were not able to demonstrate significant antitumor effects of anti-PDGFRA treatment in selected STS PDX models, neither alone nor in combination with doxorubicin. This is in line with the very recent results of the phase III clinical trial NCT02451943 ANNOUNCE, which did not confirm the clinical benefit of olaratumab in combination with doxorubicin over single agent doxorubicin.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5872-1) contains supplementary material, which is available to authorized users.

No relevant activity of olaratumab in patient-derived soft tissue sarcoma xenografts selected for expression of platelet-derived growth factor receptor a

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Background: Soft tissue sarcoma (STS) comprises a heterogeneous family of rare tumors of mesenchymal origin. Single-agent doxorubicin (DOX) remains the standard-of-care for advanced and inoperable STS, but response rates are < 15% and survival is generally poor. In 2016, Tap et al. reported impressive results of a phase Ib/II trial combining DOX and the platelet-derived growth factor receptor a (PDGFRA)-directed antibody olaratumab (OLA), suggesting an unprecedented survival advantage of the combination over DOX alone, without providing a mechanistic rationale for the observed activity (Lancet 2016;388:488-97). We decided to evaluate the efficacy of OLA in a panel of patient-derived STS xenografts (PDX). Methods: NMRI nu/nu mice were transplanted bilaterally with tumor tissue of models expressing PDGFRA, including PDX of leiomyosarcoma (UZLX-STS22), malignant peripheral nerve sheath tumor (STS39), myxofibrosarcoma (STS59) and undifferentiated pleomorphic sarcoma (STS84). Mice were randomly divided into 4 treatment groups: (1) control, (2) DOX (3 mg/kg once weekly), (3) anti-PDGFRA [OLA (60 mg/kg twice weekly) + mouse anti-PDGFRA antibody 1E10 (20 mg/kg twice weekly)] and (4) the combination of DOX and anti-PDGFRA (same dose/schedule as single treatment arms). Tumor volume, histopathology and Western blotting were used to assess treatment efficacy. Results: Anti-PDGFRA treatment as single agent did not reduce tumor growth and did not result in significant anti-proliferative or pro-apoptotic activity. Combining DOX and anti-PDGFRA did not reduce tumor burden, though a mild inhibition of proliferation was observed in models STS39 and STS59 and a pro-apoptotic effect was seen in all models except STS22. Antitumor effects on histology were not significantly different comparing DOX and the combination treatment. Anti-PDGFRA treatment, both as a single agent as well as with DOX, did not inhibit downstream MAPK and PI3K/AKT signaling pathways. Conclusions: In vivo findings in PDX models selected for PDGFRA expression support negative findings of the phase III trial NCT02451943 with OLA reported at this meeting.

Activity and safety of crizotinib in patients with alveolar soft part sarcoma with rearrangement of TFE3: European Organization for Research and Treatment of Cancer (EORTC) phase II trial 90101 'CREATE'

Background

Alveolar soft part sarcoma (ASPS) is an orphan malignancy associated with a rearrangement of transcription factor E3 (TFE3), leading to abnormal MET gene expression. We prospectively assessed the efficacy and safety of the MET tyrosine kinase inhibitor crizotinib in patients with advanced or metastatic ASPS.

Patients and methods

Eligible patients with reference pathology-confirmed ASPS received oral crizotinib 250 mg bd. By assessing the presence or absence of a TFE3 rearrangement, patients were attributed to MET+ and MET- sub-cohorts. The primary end point was the objective response rate (ORR) according to local investigator. Secondary end points included duration of response, disease control rate (DCR), progression-free survival (PFS), progression-free rate, overall survival (OS) and safety.

Results

Among 53 consenting patients, all had a centrally confirmed ASPS and 48 were treated. A total of 45 were eligible, treated and assessable. Among 40 MET+ patients, 1 achieved a confirmed partial response (PR) that lasted 215 days and 35 had stable disease (SD) as best response (ORR: 2.5%, 95% CI 0.6% to 80.6%). Further efficacy end points in MET+ cases were DCR: 90.0% (95% CI 76.3% to 97.2%), 1-year PFS rate: 37.5% (95% CI 22.9% to 52.1%) and 1-year OS rate: 97.4% (95% CI 82.8% to 99.6%). Among 4 MET- patients, 1 achieved a PR that lasted 801 days and 3 had SD (ORR: 25.0%, 95% CI 0.6% to 80.6%) for a DCR of 100% (95% CI 39.8% to 100.0%). The 1-year PFS rate in MET- cases was 50% (95% CI 5.8% to 84.5%) and the 1-year OS rate was 75% (95% CI 12.8% to 96.1%). One patient with unknown MET status due to technical failure achieved SD but stopped treatment due to progression after 17 cycles. The most common crizotinib-related adverse events were nausea [34/48 (70.8%)], vomiting [22/48 (45.8%)], blurred vision [22/48 (45.8%)], diarrhoea (20/48 (41.7%)] and fatigue [19/48 (39.6%)].

Conclusion

According to European Organization for Research and Treatment of Cancer (EORTC) efficacy criteria for soft tissue sarcoma, our study demonstrated that crizotinib has activity in TFE3 rearranged ASPS MET+ patients.

Clinical trial number

EORTC 90101, NCT01524926.

Establishment and Characterization of Histologically and Molecularly Stable Soft-tissue Sarcoma Xenograft Models for Biological Studies and Preclinical Drug Testing

Soft-tissue sarcomas (STS) represent a heterogeneous group of rare, malignant tumors of mesenchymal origin. Reliable in vivo sarcoma research models are scarce. We aimed to establish and characterize histologically and molecularly stable patient-derived xenograft (PDX) models from a broad variety of STS subtypes. A total of 188 fresh tumor samples from consenting patients with localized or advanced STS were transplanted subcutaneously in NMRI-nu/nu-immunodeficient mice. Once tumor growth was observed, the material was passaged to a next generation of mice. A patient-derived tumor sample was considered "successfully engrafted" whenever the sample was transplanted to passage 1. A PDX model was considered "established" when observing stable morphologic and molecular features for at least two passages. With every passage, histologic and molecular analyses were performed. Specific genomic alterations and copy-number profile were assessed by FISH and low coverage whole-genome sequencing. The tumor engraftment rate was 32% (61/188) and 188 patient samples generated a total of 32 PDX models, including seven models of myxofibrosarcoma, five dedifferentiated liposarcoma, five leiomyosarcoma, three undifferentiated pleomorphic sarcoma, two malignant peripheral nerve sheet tumor models, and single models of synovial sarcoma and some other (ultra)rare subtypes. Seventeen additional models are in early stages of engraftment (passage 1-2). Histopathologic and molecular features were compared with the original donor tumor and were stable throughout passaging. The platform is used for studies on sarcoma biology and suited for in vivo preclinical drug testing as illustrated by a number of completed and ongoing laboratory studies.

Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs)

BACKGROUND

Activating mutations of the receptor tyrosine kinase KIT are early events in the development of most gastrointestinal stromal tumors (GISTs). Although GISTs generally remain dependent on oncogenic KIT during tumor progression, KIT mutations alone are insufficient to induce malignant behavior. This is evidenced by KIT-mutant micro-GISTs, which are present in up to one-third of normal individuals, but virtually never progress to malignancy.

METHODS

We performed whole exome sequencing on 29 tumors obtained from 21 patients with high grade or metastatic KIT-mutant GIST (discovery set). We further validated the frequency and potential prognostic significance of aberrations in CDKN2A/B, RB1, and TP53 in an independent series of 71 patients with primary GIST (validation set).

RESULTS

Using whole exome sequencing we found significant enrichment of genomic aberrations in cell cycle-associated genes (Fisher's Exact p = 0.001), most commonly affecting CDKN2A/B, RB1, and TP53 in our discovery set. We found a low mutational tumor burden in these 29 advanced GIST samples, a finding with significant implications for the development of immunotherapy for GIST. In addition, we found mutation of spliceosome genes in a minority of cases, implicating dysregulation of splicing as a potential cancer promoting mechanism in GIST. We next assessed the prognostic significance of CDKN2A, RB1 or TP53 mutation/copy loss in an independent cohort of 71 patients with primary GIST. Genetic events (mutation, deletion, and/or LOH) involving at least one of the three genes examined were found in 17% of the very low-risk, 36% of the low-risk, 42% of the intermediate risk, 67% of the high-risk/low mitotic-count, and in 86% of the high-risk/high mitotic-count group. The presence of cell cycle-related events was associated with a significantly shorter relapse-free survival (median 67 months versus not reached; p < 0.0001) and overall survival (Log Rank, p = 0.042).

CONCLUSION

Our results demonstrate that genomic events targeting cell cycle-related genes are associated with GIST progression to malignant disease. Based on this data, we propose a model for molecular pathogenesis of malignant GIST.

Successful Perioperative and Surgical Treatment of a Rare Case of Extra-Gastrointestinal Stromal Tumor Arising in the Prostate Gland

We report a very uncommon case of a primary, non-metastatic gastrointestinal stromal tumor (GIST) arising in the prostate gland in a 60-year-old patient. The morphology and immunohistochemical profile of the disease resembled GIST of gastrointestinal origin, and the molecular driver of this malignancy was a double mutation in exons 11 and 13 of the KIT gene. The tumor was proliferating slowly, did respond to neoadjuvant therapy with the KIT-inhibiting agent imatinib and was cured by radical, retro-pubic prostatectomy followed by adjuvant imatinib treatment. We postulate that primary GIST tumors of the prostate can arise from prostatic interstitial cells, which are the pacemakers of smooth muscle contractility in the gland, and possibly share a common precursor with typical GIST and the interstitial cells of Cajal in the gastrointestinal tract.

A Case of Undifferentiated Sarcoma in the Superior Vena Cava and Bilateral Cervical Veins

BACKGROUND Intimal sarcoma (IS) is a malignant mesenchymal tumor with predominantly intraluminal growth in large vessels and the heart. Due to the rarity of cases it often poses diagnostic problems in clinical and pathological settings. Although the classification of IS is still controversial, undifferentiated type of IS has recently been found to show immunohistochemical positivity with MDM2, CDK4, or PDGFRA and amplification of MDM2/CDK4 and PDGFRA. CASE REPORT The patient was a 76 years-old Japanese man who presented with superior vena cava (SVC) syndrome. CT identified a tumor or thrombi in the SVC, bilateral brachiocephalic, and jugular veins. The histology of the biopsy specimen revealed an undifferentiated tumor without immunohistochemical positivity for all antibodies available except vimentin and smooth muscle actin. He was treated conservatively and died of respiratory failure 2 months after presentation. At autopsy, the large veins were filled by a sausage-like tumor and the cut sections revealed hemorrhagic and necrotic tumor. The tumor cells were negative with MDM2, CDK4, and PDGFRA by immunohistochemistry. Amplification of MDM2 and PDGFRA was not identified by fluorescence in-situ hybridization. CONCLUSIONS We concluded that the case was an undifferentiated sarcoma (IS without any specific phenotype) arising in the SVC, bilateral brachiocephalic, and jugular veins. We propose a way of subtyping sarcomas with predominantly intraluminal growth in large vessels and the heart based on immunohistochemistry and amplification of MDM2 and PDGFRA. However, proper subtyping of these sarcomas requires further study.

Clear Cell Odontogenic Carcinoma: Occurrence of EWSR1-CREB1 as Alternative Fusion Gene to EWSR1-ATF1

Clear cell odontogenic carcinoma (CCOC) is a rare, low-grade malignant epithelial neoplasm, occurring in the jawbones, mainly affecting the mandible of elderly patients. In addition to hyalinizing clear cell carcinoma of the salivary gland, it is one of the epithelial neoplasms known to harbor an EWSR1-ATF1 fusion. Therefore, a link between these tumors seems plausible. We describe six cases of CCOC showing EWSR1 rearrangements, with two cases being positive for the ATF1 partner gene using FISH analysis. In one case, an EWSR1-CREB1 fusion was identified using RT-PCR, which we report for the first time in this tumor type. The other three cases investigated by FISH were negative for ATF1, CREB1 and CREB3L2. In conclusion, our data show that EWSR1-CREB1 is an alternative fusion gene to EWSR1-ATF1 in CCOC.

Toward Minimal Residual Disease-Directed Therapy in Melanoma

Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD, we applied single-cell RNA sequencing to malignant cells isolated from BRAF mutant patient-derived xenograft melanoma cohorts exposed to concurrent RAF/MEK-inhibition. We identified distinct drug-tolerant transcriptional states, varying combinations of which co-occurred within MRDs from PDXs and biopsies of patients on treatment. One of these exhibited a neural crest stem cell (NCSC) transcriptional program largely driven by the nuclear receptor RXRG. An RXR antagonist mitigated accumulation of NCSCs in MRD and delayed the development of resistance. These data identify NCSCs as key drivers of resistance and illustrate the therapeutic potential of MRD-directed therapy. They also highlight how gene regulatory network architecture reprogramming may be therapeutically exploited to limit cellular heterogeneity, a key driver of disease progression and therapy resistance.

Abstract CT045: Prospective precision medicine trial of crizotinib (C) in patients (pts) with advanced, inoperable inflammatory myofibroblastic tumor (IMFT) with and without ALK alterations: EORTC phase II study 90101 "CREATE"

Background: The multi-tumor phase 2 trial EORTC 90101 (NCT01524926) assessed the activity and safety of the ALK/MET/ROS1 inhibitor C in IMFT, an orphan malignancy associated with ALK rearrangement or copy number changes.

Methods: Pts with local diagnosis of advanced/metastatic IMFT consented for shipment of a tumor tissue block and were screened for treatment after central confirmation of the diagnosis by reference pathology. Eligible ALK positive (+) and negative (-) pts received oral C 250 mg bid until RECIST 1.1 progression (PD). ALK+ was defined as at least 15% of tumor cells with rearrangement on FISH (Vysis LSI ALK Dual Color Break Apart Probe, Abbott Molecular) and/or immunohistochemical positivity (ALK MAb Clone CD246, DAKO). A Simon's optimal 2 stage design was implemented. If at least 2 out of the first 12 eligible and evaluable ALK+ pts achieved a confirmed RECIST 1.1 partial or complete response (PR, CR), a maximum of 35 pts were enrolled. If at least 6 had a confirmed PR/CR, the trial would be deemed successful.

Results: Between 10/2012 and 04/2017, 13 sites in 8 European countries recruited 35 pts with a local diagnosis of IMFT, of whom only 20 had centrally confirmed IMFT and were treated with C. Among 12 eligible and evaluable ALK+ pts, 6 achieved a confirmed PR or CR, 1 a non-confirmed PR and 5 had stable disease (SD) as best response (ORR 50.0%, 95% confidence interval: 21.1-78.9%). Further efficacy endpoints in ALK+ pts: disease control rate (DCR = CR/PR/SD as best response) 100.0% (73.5-100.0%), 1-year (y) progression free rate (PFR) 73.3 % (37.9-90.6%), 1-y OS rate (OSR) 81.8% (44.7-95.1%). Among 7 eligible and evaluable ALK- pts, 1 achieved a PR, 5 had SD and 1 PD (ORR 14.3%, 0.0-57.9%). Further data in ALK- cases: DCR 85.7% (59.8-100.0%), 1-y PFR 53.6 % (13.2-82.5%), 1-y OSR 83.3% (27.3-97.5%). One additional ALK- case was non evaluable (no measurable disease at baseline). Common related adverse events were nausea (11/20 [55%]), fatigue (9/20 [45%]), blurred vision (9/20 [45%]), vomiting (7/20 [35%]), diarrhea (7/20 [35%]).

Conclusions: EORTC can perform precision medicine phase II trials in ultra-rare cancers such as IMFT, with mandatory collection of tissue, real time reference pathology and genetic profiling. With an ORR of 50% and a DCR of 100% in ALK+ disease, C met pre-specified response rate criteria in this trial. The drug achieves long-lasting disease control in the vast majority of ALK+ pts. Sporadic responses and disease stabilization in ALK- cases either suggest limitations of the assays and their cut-offs for target positivity, or the presence of other oncogenic drivers/alternative fusions that may be sensitive to C. Based on the findings of this prospective trial, C should be considered as systemic treatment standard of care for this orphan disease.

Citation Format: Patrick Schoffski, Jozef Sufliarsky, Hans Gelderblom, Jean-Yves Blay, Sandra J. Strauss, Silvia Stacchiotti, Piotr Rutkowski, Lars H. Lindner, Michael G. Leahy, Antoine Italiano, Nicolas Isambert, Maria Debiec-Rychter, Raf Sciot, Thomas Van Cann, Sandrine Marréaud, Axelle Nzokirantevye, Sandra Collette, Agnieszka Wozniak. Prospective precision medicine trial of crizotinib (C) in patients (pts) with advanced, inoperable inflammatory myofibroblastic tumor (IMFT) with and without ALK alterations: EORTC phase II study 90101 "CREATE" [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 CT045.

Abstract 1031: XenoSarc: Patient-derived xenograft (PDX) models of soft tissue sarcoma (STS)—an update on a preclinical platform for early drug testing

Background: STS constitutes a rare family of mesenchymal tumors with more than 70 subtypes described. The limited treatment options available for advanced STS underline the need for reliable preclinical models to test novel therapeutic strategies.

Methods: Panel of PDX models was established by subcutaneous implantation of fresh tumor specimens in immunodeficient, athymic nude NMRI mice. Once tumor growth was observed, pieces of tumor were re-transplanted to next generations of animals. At each passage tumor fragments were collected for detailed characterization. A model was considered established after observing stable histological and molecular features for at least two passages.

Results: Between 09/2011 and 11/2017, 228 STS samples from 203 consenting patients treated at University Hospitals Leuven, Belgium, have been transplanted. Thirty-three stable PDX models have been established, maintaining the histopathological and molecular features of the original tumor. Detailed clinical information about a donor patient, including sensitivity to given therapy, is linked to every model. Higher engraftment rate was observed in samples collected from patients who developed metastasis throughout the course of disease (38% vs. 23%, p&lt;0.05). Moreover, patients whose tumor successfully engrafted had significantly poorer overall survival (OS) than those whose tumor did not grow in mice (median OS 83 vs. 259 months; p&lt;0.05). XenoSarc platform includes models of gastrointestinal stromal tumor (6 models), myxofibrosarcoma (6), leiomyosarcoma (5), dedifferentiated liposarcoma (4), malignant peripheral nerve sheath tumor (2), synovial sarcoma (1), pulmonary artery intimal sarcoma (1), CIC-DUX4 fusion-positive round cell sarcoma (1), epithelioid haemangioendothelioma (1), mesenchymal chondrosarcoma (1), pleomorphic rhabdomyosarcoma (1), telangiectatic extraskeletal osteosarcoma (1), and high-grade undifferentiated pleomorphic sarcoma (3). These models are well-characterized, with detailed data on copy number changes and expression profile. In addition we have constructed tissue microarray (TMA), which can be used for target identification. Some of these models have already been successfully used for in vivo testing of novel agents, including both targeted and cytotoxic (pro-)drugs, and results served as a rationale for several prospective clinical trials. In addition, 17 other xenografts are still in early stages of engraftment, not yet fulfilling our criteria of an “established model”.

Conclusion: Our XenoSarc platform contains a number of well-annotated models, characterized by stable histological and molecular features. This platform is a reliable tool for the evaluation of new anticancer treatments for STS and for studying the biology of these rare diseases. The platform is made available to collaborators from academia and industry.

Citation Format: Agnieszka Wozniak, Jasmien Cornillie, Yemarshet K. Gebreyohannes, Yannick Wang, Jasmien Wellens, Ulla Vanleeuw, Daphne Hompes, Marguerite Stas, Friedl Sinnaeve, Hazem Wafa, Maria Debiec-Rychter, Raf Sciot, Patrick Schöffski. XenoSarc: Patient-derived xenograft (PDX) models of soft tissue sarcoma (STS)—an update on a preclinical platform for early drug testing [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 1031.

Abstract 4345: Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs

Background and aim: Gastrointestinal stromal tumors (GISTs) are rare mesenchymal tumors of the gastrointestinal tract. Gain-of-function mutations in KIT or, less frequently, PDGFRA underlie the pathogenesis of the majority of these tumors. The introduction of imatinib mesylate, a selective tyrosine kinase inhibitor, has dramatically improved the outcome for GIST patients. However, half of the advanced patients treated with imatinib eventually progress and acquire resistance within two years of treatment, underscoring the need to get better insight into the resistance mechanisms. In this context we examined the miRNA and mRNA expression profiles in primary (imatinib-naïve) and imatinib resistant GIST samples.

Material and Methods: Fifty-three frozen GIST samples derived from various anatomical sites (small intestine, stomach, colon) harboring a KIT mutation including exon 9 (n=11), exon 11 (n=41) and exon 17 (n=1), were analyzed. Total RNA was isolated from imatinib naïve (IM-n; n=33) and resistant (IM-r; n=20) tumors. The resistant tumors bearing secondary mutations in exon 13 (n=3), exon 17 (n=6) or no secondary mutations (n=11). The miRNA expression profiles were determined using LNA™ oligonucleotide arrays (Exiqon) capable of detecting 725 human miRNAs. Furthermore, from a subset of samples (IM-n; n=14; IM-r; n=15) the mRNA expression profile was established using Affymetrix U133A oligonucleotide arrays. Using the mRNA expression data and the Biocarta and KEGG databases, global testing identified a number of biochemical pathways containing genes that are differentially expressed between the primary and progressive tumors.

Results: Thirty-five differentially expressed miRNAs (P&lt;0.009, FDR&lt;20%) between IM-n and IM-r GIST samples were identified. MiR-30c, miR-181a and miR-144 were among the most significantly different, with p values of 0.006, 0.006 and 0.003, respectively. Analysis of the mRNA data has revealed the up-regulation of genes (P &lt;0002, FDR&lt;30%) involved in cell cycle, DNA replication and cancer related pathways (i.e. proliferation, genomic instability, resistance to chemotherapy, evading apoptosis, etc.) in IM-r samples. To further elucidate the possible involvement of the deregulated miRNAs in the regulation of the indicated genes, the most significantly differentially expressed genes were correlated to miRNA expression. Negative correlations indicate miRNA mediated gene regulation, and were further examined in target prediction programs.

Conclusion: A molecular comparison between primary, IM-n and IM-r GIST samples revealed significant differentially expressed miRNAs and mRNAs. Bioinformatic analyses provided insight into biochemical pathways, and their putative regulation by miRNAs, that may contribute to imatinib resistance as observed in GIST patients.

Citation Format: Azadeh Amirnasr, Caroline M. Gits, Patricia F. Kuijk, Marcel Smid, Maria Debiec-Rychter, Stefan Sleijfer, Erik A. Wiemer. Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs [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 4345.

A rare case of atypical/anaplastic meningioma with MDM2 amplification

We report the exceptional occurrence of murine double minute clone 2 amplification in an atypical meningioma and its recurrent anaplastic meningioma arising in the right frontal lobe of a 75-year-old man. Murine double minute clone 2 amplification was shown by array comparative genomic hybridization and confirmed by fluorescence in situ hybridization. This is a rare finding with only one similar report in the literature. Awareness of this finding is indicated and should not lead to misdiagnosis of other entities that more commonly show this feature.

Activity and safety of crizotinib in patients with advanced clear-cell sarcoma with MET alterations: European Organization for Research and Treatment of Cancer phase II trial 90101 'CREATE'

Background

Clear-cell sarcoma (CCSA) is an orphan malignancy, characterized by a specific t(12;22) translocation, leading to rearrangement of the EWSR1 gene and overexpression of MET. We prospectively investigated the efficacy and safety of the tyrosine kinase inhibitor crizotinib in patients with advanced or metastatic CCSA.

Patients and methods

Patients with CCSA received oral crizotinib 250 mg twice daily. Primary end point was objective response rate (ORR), secondary end points included duration of response, disease control rate (DCR), progression-free survival (PFS), progression-free rate (PFR), overall survival (OS), OS rate and safety. The study design focused on MET+ disease with documented rearrangement of the EWSR1 gene by fluorescence in situ hybridization.

Results

Among 43 consenting patients with the local diagnosis of CCSA, 36 had centrally confirmed CCSA, 28 of whom were eligible, treated and assessable. Twenty-six out of the 28 patients had MET+ disease, of whom one achieved a confirmed partial response and 17 had stable disease (SD) (ORR 3.8%, 95% confidence interval: 0.1-19.6). Further efficacy end points in MET+ CCSA were DCR: 69.2% (48.2% to 85.7%), median PFS: 131 days (49-235), median OS: 277 days (232-442). The 3-, 6-, 12- and 24-month PFR was 53.8% (34.6-73.0), 26.9% (9.8-43.9), 7.7% (1.3-21.7) and 7.7% (1.3-21.7), respectively. Among two assessable MET- patients, one had stable disease and one had progression. The most common treatment-related adverse events were nausea [18/34 (52.9%)], fatigue [17/34 (50.0%)], vomiting [12/34 (35.3%)], diarrhoea [11/34 (32.4%)], constipation [9/34 (26.5%)] and blurred vision [7/34 (20.6%)].

Conclusions

The PFS with crizotinib in MET+ CCSA is similar to results achieved first-line in non-selected metastatic soft tissue sarcomas with single-agent doxorubicin. The PFS is similar to results achieved with pazopanib in previously treated sarcoma patients.

Clinical trial number

EORTC 90101, EudraCT number 2011-001988-52, NCT01524926.

Post-irradiation Sarcoma after External Beam Radiation Therapy for Localized Adenocarcinoma of the Prostate

We report a case of postirradiation sarcoma that arose in the right inguinal region 8 years after completion of external beam radiation therapy for a localized adenocarcinoma of the prostate. The patient was treated in 1995 with a “mixed-beams” technique (18 MV photons and 65 MeV fast neutrons). Eight years after the end of treatment, he presented with a radio-induced, high-grade spindle-cell sarcoma. Cytogenetic analysis was performed to confirm the diagnosis. Although the use of external beam radiation therapy for the treatment of prostate cancer has been common practice for decades, postirradiation sarcomas have been reported to be rare sequelae of irradiation and, to our knowledge, only a few of them were cytogenetically investigated.

Crizotinib in patients with advanced, inoperable inflammatory myofibroblastic tumours with and without anaplastic lymphoma kinase gene alterations (European Organisation for Research and Treatment of Cancer 90101 CREATE): a multicentre, single-drug, prospective, non-randomised phase 2 trial

BACKGROUND

An inflammatory myofibroblastic tumour (IMFT) is a rare mesenchymal neoplasm characterised by anaplastic lymphoma kinase (ALK) gene rearrangements. We assessed the activity and safety of crizotinib, a tyrosine kinase inhibitor, targeting ALK in patients with advanced IMFT either with or without ALK alterations.

METHODS

We did a multicentre, biomarker-driven, single-drug, non-randomised, open-label, two-stage phase 2 trial (European Organisation for Research and Treatment of Cancer 90101 CREATE) at 13 study sites (five university hospitals and eight specialty clinics) in eight European countries (Belgium, France, Germany, Italy, Netherlands, Poland, Slovakia, and the UK). Eligible participants were patients aged at least 15 years with a local diagnosis of advanced or metastatic IMFT deemed incurable with surgery, radiotherapy, or systemic therapy; measurable disease; an Eastern Cooperative Oncology Group performance status of 0-2; and adequate haematological, renal, and liver function. Central reference pathology was done for confirmation of the diagnosis, and ALK positivity or negativity was assessed centrally using immunohistochemistry and fluorescence in-situ hybridisation based on archival tumour tissue and defined as ALK immunopositivity or rearrangements in at least 15% of tumour cells. Eligible ALK-positive and ALK-negative patients received oral crizotinib 250 mg twice per day administered on a continuous daily dosing schedule (the duration of each treatment cycle was 21 days) until documented disease progression, unacceptable toxicity, or patient refusal. If at least two of the first 12 eligible and assessable ALK-positive patients achieved a confirmed complete or partial response according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1, a maximum of 35 patients were to be enrolled. If at least six ALK-positive patients achieved a confirmed response, the trial would be deemed successful. The primary endpoint was the proportion of patients who achieved an objective response (ie, a complete or partial response) as per RECIST 1.1, with response confirmation assessed by the local investigator every other cycle. Activity and safety endpoints were analysed in the per-protocol population. This trial is registered with ClinicalTrials.gov, number NCT01524926.

FINDINGS

Between Oct 3, 2012, and April 12, 2017, we recruited and treated 20 eligible participants, 19 of whom were assessable for the primary endpoint. Median follow-up was 863 days (IQR 358-1304). Six of 12 ALK-positive patients (50%, 95% CI 21·1-78·9) and one of seven ALK-negative patients (14%, 0·0-57·9) achieved an objective response. The most common treatment-related adverse events in the 20 participants were nausea (11 [55%]), fatigue (9 [45%]), blurred vision (nine [45%]), vomiting (seven [35%]), and diarrhoea (seven [35%]). Eight serious adverse events occurred in five patients: pneumonia, fever of unknown cause, a heart attack with increased creatinine and possible sepsis, an abdominal abscess with acute renal insufficiency, and a QT prolongation.

INTERPRETATION

With 50% of participants with ALK-positive tumours achieving an objective response, crizotinib met the prespecified criteria for success in this trial. The results presented here support the rationale for inhibiting ALK in patients with IMFT. Crizotinib could be considered as the standard of care for patients with locally advanced or metastatic ALK-positive IMFT who do not qualify for curative surgery.

FUNDING

The European Organisation for Research and Treatment of Cancer and Pfizer.

Gene expression profiling of low-grade endometrial stromal sarcoma indicates fusion protein-mediated activation of the Wnt signaling pathway

OBJECTIVE

Low-grade endometrial stromal sarcomas (LGESS) harbor chromosomal translocations that affect proteins associated with chromatin remodeling Polycomb Repressive Complex 2 (PRC2), including SUZ12, PHF1 and EPC1. Roughly half of LGESS also demonstrate nuclear accumulation of β-catenin, which is a hallmark of Wnt signaling activation. However, the targets affected by the fusion proteins and the role of Wnt signaling in the pathogenesis of these tumors remain largely unknown.

METHODS

Here we report the results of a meta-analysis of three independent gene expression profiling studies on LGESS and immunohistochemical evaluation of nuclear expression of β-catenin and Lef1 in 112 uterine sarcoma specimens obtained from 20 LGESS and 89 LMS patients.

RESULTS

Our results demonstrate that 143 out of 310 genes overexpressed in LGESS are known to be directly regulated by SUZ12. In addition, our gene expression meta-analysis shows activation of multiple genes implicated in Wnt signaling. We further emphasize the role of the Wnt signaling pathway by demonstrating concordant nuclear expression of β-catenin and Lef1 in 7/16 LGESS.

CONCLUSIONS

Based on our findings, we suggest that LGESS-specific fusion proteins disrupt the repressive function of the PRC2 complex similar to the mechanism seen in synovial sarcoma, where the SS18-SSX fusion proteins disrupt the mSWI/SNF (BAF) chromatin remodeling complex. We propose that these fusion proteins in LGESS contribute to overexpression of Wnt ligands with subsequent activation of Wnt signaling pathway and formation of an active β-catenin/Lef1 transcriptional complex. These observations could lead to novel therapeutic approaches that focus on the Wnt pathway in LGESS.

Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma

Purpose: The clinical utility of circulating tumor DNA (ctDNA) monitoring has been shown in tumors that harbor highly recurrent mutations. Leiomyosarcoma represents a type of tumor with a wide spectrum of heterogeneous genomic abnormalities; thus, targeting hotspot mutations or a narrow genomic region for ctDNA detection may not be practical. Here, we demonstrate a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single-nucleotide variants (SNV), small indels, and copy-number alterations (CNA) in ctDNA.Experimental Design: We employed Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with leiomyosarcoma.Results: We detected ctDNA in 6 of 7 of these patients with >98% specificity for mutant allele fractions down to a level of 0.01%. We show that results from CAPP-Seq and GRP are highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. By analyzing multiple tumor specimens in individual patients obtained from different sites and at different times during treatment, we observed clonal evolution of these tumors that was reflected by ctDNA profiles.Conclusions: Our strategy allows for the comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma. Our approach may be clinically useful not only in leiomyosarcoma but also in other tumor types that lack recurrent genomic alterations. Clin Cancer Res; 24(11); 2688-99. ©2018 AACR.

Effect of crizotinib on disease control in patient with advanced papillary renal cell carcinoma type 1 with MET mutations or amplification: Final results of EORTC 90101 CREATE

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Background: Papillary renal cell carcinoma type 1(PRCC1) is associated with MET alterations. Our phase II trial assessed the efficacy and safety of crizotinib in patients (pts) with advanced/metastatic PRCC1 with/without MET mutations( MET+, MET-). Methods: Eligible pts with reference pathology-confirmed PRCC1 received oral crizotinib 250mg twice-daily. Pts were attributed to MET+/ MET- sub-cohorts by sequencing of MET exons 16-19 in tumour tissue. Primary endpoint was objective response rate (ORR). If at least 2 of the first 12 eligible/evaluable MET+ pts achieved a confirmed partial (PR) or complete response (RECIST 1.1), a maximum of 35 pts were enrolled. Other endpoints included duration of response (DOR), disease control rate (DCR), progression-free survival (PFS) and rate (PFSR), overall survival (OS) and safety. Results: 23 of 41 pts consenting were eligible, treated and evaluable. In 4 MET+ pts, 2 achieved a PR and 1 had stable disease (SD) (ORR 50%; 95% CI: 6.8-93.7%), DOR was 666 and 1138 days, 1-year PFSR was 75.0% (12.8-96.1%), 1-year OS: 75.0% (12.8-96.1%). Among 16 MET- pts, 1 achieved a PR lasting 302+ days and 11 had SD (ORR: 6.3%; 0.2-30.2%), 1-year PFSR: 27.3% (8.5-50.4%), 1-year OS: 71.8% (41.1-88.4%). Among 3 pts with unknown MET status ( MET?) due to technical failure, 1 achieved a PR lasting 211+ days and 1 had SD (ORR 33.3%, 0.8%-90.6%), 1-year PFSR: 66.7% (5.4-94.5%), 1-year OS: 100%. MET amplification was found post hoc in 1 MET+ (PR, DOR: 1138 days) and 1 MET- case (SD). Common treatment-related AEs were oedema (47.8%), fatigue (47.8%), nausea (39.1%), diarrhoea (39.1%), and blurred vision (34.8%). Conclusions: Crizotinib is active and well tolerated in advanced, metastatic PRCC1, achieving objective responses and long-lasting disease control in pts with MET mutations or amplification. Sporadic, durable responses are also seen in MET-/ MET? cases, suggesting the presence of other alterations of MET or alternative pathways. Clinical trial information: NCT01524926.

Abstract A05: Circulating tumor DNA levels correlate with response to treatment in LMS patients

Circulating tumor DNA (ctDNA) has significant potential for several clinical applications, including assessment of treatment response and monitoring of recurrent/residual disease. We performed a pilot study to explore the feasibility of ctDNA monitoring in patients with leiomyosarcoma (LMS).

We profiled matching plasma and FFPE tumor specimens from 9 LMS patients. We analyzed between 2 to 6 longitudinal plasma samples (median of 5) and between 1 to 7 tumor specimens (median of 2) per patient. ctDNA analysis was performed on plasma samples collected pre-/post-surgery, throughout chemo-/radiotherapy and during follow-up. We used two separate approaches in our study: 1) targeted deep sequencing of ctDNA, tumor DNA and germline DNA to detect single nucleotide variants and indels using Cancer Personalized Profiling by deep Sequencing with integrated digital error suppression (CAPP-Seq; with a median deduplicated depth of sequencing of 2,136x); 2) copy number variant analysis in ctDNA by genome representation profiling (GRP; median coverage across the whole genome 0.23x) and in the matched tumors by SNP arrays. One patient was excluded from the analysis due to inadequate sequencing coverage in tumor specimen.

For CAPP-Seq analysis, we designed a custom 184kb capture panel targeting 89 genes that are recurrently mutated in LMS. Using strict variant calling criteria (requiring that variants be present on each strand of the original DNA “duplex” molecule) our panel identified a median of one nonsynonymous coding/splicing variant per tumor. We detected the same variants in TP53, RB1 and ATRX genes in ctDNA of 6/8 patients (with a baseline sensitivity of 87.5% and overall specificity of 98.96% calculated using plasma from 24 healthy donors). These six patients presented with advanced disease at the time of the first blood collection and were progressing throughout multiple lines of therapy. Two patients who did not have any variants detectable by CAPP-Seq in plasma had localized disease at the time of the first blood collection and/or responded well to the therapy. We found that changes in ctDNA levels appear to correspond with the extent of disease and response to treatment. Specifically, ctDNA levels decreased in a subset of patients after surgery or at the time of temporary response to chemo- and/or radiotherapy. Congruently, increases in ctDNA levels correlated with progression in most of the patients. There was a high correlation between ctDNA levels detected by CAPP-Seq (quantified as mutant molecules/mL plasma) and GRP (quantified as percent of genome showing copy number aberrations) across all plasma samples (Pearson's r= 0.88, p &lt; 0.0001), but in a few samples ctDNA was detected by only one of the two assays.

Our results suggest that serial analysis of ctDNA is a promising approach for evaluation of treatment response in LMS patients. Validation of these findings in a prospective study on a larger group of patients will be required to determine the use of this approach in a clinical setting.

References:

CAPP-Seq: PMIDs 24705333, 27018799

GRP: PMIDs 25585704, 26687610

Citation Format: Joanna Przybyl, Jacob J. Chabon, Lien Spans, Kristen Ganjoo, Sujay Vennam, Aaron M. Newman, Erna Forgó, Sushama Varma, Shirley Zhu, Maria Debiec-Rychter, Ash Alizadeh, Maximilian Diehn, Matt van de Rijn. Circulating tumor DNA levels correlate with response to treatment in LMS patients [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 A05.

New targets and therapies for gastrointestinal stromal tumors

INTRODUCTION

The majority of gastrointestinal stromal tumors (GIST) are driven by an abnormal receptor tyrosine kinase (RTK) signaling, occurring mainly due to somatic mutations in KIT or platelet derived growth factor receptor alpha (PDGFRA). Although the introduction of tyrosine kinase inhibitors (TKIs) has revolutionized therapy for GIST patients, with time the vast majority of them develop TKI resistance. Advances in understanding the molecular background of GIST resistance allows for the identification of new targets and the development of novel strategies to overcome or delay its occurrence. Areas covered: The focus of this review is on novel, promising therapeutic approaches to overcome heterogeneous resistance to registered TKIs. These approaches involve new TKIs, including drugs specific for a mutated form of KIT/PDGFRA, drugs with inhibitory effect against multiple RTKs, compounds targeting dysregulated downstream signaling pathways, drugs affecting KIT expression and degradation, inhibitors of cell cycle, and immunotherapeutics. Expert commentary: As the resistance to standard TKI treatment can be heterogeneous, a combinational approach for refractory GIST could be beneficial. Moreover, the understanding of the molecular background of resistant disease would allow development of a more personalized approach for these patients and their response to targeted therapy could be monitored closely using 'liquid biopsy'.