Multi-platform profiling of over 2000 sarcomas: Identification of biomarkers and novel therapeutic targets

Background: Drug development in sarcoma has been hampered by the rarity and heterogeneity of the disease and lack of predictive biomarkers to therapies. We assessed protein expression and gene alterations in a large number of bone and soft tissue sarcomas in order to categorize the molecular alterations, identify predictive biomarkers and discover new therapeutic targets. Methods: Data from sarcoma specimens profiled for protein expression, gene amplification/translocation and DNA sequencing was reviewed. Results: 2539 sarcoma specimens of 22 subtypes were included. TOPO2A was the most overexpressed protein at 52.8%. There was overexpression or loss of other sarcoma relevant proteins such as SPARC, PTEN and MGMT. Approximately 50% of the sarcomas expressed PD-L1 by IHC and presented with PD-1+ TILs, notably the LMS, chondrosarcomas, liposarcomas and UPS. Gene amplification/rearrangement of ALK, cMYC, HER2, PIK3CA, TOPO2A and cMET was relatively uncommon. EGFR gene amplification occurred at a rate of 16.9%. DNA sequencing of 47 genes identified mutations in 47% of the samples. The most commonly mutated genes were TP53 (26.3%) and BRCA2 (17.6%). Overexpression of TOPO2A was associated with TP53 mutation (P = 0.0001). Conclusion: This data provides the landscape of alterations in sarcoma. Future clinical trials are needed to validate these targets

FGFR1 and NTRK3 actionable alterations in “Wild-Type” gastrointestinal stromal tumors

BACKGROUND: About 10–15% of adult, and most pediatric, gastrointestinal stromal tumors (GIST) lack mutations in KIT, PDGFRA, SDHx, or RAS pathway components (KRAS, BRAF, NF1). The identification of additional mutated genes in this rare subset of tumors can have important clinical benefit to identify altered biological pathways and select targeted therapies. METHODS: We performed comprehensive genomic profiling (CGP) for coding regions in more than 300 cancer-related genes of 186 GISTs to assess for their somatic alterations. RESULTS: We identified 24 GIST lacking alterations in the canonical KIT/PDGFRA/RAS pathways, including 12 without SDHx alterations. These 24 patients were mostly adults (96%). The tumors had a 46% rate of nodal metastases. These 24 GIST were more commonly mutated at 7 genes: ARID1B, ATR, FGFR1, LTK, SUFU, PARK2 and ZNF217. Two tumors harbored FGFR1 gene fusions (FGFR1–HOOK3, FGFR1–TACC1) and one harbored an ETV6–NTRK3 fusion that responded to TRK inhibition. In an independent sample set, we identified 5 GIST cases lacking alterations in the KIT/PDGFRA/SDHx/RAS pathways, including two additional cases with FGFR1–TACC1 and ETV6–NTRK3 fusions. CONCLUSIONS: Using patient demographics, tumor characteristics, and CGP, we show that GIST lacking alterations in canonical genes occur in younger patients, frequently metastasize to lymph nodes, and most contain deleterious genomic alterations, including gene fusions involving FGFR1 and NTRK3. If confirmed in larger series, routine testing for these translocations may be indicated for this subset of GIST. Moreover, these findings can be used to guide personalized treatments for patients with GIST. Trial registration NCT 02576431. Registered October 12, 2015 ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12967-016-1075-6) contains supplementary material, which is available to authorized users

Adjuvant Chemotherapy in Uterine Leiomyosarcoma: Trends and Factors Impacting Usage

Objectives. The benefit of adjuvant chemotherapy in patients with localized uterine leiomyosarcoma (LMS) remains unclear due to a lack of randomized studies and data only from small retrospective series to rely on. We sought to identify factors associated with the administration of chemotherapy and to determine the trends in the usage of adjuvant chemotherapy in patients with nonmetastatic uterine LMS. Methods. Patients diagnosed with nonmetastatic uterine LMS between 2004 and 2014 were identified from the National Cancer Database (NCDB). Multiple regression was used to determine factors with a significant impact on patient receipt of chemotherapy. Kaplan–Meier curves and the Cox model were used to determine the effect of adjuvant chemotherapy on overall survival (OS). Results. 2,732 uterine LMS patients were identified. Patients older than 65 were less likely to receive chemotherapy than their younger counterparts. Patients with stage I or stage II cancer were less likely to receive chemotherapy, whereas individuals with positive regional lymph nodes and those who had received radiation were more likely. In this cohort, adjuvant chemotherapy had no significant impact on OS (HR, 1.04; 95% CI, 0.90–1.22; P=0.5768). However, administration of chemotherapy significantly increased from 2004 to 2014 (P<0.0001). Conclusions. Expected tumor characteristics such as higher stage of tumor were associated with receipt of chemotherapy. Although adjuvant chemotherapy demonstrated no benefit over observation on OS in patients with nonmetastatic LMS, the number of patients being treated with chemotherapy continued to increase from 2004 to 2014

A Phase I Study of the Combination of Temsirolimus with Irinotecan for Metastatic Sarcoma

mTOR inhibitors are emerging as important anti-neoplastic agents with a wide range of clinical applications. The topoisomerase I inhibitor irinotecan is a potent DNA damaging drug, with a broad spectrum of anticancer activities. mTOR appears to enhance cancer cell survival following DNA damage, thus the inhibition of mTOR after irinotecan could theoretically show synergistic activities in patients. Both mTOR inhibitors and irinotecan have been used as single agents in soft tissue sarcomas with limited efficacy. We completed a phase I trial of the combination of the mTOR inhibitor, temsirolimus, and irinotecan in patients with advanced soft tissue sarcoma. Seventeen patients were recruited. The Phase II recommended dose is 20 mg of temsirolimus and 80 mg/m2 of irinotecan administered on weekly basis for three out of four weeks. Most frequently encountered toxicities include cytopenias, fatigue, and gastrointestinal toxicities. Two patients (one with leiomyosarcoma and one with high grade undifferentiated sarcoma) had stable disease for more than 12 months