Abstract 5269: Myxofibrosarcoma: A move toward Precision Medicine
Authors: Pauli Chantal , Pauwels Jonathan , MacDonald Theresa Y. , Mosquera Juan Miguel , Sboner Andrea , Elemento Olivier , Demichelis Francesca , Prandi Davide , Rickman David , Bode Beata , Beltran Himisha , Rubin Mark A. 
Published: August 2015

Abstract
Background
Soft tissue sarcomas are rare malignant tumors that account for approximately 1% of all malignancies. Myxofibrosarcoma (MFS) is one of the most common sarcomas in elderly patients. Because of their highly complex Karyotypes with extensive intratumoral heterogeneity, no specific recurrent aberration has emerged. In our Precision Cancer Medicine Program, we enroll patients with rare malignancies, metastatic or treatment-resistant disease in order to analyze the individual patient's disease and identify druggable targets. We sequenced two macroscopically different appearing tumor areas from a patient with a primary high-grade MFS using a Whole Exome Sequencing (WES) clinical test called EXaCT-1.
Design
The patient was enrolled prospectively through our Precision Medicine Clinic under an IRB approved protocol. Genomic DNA from fresh OCT (TissueTek) - frozen tissue from a myxoid hypocellular tumor area, from a more pleomorphic hypercellular tumor area and from benign tissue were extracted using the Promega Maxwell 16 MDx. Sequencing was performed using Illumina HiSeq 2500 (2×100bp). A total of 21,522 genes were analyzed using Agilent HaloPlex Exome. Reads were aligned to GRC37/hg19 reference using BWA and processed accordingly to IPM-Exome-pipeline v0.9. Sequencing results were confirmed and further analyzed using CLONET (CLONality Estimate in Tumors) and fluorescence in situ hybridization (FISH). CDK4/6 inhibitors (PD0332991, LY2835219) were tested in a MFS monolayer cell line (OH931) and an engineered 3D mini-MFS system.
Results
Whole exome sequencing and CLONET analysis revealed a hemizygous deletion in the myxoid hypocellular tumor area and a homozygous deletion in the pleomorphic hypercellular tumor area of the tumor suppressor cyclin-dependent kinase inhibitor CDKN2A (p16/Ink4a). Looking through the genomic data published by Barretina et al. (Nat Genet. 2010), we recognized a homozygous deletion of CDKN2A in 15% of the MFS analyzed. Screening full sections of 30 MFS with FISH for CDKN2A deletion shows intratumoral heterogeneity with hemizygous deletion, homozygous deletion and amplification of CDKN2A. CDKN2A loss may be associated with increased sensitivity to CDK4/6 inhibitors. Treatment of CDKN2A null MFS cell line OH931 (kindly provided by Dr. Julia Bridge) with CDK4/6 inhibitors (PD0332991, LY2835219) showed decreased cell proliferation compared to a CDKN2A wild-type sarcoma cell line RD (ATCC CCL-136) in monolayer culture and in our newly developed 3D system.
Conclusion
Tumor suppressor cyclin-dependent kinase inhibitor CDKN2A (p16/Ink4a) deletion or methylation has been reported in multiple cancer types and is correlated with worse patient outcome. Patients suffering from a CDKN2A (p16/Ink4a) null high-grade MFS may benefit from CDK4/6 inhibition as shown in a monolayer and 3D cell culture model of a MFS cell line. This study also provides proof of principle for the benefit enrolling sarcoma patients in Precision Cancer Medicine Programs.
Citation Format: Chantal Pauli, Jonathan Pauwels, Theresa Y. MacDonald, Juan Miguel Mosquera, Andrea Sboner, Olivier Elemento, Francesca Demichelis, Davide Prandi, David Rickman, Beata Bode, Himisha Beltran, Mark A. Rubin. Myxofibrosarcoma: A move toward Precision Medicine. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5269. doi:10.1158/1538-7445.AM2015-5269