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Liposarcoma (LPS) is the most common type of soft tissue sarcoma and accounts for approximately 20% of all adult sarcomas. Due to absence of clinically effective treatment options with a high rate of recurrence and resistance to conventional therapeutics agent, a critical need exists to identify the therapeutic targets for treating this deadly disease. Our study aims to further understanding of LPS pathobiology by constructing a detailed genetic and molecular landscape of LPS through a series of integrated comprehensive genomic and transcriptomic analysis. We performed SNP CHIP array analysis on 92 LPS cases and 13 LPS cell lines, whole-exome sequencing analysis of 12 LPS-normal paired samples, transcriptome sequencing of 5 cases, targeted whole-exome sequencing of 86 LPS cases and 13 LPS cell lines and intra-tumor heterogeneity analysis in LPS. We found a variety of genomic aberrations including point mutations, copy number changes, genomic rearrangements, and fusion genes in different subtypes of LPS using next generation sequencing technology. SNP CHIP array analysis revealed significant recurrent copy number amplifications and deletions involving many important well-known cancer genes. One of the important potentially druggable alteration of carboxypeptidase M gene was emerged as new therapeutic strategy in SNP array analysis. The biological and functional characterization of carboxypeptidase M as therapeutic target was done in detail using LPS cell lines and mouse xenograft model system. Using whole exome sequencing, a total 377 potential somatic changes were identified and validated by Sanger sequencing in Discovery cohort. We analyzed the spectrum of mutations detected by whole exome sequencing and found presence of two distinct mutational signatures. Next, a Prevalence Set of additional 86 LPS patients' samples was examined by targeted exome sequencing and numerous non-synonymous mutations identified were validated using Sanger sequencing. Targeted exome sequencing revealed significant recurrent alterations in cell adhesion [60% of cases], DNA damage repair [65% of cases] and kinase [36% of cases] signalling pathways leading to identification of genes that can be potentially targeted using currently available drugs. A class of genes with regulatory roles in axon guidance and cancer cell growth, survival, invasion and angiogenesis were also found to be mutated. RNA sequencing was performed on 5 LPS samples of different histotypes to explore fusion genes. We identified various fusion genes and validated 29 chimeric fusion transcripts using RT-PCR followed by Sanger sequencing across the fusion junctions. We also found the well-known and established classical fusion in LPS cases. Intra-tumor heterogeneity analysis indicates ongoing regional clonal evolution due to the presence of unique mutations in different tumor regions of the same patient tumor sample. Mutations confined to only one of the three tumor regions indicate that interrogation of a single tumor site is not representative of the entire mutational landscape of a patient's tumor. A phylogenetic tree of different tumor regions by clonal ordering shows branching tumor evolution indicating that the majority of genetic events occurred after tumors diverged. The present investigation provides insights into the underlying mechanism driving liposarcomagenesis and also identifies new therapeutic targets which need to be further investigated. Comprehensive genomic characterization will improve our understanding of the LPS molecular genetics and lay the foundation to refine diagnostic classifications, determine prognosis and develop new therapeutics for treating LPS. Note: This abstract was not presented at the conference. Citation Format: Deepika Kanojia, Manoj Garg, Yasunobu Nagata, Dhong Hyun Lee, Hans-Ulrich Klein, Christoph Bartenhagen, Anand M T, Ngan B Doan, Jonathan W Said, Henry Yang, Charles Forscher, Martin Dugas, Seishi Ogawa, H Phillip Koeffler. Integrative study of genomic alterations in liposarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-20.

Anaplastic thyroid cancer (ATC) has no effective treatment, resulting in a high rate of mortality. We established cell lines from a primary ATC and its lymph node metastasis, and investigated the molecular factors and genomic changes associated with tumor growth.The aim of the study was to understand the molecular and genomic changes of highly aggressive ATC and its clonal evolution to develop rational therapies.We established unique cell lines from primary (OGK-P) and metastatic (OGK-M) ATC specimen, as well as primagraft from the metastatic ATC, which was serially xeno-transplanted for more than 1 year in NOD scid gamma mice were established. These cell lines and primagraft were used as tools to examine gene expression, copy number changes, and somatic mutations using RNA array, SNP Chip, and whole exome sequencing.Mice carrying sc (OGK-P and OGK-M) tumors developed splenomegaly and neutrophilia with high expression of cytokines including CSF1, CSF2, CSF3, IL-1β, and IL-6. Levels of HIF-1α and its targeted genes were also elevated in these tumors. The treatment of tumor carrying mice with Bevacizumab effectively decreased tumor growth, macrophage infiltration, and peripheral WBCs. SNP chip analysis showed homozygous deletion of exons 3-22 of the PARD3 gene in the cells. Forced expression of PARD3 decreased cell proliferation, motility, and invasiveness, restores cell-cell contacts and enhanced cell adhesion. Next generation exome sequencing identified the somatic changes present in the primary, metastatic, and primagraft tumors demonstrating evolution of the mutational signature over the year of passage in vivo.To our knowledge, we established the first paired human primary and metastatic ATC cell lines offering unique possibilities for comparative functional investigations in vitro and in vivo. Our exome sequencing also identified novel mutations, as well as clonal evolution in both the metastasis and primagraft.