Importance of the Dataset

Sarcoma is a malignant tumor of the mesenchymal cells forming the connective tissue. Champions Oncology currently has 135 Sarcoma PDX models available to oncology pharmacology studies and drug development. Champions’ Sarcoma models represent several disease subtypes, both pediatric and adult, including Ewing Sarcoma, Leiomyosarcoma, Liposarcoma, Angiosarcoma, Synovial Sarcoma, and others. These models are well characterized with patient clinical annotations, disease status, treatment history, and in vivo and ex vivo drug responses to standard of care therapies, such as cisplatin, doxorubicin, docetaxel, ifosfamide, and many more. Champions’ Sarcoma model cohort encompass mutations in numerous key pathways including DNA repair, cell cycle, cell proliferation and invasion, and angiogenesis.

Experimental Design

Each model included in this cohort was characterized by NGS sequencing (WES and RNA-Seq), proteomics and phospho-proteomics analyses. Our NGS workflow is a multi-step procedure; specifically, a primary sample undergoes preparation by thawing and subsequent extraction of gDNA and RNA. A library is then prepared and NGS sequencing (WES and RNA-Seq) is performed using Illumina Nextseq2000. Subsequently, raw data is collected, processed, and analyzed. The data must meet Champions’ Quality Control requirements, including sample QC, library QC and sequencing data QC. Finally, data is uploaded and stored in the user’s unique Lumin instance, where it can be visualized and further analyzed in various modules.

Champions has partnered with BGI Genomics to obtain proteomics and phospho-proteomics data; specifically, proteins are extracted from cells and/or tissues to obtain a protein mixture, which are broken down by digestion enzymes to yield a peptide mixture. This peptide mixture undergoes phospho-peptide enrichment to give a phospho-peptide mixture, which is then analyzed by LC/MS, using either data-dependent acquisition (DDA) or label-free data-independent acquisition (DIA) for data quantification.

Applications of the Dataset

The Sarcoma model cohort dataset has been integrated into our revolutionary visualization and data analytics software, Lumin Bioinformatics. With a Lumin Bioinformatics or Workspaces subscription, you can access multi-omic data from our Sarcoma model cohort.

The following modules can be used in Lumin Bioinformatics to access proteomics and phospho-proteomics data:

• Clustergrammer: Create hierarchical clustered heatmaps using gene expression, protein abundance, phosphorylation intensity or kinase activity. Users can also overlay %TGI values and mutation status for model cohorts.
  
  
• Molecular Graphing: Quickly create box plots to show protein abundance of your proteins of interest across different indications.
  
• Network Viewer: Within the network viewer, users can color protein nodes based on gene expression, mutational status, quantitative protein expression or include molecular signatures. This tool overlays proteomics data from Champions’ PDX models or the public CPTAC database. Users can then evaluate quantitative protein abundance, kinase activity and specific phosphorylation status across cancer types or within a defined tumor model.
  
• Mutation Mapper: Researchers can visualize protein amino acid domains and mutations identified within Champions' PDX models. Through Champions’ phospho-proteomic sequencing, phosphorylation sites identified within our tumor bank were detected, and are aligned within the context of protein amino acid domains. Users can also visualize phosphorylation sites detected within the public CPTAC database as well as those predicted by PhosphositePlus.

Watch our quick video to discover more about Champions’ Sarcoma Models in Lumin Bioinformatics: