title: Functional genomics analysis reveals a MYC signature associated with a poor clinical prognosis in liposarcomas.
abstract: Liposarcomas, which are malignant fatty tumors, are the second most common soft-tissue sarcomas. Several histologically defined liposarcoma subtypes exist, yet little is known about the molecular pathology that drives the diversity in these tumors. We used functional genomics to classify a panel of diverse liposarcoma cell lines based on hierarchical clustering of their gene expression profiles, indicating that liposarcoma gene expression profiles and histologic classification are not directly correlated. Boolean probability approaches based on cancer-associated properties identified differential expression in multiple genes, including MYC, as potentially affecting liposarcoma signaling networks and cancer outcome. We confirmed our method with a large panel of lipomatous tumors, revealing that MYC protein expression is correlated with patient survival. These data encourage increased reliance on genomic features in conjunction with histologic features for liposarcoma clinical characterization and lay the groundwork for using Boolean-based probabilities to identify prognostic biomarkers for clinical outcome in tumor patients.
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Dat
authors.initials: D
authors.lastname: Tran
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Kundan
authors.initials: K
authors.lastname: Verma
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Kristin
authors.initials: K
authors.lastname: Ward
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Dolores
authors.initials: D
authors.lastname: Diaz
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Esha
authors.initials: E
authors.lastname: Kataria
authors.affiliation: Department of Pathology, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Alireza
authors.initials: A
authors.lastname: Torabi
authors.affiliation: Curie Institute Research Center, Paris, France.
authors.forename: Anna
authors.initials: A
authors.lastname: Almeida
authors.affiliation: Curie Institute Research Center, Paris, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Malfoy
authors.affiliation: Cancer Stem Cell Innovation Centre and the Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.
authors.forename: Eva W
authors.initials: EW
authors.lastname: Stratford
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
authors.forename: Dianne C
authors.initials: DC
authors.lastname: Mitchell
authors.affiliation: Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas. Electronic address: brad.bryan@ttuhsc.edu.
authors.forename: Brad A
authors.initials: BA
authors.lastname: Bryan
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D045744:Cell Line, Tumor; D005260:Female; D023281:Genomics; D006801:Humans; D008080:Liposarcoma / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D008297:Male; D008875:Middle Aged; D011379:Prognosis; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics*; D012983:Soft Tissue Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D015996:Survival Rate; D059467:Transcriptome
chemical_list: C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc