title: Whole-transcriptome analysis of chordoma of the skull base.
abstract: Fourteen skull base chordoma specimens and three normal specimens were microdissected from paraffin-embedded tissue. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using whole-transcriptome shotgun sequencing. Using strict criteria, 294 differentially expressed transcripts were found, with 28 % upregulated and 72 % downregulated. The transcripts were annotated using NCBI Entrez Gene and computationally analyzed with the Ingenuity Pathway Analysis program. From these significantly changed expressions, the analysis identified 222 cancer-related transcripts. These 294 differentially expressed genes and non-coding RNA transcripts provide here a set to specifically define skull base chordomas and to identify novel and potentially important targets for diagnosis, prognosis, and therapy of this cancer. Significance Genomic profiling to subtype skull base chordoma reveals potential candidates for specific biomarkers, with validation by IHC for selected candidates. The highly expressed developmental genes T, LMX1A, ZIC4, LHX4, and HOXA1 may be potential drivers of this disease.
authors.affiliation: Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA. diana.bell@mdanderson.org.|Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA. diana.bell@mdanderson.org.
authors.forename: Diana
authors.initials: D
authors.lastname: Bell
authors.affiliation: Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA.|Department of Neurosurgery, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
authors.forename: Shaan M
authors.initials: SM
authors.lastname: Raza
authors.affiliation: Lone Star College, Houston, TX, USA.
authors.forename: Achim H
authors.initials: AH
authors.lastname: Bell
authors.affiliation: Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
authors.forename: Gregory N
authors.initials: GN
authors.lastname: Fuller
authors.affiliation: Department of Neurosurgery, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA. fdemonte@mdanderson.org.
authors.forename: Franco
authors.initials: F
authors.lastname: DeMonte
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000032:analysis / Q000378:metabolism*; D002648:Child; D002817:Chordoma / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008875:Middle Aged; D011379:Prognosis; D019292:Skull Base Neoplasms / Q000378:metabolism* / Q000473:pathology*
chemical_list: D014408:Biomarkers, Tumor
keywords: Chordoma; Skull base; Transcriptome