Whole-transcriptome Analysis of Chordoma of the Skull Base

Overview

Journal Virchows Arch

Specialties Cell Biology
Molecular Biology
Pathology

Date 2016 Jul 13

PMID 27401718

Citations 16

Authors

Diana Bell

Shaan M Raza

Achim H Bell

Gregory N Fuller

Franco DeMonte

Affiliations

Soon will be listed here.

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.

Citing Articles

Radiogenomic method combining DNA methylation profiles and magnetic resonance imaging radiomics predicts patient prognosis in skull base chordoma.

Deng X, Li P, Tian K, Zhang F, Yan Y, Fan Y Clin Epigenetics. 2025; 17(1):23.

PMID: 39962547 PMC: 11831810. DOI: 10.1186/s13148-025-01836-w.

Chordoma cells possess bone-dissolving activity at the bone invasion front.

Kawaai K, Oishi Y, Kuroda Y, Tamura R, Toda M, Matsuo K Cell Oncol (Dordr). 2024; 47(5):1663-1677.

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Organelle resolved proteomics uncovers PLA2R1 as a novel cell surface marker required for chordoma growth.

Khan S, Zuccato J, Ignatchenko V, Singh O, Govindarajan M, Waas M Acta Neuropathol Commun. 2024; 12(1):39.

PMID: 38454495 PMC: 10921702. DOI: 10.1186/s40478-024-01751-w.

Integrated Molecular and Histological Insights for Targeted Therapies in Mesenchymal Sinonasal Tract Tumors.

Hoch C, Knoedler L, Knoedler S, Bashiri Dezfouli A, Schmidl B, Trill A Curr Oncol Rep. 2024; 26(3):272-291.

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Linc01116 Silencing Inhibits the Proliferation and Invasion, Promotes Apoptosis of Chordoma Cells Regulating the Expression of Mir-9-5p/PKG1.

Liu J, Qi Y, Hou S, Zhang S, Wang Z Curr Mol Med. 2023; 24(8):1056-1071.

PMID: 37489776 DOI: 10.2174/1566524023666230719121758.

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