Relevance of a TCGA-derived Glioblastoma Subtype Gene-Classifier among Patient Populations

Wan Yee Teo, Karthik Sekar, Pratap Seshachalam, Jianhe Shen, Wing Yuk Chow, Ching C. Lau, Hee Kyoung Yang, Junseong Park, Seok Gu Kang, Xiaonan Li, Do Hyun Nam, Kam M. Hui

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Abstract

Glioblastoma multiforme (GBM), a deadly cancer, is the most lethal and common malignant brain tumor, and the leading cause of death in adult brain tumors. While genomic data continues to rocket, clinical application and translation to patient care are lagging behind. Big data now deposited in the TCGA network offers a window to generate novel clinical hypotheses. We hypothesized that a TCGA-derived gene-classifier can be applied across different gene profiling platforms and population groups. This gene-classifier validated three robust GBM-subtypes across six different platforms, among Caucasian, Korean and Chinese populations: Three Caucasian-predominant TCGA-cohorts (Affymetrix U133A = 548, Agilent Custom-Array = 588, RNA-seq = 168), and three Asian-cohorts (Affymetrix Human Gene 1.0ST-Array = 61, Illumina = 52, Agilent 4 × 44 K = 60). To understand subtype-relevance in patient therapy, we investigated retrospective TCGA patient clinical sets. Subtype-specific patient survival outcome was similarly poor and reflected the net result of a mixture of treatment regimens with/without surgical resection. As a proof-of-concept, in subtype-specific patient-derived orthotopic xenograft (PDOX) mice, Classical-subtype demonstrated no survival difference comparing radiation-therapy versus temozolomide monotherapies. Though preliminary, a PDOX model of Proneural/Neural-subtype demonstrated significantly improved survival with temozolomide compared to radiation-therapy. A larger scale study using this gene-classifier may be useful in clinical outcome prediction and patient selection for trials based on subtyping.

Original languageEnglish
Article number7442
JournalScientific reports
Volume9
Issue number1
DOIs
Publication statusPublished - 2019 Dec 1

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Teo, W. Y., Sekar, K., Seshachalam, P., Shen, J., Chow, W. Y., Lau, C. C., Yang, H. K., Park, J., Kang, S. G., Li, X., Nam, D. H., & Hui, K. M. (2019). Relevance of a TCGA-derived Glioblastoma Subtype Gene-Classifier among Patient Populations. Scientific reports, 9(1), [7442]. https://doi.org/10.1038/s41598-019-43173-y