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Microarray analysis of gliomas reveals chromosomal position-associated gene expression patterns and identifies potential immunotherapy targets

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Abstract

Gliomas are among the most aggressive malignant tumors and the most refractory to therapy, in part due to the propensity for malignant cells to disseminate diffusely throughout the brain. Here, we have used 27 K cDNA microarrays to investigate global gene expression changes between normal brain and high-grade glioma (glioblastoma multiforme) to try and better understand gliomagenesis and to identify new therapeutic targets. We have also included smaller groups of grade II and grade III tumors of mixed astrocytic and oligodendroglial origin as comparison. We found that the expression of hundreds of genes was significantly correlated to each group, and employed a naïve Bayesian classifier with leave-one-out cross-validation to accurately classify the samples. We developed a novel algorithm to analyze the gene expression data from the perspective of chromosomal position, and identified distinct regions of the genome that displayed coordinated expression patterns that correlated significantly to tumor grade. The regions identified corresponded to previously known genetic copy number changes in glioma (e.g. 10q23, 10q25, 7q, 7p) as well as regions not previously associated significantly with glioma (e.g. 1p13, 6p22). Furthermore, to enrich for more suitable targets for therapy, we took a bioinformatics approach and annotated our signatures with two published datasets that identified membrane/secreted genes from cytosolic genes. The resulting focused list of 31 genes included interesting novel potential targets as well as several proteins already being investigated for immunotherapy (e.g. CD44 and tenascin-C). Software for the chromosome analysis was developed and is freely available at http://base.thep.lu.se.

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Acknowledgements

We would like to thank Karolina Holm and Kristina Lövgren for technical guidance.

The Märit and Hans Rausing Charitable Foundation and The Swedish Children’s Cancer Foundation (to L.G.S.), and from National Institutes of Health, Medical Scientist Training Grant 5T32 GM07367-29 (L.H.S.), Grant CA082783 (R.P.), and from the Avon Foundation (R.P.), and from the Swedish Cancer Society, the Mrs. Berta Kamprad Foundation, the Gunnar Nilsson Cancer Foundation, the Lund University Hospital Foundations, the King Gustav V:s Jubilee Foundation and the Ingabritt and Arne Lundberg Foundation (Å.B.), and from The Swedish Foundation for Strategic Research (M.K.).

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Authors and Affiliations

  1. Department of Neurosurgery, The Rausing Laboratory, Lund University, 22100, Lund, Sweden

    Oscar Persson, Bengt Widegren & Leif G. Salford

  2. Department of Theoretical Physics, Lund University, Lund, Sweden

    Morten Krogh

  3. Department of Oncology, Lund University, Lund, Sweden

    Lao H. Saal, Jian Liu & Åke Borg

  4. Department of Pathology, Lund University, Lund, Sweden

    Elisabet Englund

  5. Department of Clinical Genetics, Lund University, Lund, Sweden

    Nils Mandahl

  6. Division of Tumor Immunology, Lund University, Lund, Sweden

    Bengt Widegren

  7. Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA

    Lao H. Saal & Ramon Parsons

  8. Departments of Pathology and Medicine, Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA

    Ramon Parsons

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  1. Oscar Persson
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Correspondence to Leif G. Salford.

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Oscar Persson, Morten Krogh and Lao H. Saal contributed equally and are joint co-first authors.

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Persson, O., Krogh, M., Saal, L.H. et al. Microarray analysis of gliomas reveals chromosomal position-associated gene expression patterns and identifies potential immunotherapy targets. J Neurooncol 85, 11–24 (2007). https://doi.org/10.1007/s11060-007-9383-6

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