OMICS and brain tumour biomarkers

Currently, brain tumours are diagnosed by surgical biopsy and light microscopic examination of tissue, with immunohistochemistry in difficult cases. We review research in the field of brain tumour diagnosis and discuss several new approaches. In future, tumour type, optimal treatment, and prognosis could be obtained by studying the gene (genomics), protein (proteomics) or metabolite (metabolomics) content of tumour cells. These techniques generate complex data, analysed using techniques such as pattern recognition software to identify biomarker signatures of different tumours. Compared with individual biomarkers, biomarker signatures appear to increase diagnostic accuracy and may produce an improved brain tumour classification system.

[1]  D. Botstein,et al.  A gene expression database for the molecular pharmacology of cancer , 2000, Nature Genetics.

[2]  L Verhey,et al.  Serial proton MR spectroscopic imaging of recurrent malignant gliomas after gamma knife radiosurgery. , 2001, AJNR. American journal of neuroradiology.

[3]  P. Davidsson,et al.  Elevated Levels of alpha-2-Heremans-Schmid Glycoprotein in CSF of Patients with Low-Grade Gliomas , 2003, Tumor Biology.

[4]  F. Kokocinski,et al.  Microarray-based screening for molecular markers in medulloblastoma revealed STK15 as independent predictor for survival. , 2004, Cancer research.

[5]  Wei Huang,et al.  Functional outcomes and survival in patients with high-grade gliomas in dominant and nondominant hemispheres. , 2005, Journal of neurosurgery.

[6]  M. Bernstein,et al.  Failed stereotactic biopsy in a series of 518 cases. , 1995, Stereotactic and functional neurosurgery.

[7]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian cancer , 2002, The Lancet.

[8]  E. Petricoin,et al.  Clinical potential of proteomics in the diagnosis of ovarian cancer , 2002, Expert review of molecular diagnostics.

[9]  A. Alaiya,et al.  Clinical cancer proteomics: promises and pitfalls. , 2005, Journal of proteome research.

[10]  I. Whittle,et al.  Pineal region tumors and the role of stereotactic biopsy: review of the mortality, morbidity, and diagnostic rates in 370 cases. , 1998, Neurosurgery.

[11]  P. Graham Meta‐analysis of radiation therapy with and without adjuvant chemotherapy for malignant gliomas in adults , 1993, Cancer.

[12]  Timothy Planche,et al.  A novel and accurate diagnostic test for human African trypanosomiasis , 2004, The Lancet.

[13]  P. Angenendt Progress in protein and antibody microarray technology. , 2005, Drug discovery today.

[14]  M. Bernstein,et al.  Complications of CT-guided stereotactic biopsy of intra-axial brain lesions. , 1994, Journal of neurosurgery.

[15]  Liliana Gheorghiu,et al.  Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands , 2005, Electrophoresis.

[16]  Enrique Querol,et al.  Identification of protein ligands in complex biological samples using intensity-fading MALDI-TOF mass spectrometry. , 2003, Analytical chemistry.

[17]  W. Hall,et al.  Preliminary assessment of turbo spectroscopic imaging for targeting in brain biopsy. , 2001, AJNR. American journal of neuroradiology.

[18]  Allan J. Hamilton,et al.  Stereotactic Biopsy of Intracranial Brain Lesions , 1999, Stereotactic and Functional Neurosurgery.

[19]  F. Valafar Pattern Recognition Techniques in Microarray Data Analysis : A Survey , 2002 .

[20]  N. Seki,et al.  Cathepsin D is a potential serum marker for poor prognosis in glioma patients. , 2005, Cancer research.

[21]  S. Nelson,et al.  DNA-microarray analysis of brain cancer: molecular classification for therapy , 2004, Nature Reviews Neuroscience.

[22]  A. Butte,et al.  Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Yu Shyr,et al.  Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. , 2005, Cancer research.

[24]  O. Kallioniemi,et al.  Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. , 2000, Cancer research.

[25]  A. von Deimling,et al.  Molecular Genetic Analysis of Oligodendroglial Tumors , 2005, Journal of neuropathology and experimental neurology.

[26]  Mark R Gilbert,et al.  Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. , 2002, Cancer research.

[27]  S. Green,et al.  Glioblastoma multiforme and anaplastic astrocytoma pathologic criteria and prognostic implications , 1985, Cancer.

[28]  Debashis Ghosh,et al.  Autoantibody signatures in prostate cancer. , 2005, The New England journal of medicine.

[29]  L. Liotta,et al.  CSF proteome: a protein repository for potential biomarker identification , 2005, Expert review of proteomics.

[30]  E. Alexander,et al.  Evaluation of BCNU and/or radiotherapy in the treatment of anaplastic gliomas. A cooperative clinical trial. , 1978, Journal of neurosurgery.

[31]  A. Larsson,et al.  Growth factor analysis of low-grade glioma CSF: PDGF and VEGF are not detectable , 2003, Neurological Sciences.

[32]  Webster K. Cavenee,et al.  Pathology and genetics of tumours of the nervous system. , 2000 .

[33]  Xiao-Ying Meng,et al.  Classification of cancer types by measuring variants of host response proteins using SELDI serum assays , 2005, International journal of cancer.

[34]  Anthony Asher,et al.  Survival following surgery and prognostic factors for recently diagnosed malignant glioma: data from the Glioma Outcomes Project. , 2003, Journal of neurosurgery.

[35]  M. Papadopoulos,et al.  Emerging molecular mechanisms of brain tumour oedema. , 2001, British journal of neurosurgery.

[36]  M. Brada Pathology and Genetics of Tumours of the Nervous System , 2001, British Journal of Cancer.

[37]  L. Arckens,et al.  Proteomic approaches in brain research and neuropharmacology. , 2004, European journal of pharmacology.

[38]  Nathalie Wong,et al.  Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting: a pilot study. , 2005, Clinical chemistry.

[39]  D. Koller,et al.  From signatures to models: understanding cancer using microarrays , 2005, Nature Genetics.

[40]  W. Hop,et al.  Low-Molecular Weight Caldesmon as a Potential Serum Marker for Glioma , 2005, Clinical Cancer Research.

[41]  T. Barrette,et al.  Mining for regulatory programs in the cancer transcriptome , 2005, Nature Genetics.

[42]  Susan M. Chang,et al.  Serial proton magnetic resonance spectroscopy imaging of glioblastoma multiforme after brachytherapy. , 1997, Journal of neurosurgery.

[43]  L. Liau,et al.  Cellular immunity and immunotherapy of brain tumors. , 2004, Frontiers in bioscience : a journal and virtual library.

[44]  Rob Pieters,et al.  Identification of Tumor‐Related Proteins by Proteomic Analysis of Cerebrospinal Fluid from Patients with Primary Brain Tumors , 2003, Journal of neuropathology and experimental neurology.

[45]  P. Thibault,et al.  Identification of differentially expressed proteins in human glioblastoma cell lines and tumors , 2003, Glia.

[46]  F. Heppner,et al.  Gene expression profiling and subgroup identification of oligodendrogliomas , 2004, Oncogene.

[47]  Stefan Müllner,et al.  Protein biochips: A new and versatile platform technology for molecular medicine. , 2005, Drug discovery today.

[48]  L. Stewart,et al.  Chemotherapy in adult high-grade glioma: a systematic review and meta-analysis of individual patient data from 12 randomised trials , 2002, The Lancet.

[49]  M. Oshimura,et al.  Proteomics-based identification of differentially expressed genes in human gliomas: down-regulation of SIRT2 gene. , 2003, Biochemical and biophysical research communications.

[50]  T. Poggio,et al.  Prediction of central nervous system embryonal tumour outcome based on gene expression , 2002, Nature.

[51]  A. Chinnaiyan,et al.  Integrative analysis of the cancer transcriptome , 2005, Nature Genetics.

[52]  Witham,et al.  Comprehensive assessment of hemorrhage risks and outcomes after stereotactic brain biopsy. , 2001, Journal of neurosurgery.

[53]  F Ståhlberg,et al.  Proton MR spectroscopy and preoperative diagnostic accuracy: an evaluation of intracranial mass lesions characterized by stereotactic biopsy findings. , 2000, AJNR. American journal of neuroradiology.

[54]  P J Kelly,et al.  Resection, biopsy, and survival in malignant glial neoplasms. A retrospective study of clinical parameters, therapy, and outcome. , 1993, Journal of neurosurgery.

[55]  L. Liau,et al.  Tumor immunology, immunomics and targeted immunotherapy for central nervous system malignancies , 2005, Neurological research.

[56]  Daniel B Vigneron,et al.  In vivo molecular imaging for planning radiation therapy of gliomas: An application of 1H MRSI , 2002, Journal of magnetic resonance imaging : JMRI.

[57]  F. Valafar Pattern Recognition Techniques in Microarray Data Analysis , 2002 .

[58]  W P Dillon,et al.  Preoperative proton MR spectroscopic imaging of brain tumors: correlation with histopathologic analysis of resection specimens. , 2001, AJNR. American journal of neuroradiology.

[59]  J. Mesirov,et al.  Chemosensitivity prediction by transcriptional profiling , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[60]  P. Black,et al.  Neuroimaging in pediatric brain tumors: Gd-DTPA-enhanced, hemodynamic, and diffusion MR imaging compared with MR spectroscopic imaging. , 2002, AJNR. American journal of neuroradiology.

[61]  P. Warnke,et al.  Surgical resection and radiation therapy versus biopsy and radiation therapy in the treatment of glioblastoma multiforme. , 1993, Journal of neurosurgery.

[62]  M. Izquierdo,et al.  Parent Phenotype and Age Dependence, on Rat Glioma Tumor Rejection , 2004, Journal of Neuro-Oncology.

[63]  D. Botstein,et al.  Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Glyn Johnson,et al.  High-grade gliomas and solitary metastases: differentiation by using perfusion and proton spectroscopic MR imaging. , 2002, Radiology.

[65]  Z L Gokaslan,et al.  A multivariate analysis of 416 patients with glioblastoma multiforme: prognosis, extent of resection, and survival. , 2001, Journal of neurosurgery.

[66]  V. L. Doyle,et al.  Metabolic profiles of human brain tumors using quantitative in vivo 1H magnetic resonance spectroscopy , 2003, Magnetic resonance in medicine.

[67]  K. Laxer Clinical Applications of Magnetic Resonance Spectroscopy , 1997, Epilepsia.

[68]  P. Wesseling,et al.  Neuropathological diagnostic accuracy , 2002, British journal of neurosurgery.

[69]  M. Zweig,et al.  Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. , 1993, Clinical chemistry.

[70]  Akira Yamaura,et al.  Molecular Classification and Survival Prediction in Human Gliomas Based on Proteome Analysis , 2004, Cancer Research.

[71]  Shu Zheng,et al.  Serum protein fingerprinting coupled with artificial neural network distinguishes glioma from healthy population or brain benign tumor. , 2005, Journal of Zhejiang University. Science. B.

[72]  L. D.,et al.  Brain tumors , 2005, Psychiatric Quarterly.

[73]  P. Lichter,et al.  Gene expression patterns in ependymomas correlate with tumor location, grade, and patient age. , 2003, The American journal of pathology.

[74]  C. Gladson,et al.  Endogenous inhibitors of angiogenesis in malignant gliomas: nature's antiangiogenic therapy. , 2005, Neuro-oncology.

[75]  M. Pfreundschuh,et al.  Human neoplasms elicit multiple specific immune responses in the autologous host. , 1995, Proceedings of the National Academy of Sciences of the United States of America.