Molecular genetic and proteomic analysis of synchronous malignant gliomas

Demography, Pattern of Care, and Survival in Patients with Xanthoastrocytoma: A Systematic Review and Individual Patient Data Analysis of 325 Cases

Objectives Xanthoastrocytoma (XA) is a low-grade glial tumor seen in young adults and there is lack of robust data on treatment of this rare tumor. In this systematic review and individual patient's data analysis, we aimed to look into the demography, pattern of care, survival outcomes, and prognostic factors in patients with both Grade II and III XA.

Methods A comprehensive search was conducted with the Medical Subject Heading terms: “Xanthoastrocytoma; Pleomorphic Xanthoastrocytoma; Anaplastic Xanthoastrocytoma; Xanthoastrocytoma AND treatment; and Anaplastic Xanthoastrocytoma AND survival” to find all possible publications.

Results A total of 325 individual patients from a total of 138 publications pertaining to XA were retrieved. Median age of the entire cohort was 19 years. About 56.1% of the patients underwent a gross total resection (GTR) and 31.4% underwent a subtotal resection. Nearly, 76.6% of the patients had a Grade II tumor and adjuvant radiation was delivered in 27.4% of the patients. Estimated 2- and 5-year progression-free survival (PFS) were 68.5 and 51.2%, respectively. Age, grade, and extent of surgery were significant factors affecting PFS. Estimated 2- and 5-year overall survival (OS) was 88.8 and 78%, respectively. The median OS for Grade II and Grade III tumors were 209 and 49 months, respectively. Age and extent of surgery were significant factors affecting OS.

Conclusion XA is a disease of young adults with favorable prognosis. Younger patients (<20 years), patients who undergo a GTR, and patients with a lower grade tumor have a better treatment outcome.

Primary anaplastic pleomorphic xanthoastrocytoma in adults. Case report and review of literature

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A case report and literature review of anaplastic pleomorphic xanthoastrocytoma in adults.

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The tumor shows an aggressive clinical course compared with its benign variant.

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APXA shows histological characteristics comparable with grade III astrocytomas.

Background

Pleomorphic xanthoastrocytoma (PXA) classified as a low Grade (WHO II) astrocytic neoplasm. It is known for its relatively favorable prognosis. It most commonly occurs in young adults. Malignant progression in PXA has been frequently reported since its first description in 1979; however, the presentation of a primary anaplastic PXA tumor with an aggressive clinical course in adults is rare especially in the later age group.

Case description

We present a case of primary anaplastic PXA in a 53 year old male that manifested with an early recurrence pattern at 9 weeks. Treatment performed was surgical excision and external beam radiotherapy. The aforementioned tumor followed an aggressive clinical course. Tumor cells exhibited the characteristic expression of GFAP (Glial fibrillary acidic protein), higher proliferative index (8–10%) on Ki-67 staining along with the presence of increased mitoses ( >5/10hpf). A review of previously reported primary anaplastic pleomorphic xanthoastrocytoma cases in adults with histological features was also done.

Conclusion

Our review of all reported cases of APXA in adults concludes that the clinical behavior of this tumor varies considerably from its benign variant. Early disease recurrence in anaplastic pleomorphic xanthoastrocytomas is associated with fatal outcomes. As per our review of literature it is seen that anaplastic variant of PXA shows histological characteristics as well as clinical course comparable with Grade III astrocytomas.

We recommend further evaluation of PXA with anaplastic features regarding their genetic characteristics to understand the origin as well as behavior of this tumor.

Tissue proteomics using capillary isoelectric focusing-based multidimensional separations

The capabilities of capillary isoelectric focusing-based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. In this article, recent advances in online integration of capillary isoelectric focusing with nano-reversed phase liquid chromatography for achieving high-resolution peptide and protein separations prior to mass spectrometry analysis are reviewed, along with its potential application to tissue proteomics. These proteome technological advances combined with recently developed tissue microdissection techniques, provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.

Targeted tissue proteomic analysis of human astrocytomas

Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not only serves as a synergistic strategy to characterize low abundance proteins, but it can also be employed to conduct comparative proteomic studies of human astrocytomas. A set of fresh frozen brain biopsies were selectively microdissected to provide an enriched, high quality, and reproducible sample of tumor cells. Despite sharing many common proteins, there are significant differences in the protein expression level among different grades of astrocytomas. A large number of proteins, such as plasma membrane proteins EGFR and Erbb2, are up-regulated in glioblastoma. Besides facilitating the prioritization of follow-on biomarker selection and validation, comparative proteomics involving measurements in changes of pathways are expected to reveal the molecular relationships among different pathological grades of gliomas and potential molecular mechanisms that drive gliomagenesis.

Clonal analysis in recurrent astrocytic, oligoastrocytic and oligodendroglial tumors implicates IDH1- mutation as common tumor initiating event

Background

To investigate the dynamics of inter- and intratumoral molecular alterations during tumor progression in recurrent gliomas.

Methodology/Principal Findings

To address intertumoral heterogeneity we investigated non- microdissected tumor tissue of 106 gliomas representing 51 recurrent tumors. To address intratumoral heterogeneity a set of 16 gliomas representing 7 tumor pairs with at least one recurrence, and 4 single mixed gliomas were investigated by microdissection of distinct oligodendroglial and astrocytic tumor components. All tumors and tumor components were analyzed for allelic loss of 1p/19q (LOH 1p/19q), for TP53- mutations and for R132 mutations in the IDH1 gene. The investigation of non- microdissected tumor tissue revealed clonality in 75% (38/51). Aberrant molecular alterations upon recurrence were detected in 25% (13/51). 64% (9/14) of these were novel and associated with tumor progression. Loss of previously detected alterations was observed in 36% (5/14). One tumor pair (1/14; 7%) was significant for both. Intratumoral clonality was detected in 57% (4/7) of the microdissected tumor pairs and in 75% (3/4) of single microdissected tumors. 43% (3/7) of tumor pairs and one single tumor (25%) revealed intratumoral heterogeneity. While intratumoral heterogeneity affected both the TP53- mutational status and the LOH1p/19q status, all tumors with intratumoral heterogeneity shared the R132 IDH1- mutation as a common feature in both their microdissected components.

Conclusions/Significance

The majority of recurrent gliomas are of monoclonal origin. However, the detection of divertive tumor cell clones in morphological distinct tumor components sharing IDH1- mutations as early event may provide insight into the tumorigenesis of true mixed gliomas.

Malignant potential of pleomorphic xanthoastrocytoma

Pleomorphic xanthoastrocytoma (PXA) is a low-grade astrocytic tumour that occasionally progresses to a higher grade. We have extensively reviewed the literature on the potential for malignant transformation of PXA. An illustrative case of a PXA transforming to glioblastoma multiforme is presented.

Comparison of multidimensional shotgun technologies targeting tissue proteomics

A compelling need exists for the development of technologies that facilitate and accelerate the discovery of novel protein biomarkers with therapeutic and diagnostic potential. Comparisons among shotgun proteome technologies, including capillary isotachophoresis (CITP)-based multidimensional separations and multidimensional LC system, are therefore performed in this study regarding their abilities to address the challenges of protein complexity and relative abundance inherent in glioblastoma multiforme-derived cancer stem cells. Comparisons are conducted using a single processed protein digest with equal sample loading, identical second-dimension separation (RPLC) and MS conditions, and consistent search parameters and cutoff established by the target-decoy determined false-discovery rate. Besides achieving superior overall proteome performance in total peptide, distinct peptide, and distinct protein identifications; analytical reproducibility of the CITP proteome platform coupled with the spectral counting approach are determined by a Pearson R(2) value of 0.98 and a CV of 15% across all proteins quantified. In contrast, extensive fraction overlapping in strong cation exchange greatly limits the ability of multidimensional LC separations for mining deeper into the tissue proteome as evidenced by the poor coverage in various protein functional categories and key protein pathways. The CITP proteomic technology, equipped with selective analyte enrichment and ultrahigh resolving power, is expected to serve as a critical component in the overall toolset required for biomarker discovery via shotgun proteomic analysis of tissue specimens.

Subtelomeric analysis of pediatric astrocytoma: subchromosomal instability is a distinctive feature of pleomorphic xanthoastrocytoma

Astrocytic neoplasms are genetically heterogeneous; however a low frequency of genomic changes has been found in juvenile pilocytic astrocytoma (PA) in molecular studies. Concerning pleomorphic xanthoastrocytomas (PXA), recent studies have given heterogeneous results for chromosomal alterations. We studied the subtelomeric regions of 19 primary astrocytoma tumors. Results were near normality for the PA group with relative scarcity of chromosomal imbalances, except for the duplication of 3pter in 4/15 and deletion of 21qter in 5/15 of them. In contrast, a specific profile was observed in the 4 PXA tumoral samples. This involved 3pter, 14qter and 19pter duplication and 4qter, 6qter, 9qter, 13cen, 17pter, 18qter and 21qter deletion. Our results indicate that the chromosomal and genetic aberrations in PXAs differed from those typically associated with the diffusely infiltrating astrocytic and oligodendroglial gliomas. These genetic differences would likely contribute to the more favorable behavior of PXAs and may be helpful for molecular differential diagnosis of pediatric cerebral tumors.

Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens

Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique.

Mass spectrometry-based tissue proteomics for cancer biomarker discovery

There is an urgent need for the development of technologies that allow the monitoring of protein expression and processing in tumor tissues resulting from development, physiology and disease state. To address the issue of cell heterogeneity in the tissue section, several microdissection techniques have been developed to provide a rapid and straightforward method for isolating selected subpopulations of cells for downstream molecular analysis. Development and demonstration of an effective discovery-based proteome platform, Gemini, are particularly highlighted for its capabilities of achieving ultrasensitive and comprehensive analysis of minute proteins extracted from targeted cells in tissue specimens. The greatest expectations for targeted proteomics research using enriched nonmalignant and malignant cells from high-quality fresh-frozen, formalin-fixed and paraffin-embedded specimens reside in the identification of diagnostic, prognostic and predictive biological markers in the clinical setting, as well as the discovery and validation of new protein targets in the biopharmaceutical industry.

Malignant progression in pleomorphic xanthoastrocytoma: Personal experience and review of the literature

Pleomorphic xanthoastrocytoma (PXA) is a rare primary low-grade astrocytic tumor, recently classified as a neuroglial tumor. It generally occurs in children and young adults and shows benign behaviour (WHO II), although an anaplastic variant and malignant potential have been described. Pleomorphic xanthoastrocytomas with malignant transformation have been reported in three out of eight patients operated on for this type of tumor in our department in the last 15 years. The three patients were two adult women and a child, the primary tumors were located in the cortex of the right temporal lobe, and treatment consisted of complete surgical resection. Histological examination revealed simple PXA in two patients and a PXA with anaplastic foci in the other. Mean recurrence time was 5.7 years, with the original xanthoastrocytoma evolving to glioblastoma in two cases and anaplastic astrocytoma in the third. All three patients underwent a second operation, followed by adjuvant therapies. Two died from tumor progression and one from brain edema after intracerebral haemorrhage. A review of the available PXA literature dating back to 1979 revealed 16 cases of primary anaplastic astrocytoma and 21 cases of PXA with malignant transformation. Our experience adds three more cases of malignant transformations, outlining once again the potential malignancy of pleomorphic xanthoastrocytomas and the fact that prognosis in these cases is the same as for primary anaplastic astrocytoma and glioblastoma. Analysis of glioneuronal markers, Ki67 and p53 in all pleomorphic xanthoastrocytomas did not prove to be a discriminating factor to identify a subgroup of xanthoastrocytomas prone to malignancy. Accordingly, these tumors demand close long-term clinical and radiological follow-up.

Capillary separations enabling tissue proteomics-based biomarker discovery

Development of the capability to enable large-scale proteome studies, analogous to comprehensive gene expression analysis, will clearly have far-reaching impacts on protein biomarker investigations of human diseases such as cancer through interrogation of the archived fresh frozen and formalin-fixed and paraffin-embedded tissue collections. This review therefore focuses on the most recent advances in microdissection techniques and proteome platforms for procuring homogeneous subpopulations of tumor cells or structures and performing comprehensive analysis of protein profiles within tissue specimens, respectively. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state-of-the-art integrated tissue proteome effort. The capabilities of CIEF-based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. These proteome technological advances combined with recently developed tissue microdissection techniques provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.

Proteins and protein pattern differences between glioma cell lines and glioblastoma multiforme

INTRODUCTION

Research into the pathogenesis, molecular signaling, and treatment of glioblastoma multiforme (GBM) has traditionally been conducted using cell lines derived from malignant gliomas. We compared protein expression patterns between solid primary GBMs and GBM cell lines to identify proteins whose expression may be altered in cell culture.

METHODS

We cultured cell lines U87, U118, U251, and A172 and used tissue-selective microdissection of eight primary GBMs to obtain pure populations of tumor cells, which we studied using two-dimensional gel electrophoresis (2DGE) and examined using differential expression software. Select protein targets expressed differentially between GBM tumors and GBM cell lines were sequenced using tandem mass spectrometry.

RESULTS

Analysis of the primary GBM tumor samples (n = 8) and the GBM cell lines revealed reproducibly similar proteomic patterns for each group, which distinguished tumors from the cell lines. Gels contained up to 500 proteins that were consistently identified in the pH 4 to 7 range. Comparison of proteins identified in the GBM tumors and in the cell lines showed approximately 160 proteins that were gained and 60 proteins that were lost on culture. Using normalized intensity patterns from the 2DGE images, ANOVA tests were done and statistically significant spots were identified. Seven proteins found in the cell lines were significantly increased when compared with the GBM tumors (P < 0.05), whereas 10 proteins were significantly decreased from cell lines compared with the GBM tumors. Proteins identified included transcription factors, tumor suppressor genes, cytoskeletal proteins, and cellular metabolic proteins.

CONCLUSION

Global protein and proteomic differences were identified between primary GBM tumor samples and GBM cell lines. The proteins identified by 2DGE analysis elucidate some of the selection pressures of in vitro culture, help accentuate the advantages and limitations of cell culture, and may aid comprehension of gliomagenesis and enhance development of new therapeutics.