Identification of Predictive Response Markers and Novel Treatment Targets for Gliomas

Gliomas are the most frequent primary brain tumors in adults. Despite multimodality treatment strategies, the survival of patients with a diffuse glioma remains poor. There has been an increasing use of molecular markers to assist diagnosis and predict prognosis and response to therapy. Although several prognostic and predictive response markers have been identified, considerable research still needs to be done to improve on these. Therefore, the identification of novel predictive response markers and therapeutic targets are desperately needed for this dismal disease. In this thesis, we describe prognostic and identify novel predictive markers in randomized clinical trials. We determined the gene expression profiles of samples of anaplastic oligodendrogliomas and oligoastrocytomas from the EORTC 26951 study and samples of recurrent glioblastomas of the BELOB study to evaluate the treatment responses within defined intrinsic glioma subtypes (IGSs). IGSs are molecularly similar tumors that have been previously identified by unsupervised gene expression analysis. We found that IGSs can be used to assess the molecular heterogeneity within clinical trials. In addition, we confirmed that IGS subtypes are prognostic for survival and predictive. Tumors assigned to IGS-9 showed benefit from adjuvant PCV chemotherapy. In the BELOB study, we found that tumors assigned to IGS-18 (classical GBMs) showed a trend towards benefit from Beva+CCNU treatment. Expression of FMO4 and OSBPL3 were particularly associated with treatment response. Intrinsic subtypes can therefore be used to assess the molecular heterogeneity within clinical trials and may be used as a prognostic and predictive marker. Another method to profile gliomas is based on DNA methylation. We performed genome-wide methylation profiling on material from EORTC 26951 and assessed CIMP and MGMT-STP27 status. We have shown that survival in patients with CIMP+ or MGMT-STP27 methylated tumors was improved compared to CIMP- and/or MGMT-STP27 unmethylated tumors. Importantly, the MGMT-STP27 status was predictive for response to adjuvant PCV chemotherapy in these tumors. MGMT-STP27 may therefore be used to identify AODs and AOAs with improved prognosis and identify patients that are likely to benefit from adjuvant PCV chemotherapy. We also performed functional analysis on different mutations on the EGFR gene and infrequently mutated genes in oligodendrogliomas. We have shown that different mutations within a single gene (EGFR) can have different molecular consequences and have different binding partners for EGFRvIII, EGFRL858 and EGFRwildtype. As these mutations have different functions, each mutation may need its own unique treatment. Functional analysis on infrequently mutated genes showed that the function of many of ‘low frequency’ genes, differs from its wildtype counterpart. This differential effect suggests that these genes can contribute to the disease and therefore may offer new therapeutic targets for oligodendrogliomas

Tumor-specific mutations in low-frequency genes affect their functional properties

Causal genetic changes in oligodendrogliomas (OD) with 1p/19q co-deletion include mutations in IDH1, IDH2, CIC, FUBP1, TERT promoter and NOTCH1. However, it is generally assumed that more somatic mutations are required for tumorigenesis. This study aimed to establish whether genes mutated at low frequency can be involved in OD initiation and/or progression. We performed whole-genome sequencing on three anaplastic ODs with 1p/19q co-deletion. To estimate mutation frequency, we performed targeted resequencing on an additional 39 ODs. Whole-genome sequencing identified a total of 55 coding mutations (range 8–32 mutations per tumor), including known abnormalities in IDH1, IDH2, CIC and FUBP1. We also identified mutations in genes, most of which were previously not implicated in ODs. Targeted resequencing on 39 additional ODs confirmed that these genes are mutated at low frequency. Most of the mutations identified were predicted to have a deleterious functional effect. Functional analysis on a subset of these genes (e.g. NTN4 and MAGEH1) showed that the mutation affects the subcellular localization of the protein (n = 2/12). In addition, HOG cells stably expressing mutant GDI1 or XPO7 showed altered cell proliferation compared to those expressing wildtype constructs. Similarly, HOG cells expressing mutant SASH3 or GDI1 showed altered migration. The significantly higher rate of predicted deleterious mutations, the changes in subcellular localization and the effects on proliferation and/or migration indicate that many of these genes functionally may contribute to gliomagenesis and/or progression. These low-frequency genes and their affected pathways may provide new treatment targets for this tumor type

Absence of common somatic alterations in genes on 1p and 19q in oligodendrogliomas

A common and histologically well defined subtype of glioma are the oligodendroglial brain tumors. Approximately 70% of all oligodendrogliomas have a combined loss of the entire 1p and 19q chromosomal arms. This remarkably high frequency suggests that the remaining arms harbor yet to be identified tumor suppressor genes. Identification of these causal genetic changes in oligodendrogliomas is important because they form direct targets for treatment. In this study we therefore performed targeted resequencing of all exons, microRNAs, splice sites and promoter regions residing on 1p and 19q on 7 oligodendrogliomas and 4 matched controls. Only one missense mutation was identified in a single sample in the ARHGEF16 gene. This mutation lies within- and disrupts the conserved PDZ binding domain. No similar ARHGEF16 mutations or deletions were found in a larger set of oligodendrogliomas. The absence of common somatic changes within genes located on 1p and 19q in three out of four samples indicates that no additional "second hit" is required to drive oncogenic transformation on either chromosomal arm

Awareness of drug laboratory test interactions is important for prevention of unnecessary additional diagnostics: An example

Background: Elevated levels of Chromogranin A (CgA) may be indicative of a neuroendocrine tumour (NET), but increased levels are also observed after intake of proton pump inhibitors (PPIs). The incidence of diagnostic confusion because of this drug-laboratory test interaction (DLTI) was examined. Methods: Medical records of 238 patients with elevated CgA concentrations were obtained from three hospitals. The following data were extracted: PPI prescription at the time of CgA measurement, medical decision making based on elevated CgA concentrations, final diagnosis, comorbidity and other prescribed drugs. Results: From 238 patients with elevated CgA concentrations, 132 used PPIs. Of these patients, 57 patients did not have a NET. In 9 of these 57 patients (16%), diagnostic work up revealed no medical cause of an elevated CgA concentration. Somatostatin receptor imaging was ordered in 4 out of 9 cases, with no abnormalities observed. In 6 out of 9 cases, CgA measurement was repeated after PPI discontinuation resulting in normalisation of CgA concentrations. Conclusion: In this retrospective patient record study we observed that part of the elevated CgA concentrations in patients could be caused by the usage of PPIs causing unnecessary diagnostic work-up for the exclusion of a NET. These observations illustrate the need for better DLTI awareness

Awareness of drug laboratory test interactions is important for prevention of unnecessary additional diagnostics: An example

Background: Elevated levels of Chromogranin A (CgA) may be indicative of a neuroendocrine tumour (NET), but increased levels are also observed after intake of proton pump inhibitors (PPIs). The incidence of diagnostic confusion because of this drug-laboratory test interaction (DLTI) was examined. Methods: Medical records of 238 patients with elevated CgA concentrations were obtained from three hospitals. The following data were extracted: PPI prescription at the time of CgA measurement, medical decision making based on elevated CgA concentrations, final diagnosis, comorbidity and other prescribed drugs. Results: From 238 patients with elevated CgA concentrations, 132 used PPIs. Of these patients, 57 patients did not have a NET. In 9 of these 57 patients (16%), diagnostic work up revealed no medical cause of an elevated CgA concentration. Somatostatin receptor imaging was ordered in 4 out of 9 cases, with no abnormalities observed. In 6 out of 9 cases, CgA measurement was repeated after PPI discontinuation resulting in normalisation of CgA concentrations. Conclusion: In this retrospective patient record study we observed that part of the elevated CgA concentrations in patients could be caused by the usage of PPIs causing unnecessary diagnostic work-up for the exclusion of a NET. These observations illustrate the need for better DLTI awareness

Mutation specific functions of EGFR result in a mutation-specific downstream pathway activation

Background: Epidermal growth factor receptor (EGFR) is frequently mutated in various types of cancer. Although all oncogenic mutations are considered activating, different tumour types have different mutation spectra. It is possible that functional differences underlie this tumour-type specific mutation spectrum. Methods: We have determined whether specific mutations in EGFR (EGFR, EGFRvIII and EGFR-L858R) have differences in binding partners, differences in downstream pathway activation (gene expression and phosphoproteins), and have functional consequences on cellular growth and migration. Results: Using biotin pulldown and subsequent mass spectrometry we were able to detect mutation specific binding partners for EGFR. Differential binding was confirmed using a proximity ligation assay and/or Western Blot for the dedicator of cytokinesis 4 (DOCK4), UDP-glucose glycoprotein glucosyltransferase 1 (UGGT1), MYC binding protein 2 (MYCBP2) and Smoothelin (SMTN). We also demonstrate that each mutation induces the expression of a specific set of genes, and that each mutation is associated with specific phosphorylation patterns. Finally, we demonstrate using stably expressing cell lines that EGFRvIII and EGFL858R display reduced growth and migration compared to EGFR ildtype expressing cells

MGMT-STP27 Methylation Status as Predictive Marker for Response to PCV in Anaplastic Oligodendrogliomas and Oligoastrocytomas. A Report from EORTC Study 26951

<p>Purpose: The long-term follow-up results from the EORTC-26951 trial showed that the addition of procarbazine, CCNU, and vincristine (PCV) after radiotherapy increases survival in anaplastic oligodendrogliomas/oligoastrocytomas (AOD/AOA). However, some patients appeared to benefit more from PCV treatment than others.</p><p>Experimental Design: We conducted genome-wide methylation profiling of 115 samples included in the EORTC-26951 trial and extracted the CpG island hypermethylated phenotype (CIMP) and MGMT promoter methylation (MGMT-STP27) status.</p><p>Results: We first show that methylation profiling can be conducted on archival tissues with a performance that is similar to snap-frozen tissue samples. We then conducted methylation profiling on EORTC-26951 clinical trial samples. Univariate analysis indicated that CIMP+ or MGMT-STP27 methylated tumors had an improved survival compared with CIMP- and/or MGMT-STP27 unmethylated tumors [median overall survival (OS), 1.05 vs. 6.46 years and 1.06 vs. 3.8 years, both P <0.0001 for CIMP and MGMT-STP27 status, respectively]. Multivariable analysis indicates that CIMP and MGMT-STP27 are significant prognostic factors for survival in presence of age, sex, performance score, and review diagnosis in the model. CIMP+ and MGMT-STP27 methylated tumors showed a clear benefit from adjuvant PCV chemotherapy: the median OS of CIMP+ samples in the RT and RT-PCV arms was 3.27 and 9.51 years, respectively (P = 0.0033); for MGMT-STP27 methylated samples, it was 1.98 and 8.65 years. There was no such benefit for CIMP- or for MGMT-STP27 unmethylated tumors. MGMT-STP27 status remained significant in an interaction test (P = 0.003). Statistical analysis of microarray (SAM) identified 259 novel CpGs associated with treatment response.</p><p>Conclusions: MGMT-STP27 may be used to guide treatment decisions in this tumor type. (C) 2013 AACR.</p>

Impact of interactions between drugs and laboratory test results on diagnostic test interpretation - a systematic review

Intake of drugs may influence the interpretation of laboratory test results. Knowledge and correct interpretation of possible drug-laboratory test interactions (DLTIs) is important for physicians, pharmacists and laboratory specialists. Laboratory results may be affected by analytical or physiological effects of medication. Failure to take into account the possible unintended influence of drug use on a laboratory test result may lead to incorrect diagnosis, incorrect treatment and unnecessary follow-up. The aim of this review is to give an overview of the literature investigating the clinical impact and use of DLTI decision support systems on laboratory test interpretation. Particular interactions were reported in a large number of articles, but they were fragmentarily described and some papers even reported contradictory findings. To provide an overview of information that clinicians and laboratory staff need to interpret test results, DLTI databases have been made by several groups. In a literature search, only four relevant studies have been found on DLTI decision support applications for laboratory test interpretation in clinical practice. These studies show a potential benefit of automated DLTI messages to physicians for the correct interpretation of laboratory test results. Physicians reported 30-100% usefulness of DLTI messages. In one study 74% of physicians sometimes even refrained from further additional examination. The benefit of decision support increases when a refined set of clinical rules is determined in cooperation with health care professionals. The prevalence of DLTIs is high in a broad range of combinations of laboratory tests and drugs and these frequently remain unrecognized