Anneleen Daemen

Intrinsic Gene Expression Profiles of Gliomas Are a Better Predictor of Survival than Histology

Gliomas are the most common primary brain tumors with heterogeneous morphology and variable prognosis. Treatment decisions in patients rely mainly on histologic classification and clinical parameters. However, differences between histologic subclasses and grades are subtle, and classifying gliomas is subject to a large interobserver variability. To improve current classification standards, we have performed gene expression profiling on a large cohort of glioma samples of all histologic subtypes and grades. We identified seven distinct molecular subgroups that correlate with survival. These include two favorable prognostic subgroups (median survival, >4.7 years), two with intermediate prognosis (median survival, 1-4 years), two with poor prognosis (median survival, <1 year), and one control group. The intrinsic molecular subtypes of glioma are different from histologic subgroups and correlate better to patient survival. The prognostic value of molecular subgroups was validated on five independent sample cohorts (The Cancer Genome Atlas, Repository for Molecular Brain Neoplasia Data, GSE12907, GSE4271, and Li and colleagues). The power of intrinsic subtyping is shown by its ability to identify a subset of prognostically favorable tumors within an external data set that contains only histologically confirmed glioblastomas (GBM). Specific genetic changes (epidermal growth factor receptor amplification, IDH1 mutation, and 1p/19q loss of heterozygosity) segregate in distinct molecular subgroups. We identified a subgroup with molecular features associated with secondary GBM, suggesting that different genetic changes drive gene expression profiles. Finally, we assessed response to treatment in molecular subgroups. Our data provide compelling evidence that expression profiling is a more accurate and objective method to classify gliomas than histologic classification. Molecular classification therefore may aid diagnosis and can guide clinical decision making.

Molecular Response to Cetuximab and Efficacy of Preoperative Cetuximab-Based Chemoradiation in Rectal Cancer

PURPOSE To characterize the molecular pathways activated or inhibited by cetuximab when combined with chemoradiotherapy (CRT) in rectal cancer and to identify molecular profiles and biomarkers that might improve patient selection for such treatments. PATIENTS AND METHODS Forty-one patients with rectal cancer (T3-4 and/or N+) received preoperative radiotherapy (1.8 Gy, 5 days/wk, 45 Gy) in combination with capecitabine and cetuximab (400 mg/m2 as initial dose 1 week before CRT followed by 250 mg/m2 /wk for 5 weeks). Biopsies and plasma samples were taken before treatment, after cetuximab but before CRT, and at the time of surgery. Proteomics and microarrays were used to monitor the molecular response to cetuximab and to identify profiles and biomarkers to predict treatment efficacy. RESULTS Cetuximab on its own downregulated genes involved in proliferation and invasion and upregulated inflammatory gene expression, with 16 genes being significantly influenced in microarray analysis. The decrease in proliferation was confirmed by immunohistochemistry for Ki67 (P = .01) and was accompanied by an increase in transforming growth factor-alpha in plasma samples (P < .001). Disease-free survival (DFS) was better in patients if epidermal growth factor receptor expression was upregulated in the tumor after the initial cetuximab dose (P = .02) and when fibro-inflammatory changes were present in the surgical specimen (P = .03). Microarray and proteomic profiles were predictive of DFS. CONCLUSION Our study showed that a single dose of cetuximab has a significant impact on the expression of genes involved in tumor proliferation and inflammation. We identified potential biomarkers that might predict response to cetuximab-based CRT.

Limitations of current definitions of miscarriage using mean gestational sac diameter and crown–rump length measurements: a multicenter observational study

There is significant variation in cut‐off values for mean gestational sac diameter (MSD) and embryo crown–rump length (CRL) used to define miscarriage, values suggested in the literature ranging from 13 to 25 mm for MSD and from 3 to 8 mm for CRL. We aimed to define the false‐positive rate (FPR) for the diagnosis of miscarriage associated with different CRL and MSD measurements with or without a yolk sac in a large study population of patients attending early pregnancy clinics. We also aimed to define cut‐off values for CRL and MSD that, on the basis of a single measurement, can definitively diagnose a miscarriage and so exclude possible inadvertent termination of pregnancy.

A kernel-based integration of genome-wide data for clinical decision support.

BackgroundAlthough microarray technology allows the investigation of the transcriptomic make-up of a tumor in one experiment, the transcriptome does not completely reflect the underlying biology due to alternative splicing, post-translational modifications, as well as the influence of pathological conditions (for example, cancer) on transcription and translation. This increases the importance of fusing more than one source of genome-wide data, such as the genome, transcriptome, proteome, and epigenome. The current increase in the amount of available omics data emphasizes the need for a methodological integration framework.MethodsWe propose a kernel-based approach for clinical decision support in which many genome-wide data sources are combined. Integration occurs within the patient domain at the level of kernel matrices before building the classifier. As supervised classification algorithm, a weighted least squares support vector machine is used. We apply this framework to two cancer cases, namely, a rectal cancer data set containing microarray and proteomics data and a prostate cancer data set containing microarray and genomics data. For both cases, multiple outcomes are predicted.ResultsFor the rectal cancer outcomes, the highest leave-one-out (LOO) areas under the receiver operating characteristic curves (AUC) were obtained when combining microarray and proteomics data gathered during therapy and ranged from 0.927 to 0.987. For prostate cancer, all four outcomes had a better LOO AUC when combining microarray and genomics data, ranging from 0.786 for recurrence to 0.987 for metastasis.ConclusionsFor both cancer sites the prediction of all outcomes improved when more than one genome-wide data set was considered. This suggests that integrating multiple genome-wide data sources increases the predictive performance of clinical decision support models. This emphasizes the need for comprehensive multi-modal data. We acknowledge that, in a first phase, this will substantially increase costs; however, this is a necessary investment to ultimately obtain cost-efficient models usable in patient tailored therapy.

Assessing first trimester growth: the influence of ethnic background and maternal age

BACKGROUND First trimester growth restriction may predict miscarriage or adverse outcome later in the pregnancy, but determinants of early growth are not well described. Our objective was to examine factors influencing fetal and gestational sac size in the first trimester. METHODS Prospective observational study of 1828 singleton pregnancies before 12 weeks gestation. Maternal characteristics (ethnicity, maternal age, obstetric history, abdominal pain and vaginal bleeding), crown rump length (CRL) and mean gestational sac diameter (MSD) were recorded. A stepwise linear mixed effects analysis was performed to determine factors influencing rate of change in CRL and MSD. RESULTS 1063 scans, in 464 women, were included. Rate of increase in CRL was higher in women of black ethnic origin (P = 0.0261) compared with white, and increased with advancing maternal age (P = 0.0046). Maternal age also influenced MSD: older women had gestational sacs which were 0.118 mm larger for each one year increase in maternal age (P = 0.0073). Bleeding, pain and prior obstetric history did not influence CRL or MSD. CONCLUSIONS Rate of increase in CRL was greater in fetuses of black versus white women and increased with advancing maternal age. As CRL is used to date pregnancies, and this influences further growth assessment, consideration should be given to the use of individualized growth charts which take account of maternal factors found to influence first trimester growth.

A seven-gene set associated with chronic hypoxia of prognostic importance in hepatocellular carcinoma

Purpose: Hepatocellular carcinomas (HCC) have an unpredictable clinical course, and molecular classification could provide better insights into prognosis and patient-directed therapy. We hypothesized that in HCC, certain microenvironmental regions exist with a characteristic gene expression related to chronic hypoxia which would induce aggressive behavior. Experimental Design: We determined the gene expression pattern for human HepG2 liver cells under chronic hypoxia by microarray analysis. Differentially expressed genes were selected and their clinical values were assessed. In our hypothesis-driven analysis, we included available independent microarray studies of patients with HCC in one single analysis. Three microarray studies encompassing 272 patients were used as training sets to determine a minimal prognostic gene set, and one recent study of 91 patients was used for validation. Results: Using computational methods, we identified seven genes (out of 3,592 differentially expressed under chronic hypoxia) that showed correlation with poor prognostic indicators in all three training sets (65/139/73 patients) and this was validated in a fourth data set (91 patients). Retrospectively, the seven-gene set was associated with poor survival (hazard ratio, 1.39; P = 0.007) and early recurrence (hazard ratio, 2.92; P = 0.007) in 135 patients. Moreover, using a hypoxia score based on this seven-gene set, we found that patients with a score of >0.35 (n = 42) had a median survival of 307 days, whereas patients with a score of ≤0.35 (n = 93) had a median survival of 1,602 days (P = 0.005). Conclusions: We identified a unique, liver-specific, seven-gene signature associated with chronic hypoxia that correlates with poor prognosis in HCCs. Clin Cancer Res; 16(16); 4278–88. ©2010 AACR.

Why are some ectopic pregnancies characterized as pregnancies of unknown location at the initial transvaginal ultrasound examination

Objective. To compare the appearance and behavior of ectopic pregnancies (EPs) initially classified as pregnancies of unknown location (PULs) to those visualized on the initial transvaginal ultrasound scan (TVS). Methods. An observational study over a four‐year period on women undergoing a TVS prior to diagnosis of a tubal EP. Demographic details, presenting symptoms, TVS findings, serum hCG and progesterone levels were recorded at the time of the initial TVS and at the time of diagnosis of the EP in those initially classified as a PUL. Results. 411 women with a tubal EP underwent a TVS prior to treatment. In 85.9% (353/411) the EP was visualized on the initial TVS while 14.1%(58/411) were initially classified as PULs. Those initially classified as PULs had significantly lower mean gestational age and mean initial human chorionic gonadotrophin (hCG) levels, and significantly higher mean progesterone level at presentation than those where the EP was visualized on the initial TVS. Of those with a PUL, 60.3% (35/58) had the EP subsequently visualized on TVS. At the time of diagnosis these EPs were significantly smaller (p<0.0001); the appearance of the EPs, serum hCG and progesterone levels at the time of visualization on TVS were not significantly different from those visualized on the initial TVS. Conclusion. In women with EPs who are initially classified as PULs, failure of visualization of the EP on the initial TVS is likely to be due to the fact that they are too small and probably too early in the disease process.

Gestational sac and embryonic growth are not useful as criteria to define miscarriage: a multicenter observational study

We studied changes in mean gestational sac diameter (MSD) and embryonic crown–rump length (CRL) in intrauterine pregnancies of uncertain viability (IPUVs). We aimed to establish cut‐off values for MSD and CRL growth that could be definitively associated with either viability or miscarriage, and to establish the relationship between growth in MSD and appearance of embryonic structures in the gestational sac.

Occurrence and Outcome of Residual Trophoblastic Tissue A Prospective Study

The purpose of this study was to evaluate the occurrence of residual trophoblastic tissue after miscarriage or delivery, to assess the diagnostic value of sonography with color Doppler examination in the detection of retained tissue, and to define in what cases expectant management may be an option.

Pain experienced during transvaginal ultrasound, saline contrast sonohysterography, hysteroscopy and office sampling: a comparative study

To evaluate and compare the pain experienced by women during transvaginal ultrasound, saline contrast sonohysterography (SCSH), diagnostic hysteroscopy and office sampling.