Robust Prognostic Markers Research Articles

Metabolic phenotyping for monitoring surgical patients

Operating theatres are traditionally largely free of chemical diagnostic information, because the timescale for surgical decision making is shorter than that for most clinical analytical procedures. 1 Garcia-Miguel FJ Serrano-Aguilar PG López-Bastida J Preoperative assessment. Lancet. 2003; 362: 1749-1757 Summary Full Text Full Text PDF PubMed Scopus (148) Google Scholar Clinical risk scores have variable sensitivity and specificity, 2 Can MF Yagci G Tufan T Ozturk E Zeybek N Cetiner S Can SAPS II predict operative mortality more accurately than POSSUM and P-POSSUM in patients with colorectal carcinoma undergoing resection?. World J Surg. 2008; 32: 589-595 Crossref PubMed Scopus (14) Google Scholar and by definition they are not personalised, so more robust prognostic markers are needed to improve the quality of surgical care. 3 The LancetWhat is the point of surgery?. Lancet. 2010; 376: 1025 Summary Full Text Full Text PDF PubMed Scopus (5) Google Scholar Rapid metabolic phenotyping approaches (known as metabotyping), which use nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry of tissue biopsy or biofluid samples, 4 Lindon JC Nicholson JK Analytical technologies for metabonomics and metabolomics, and multi-omic information recovery. Trends Analyt Chem. 2008; 3: 194-204 Crossref Scopus (125) Google Scholar have proven useful for generation of diagnostic biomarker information about many diseases in human beings. 5 Holmes E Wilson ID Nicholson JK Metabolic phenotyping in health and disease. Cell. 2008; 134: 714-717 Summary Full Text Full Text PDF PubMed Scopus (573) Google Scholar , 6 Holmes E Loo RL Stamler J et al. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature. 2008; 453: 396-400 Crossref PubMed Scopus (866) Google Scholar , 7 Nicholson JK Lindon JC Systems biology: metabonomics. Nature. 2008; 455: 1054-1105 Crossref PubMed Scopus (1429) Google Scholar The techniques have also been widely used in animals to investigate disease, including the effects of surgical trauma on host physiology. 8 Kinross JM Alkhamesi N Barton RH et al. Global metabolic phenotyping in an experimental laparotomy model of surgical trauma. J Proteome Res. 2011; 10: 277-287 Crossref PubMed Scopus (59) Google Scholar The deployment of such technologies in operating theatres could provide sensitive, specific, and efficient vehicles for the delivery of novel real-time diagnostic information, to aid surgical decision making.

Mirna EXPRESSION SIGNATURES as PROGNOSTIC Markers IN ADVANCED Classical HODGKIN LYMPHOMA

AbstractAbstract 4157In spite of the progress in the therapy of advanced stage classic Hodgkin lymphoma (cHL), still a significant proportion of patients fail to respond or relapse after complete remission. MicroRNAs (miRNA) are essential regulators of cell differentiation, emerging as robust predictor and prognostic markers. Specific miRNA signatures from the Hodgkin and Reed Sternberg cells (HRS) cells and their microenvironment have been proposed, but the potential prognostic role of them remains unclear. Here, we investigated whether miRNA signatures can allow to a better understanding of cHL pathogenesis and being applied in patient outcome prognostication.We have used mirRNA gene expression data from 32 samples of advanced cHL patients and 5 cHL derived cell lines (L540, L1236, L428, HDLM2, and KHMZ) to identify specific miRNA profiles from the tumoral cells and their non-tumoral microenvironment. A miRNA signature was identified in the cHL cell lines, probably reflecting functional properties of the HRS, whereas the others informed from properties of the reactive infiltrate. Selected miRNAs were further validated by performing laser capture microdissection using frozen samples in order to look for specific miRNAS preferentially expressed for either HRS cells and their surrounding microenvironment.In addition, logistic regression and Cox analysis allowed us to identify a set of 102 miRNAs differentially expressed (p<0.05) among patients with favourable and unfavourable outcome that included members of the miR-17-92 cluster such us mir-17, mir-92a and mir-92b* and other miRNAs known to be involved in cancerogenesis. A restricted group of 32 miRNAS with better prognostic capacity was further selected to set up a quantitative RT-PCR assay and explore the potential diagnostic application of their expression in an independent series of 96 formalin-fixed paraffin-embedded (FFPE) cHL samples.Bioinformatics target prediction (miRBase and TargetScan) and the web based computational tool DIANA-mirPath, were used in the identification of molecular pathways and target genes potentially regulated by the expression of these mirRNAs. Combined analysis of miRNAs, paired with bioinformatic target prediction, revealed a series of genes and pathways targeted by a small number of miRNAs, including essential pathways for lymphoma survival like MAPK signaling pathway, cell cycle, Jak-STAT signaling pathway and others.In conclusion, specific miRNA signatures for the HRS cells and their microenvironment can be identified in cHL samples, and improve our understanding in cHL pathogenesis. Selected miRNAs can be used in paraffin-embedded tissue for prognosis of advanced cHL cases, and can be incorporated in an RT-PCR assay with potential clinical application in advanced cHL. Disclosures:No relevant conflicts of interest to declare.

Genetics of medulloblastoma: clues for novel therapies

Medulloblastoma is the most common malignant brain tumor in children. Current medulloblastoma therapy entails surgery, radiation and chemotherapy. The 5-year survival rate for patients ranges from 40 to 70%, with most survivors suffering from serious long-term treatment-related sequelae. Additional research on the molecular biology and genetics of medulloblastoma is needed to identify robust prognostic markers for disease-risk stratification, to improve current treatment regimes and to discover novel and more effective molecular-targeted therapies. Recent advances in molecular biology have led to the development of powerful tools for the study of medulloblastoma tumorigenesis, which have revealed new insights into the molecular underpinnings of this disease. Here we discuss the signaling pathway alterations implicated in medulloblastoma pathogenesis, the techniques used in molecular profiling of these tumors and recent molecular subclassification schemes. Particular emphasis is given to the identification of novel molecular targets for less toxic, patient-tailored therapeutic approaches.

Deletion of Chromosome 4q Predicts Outcome in Stage II Colon Cancer Patients

Background: Around 30% of all stage II colon cancer patients will relapse and die of their disease. At present no objective parameters to identify high-risk stage II colon cancer patients, who will benefit from adjuvant chemotherapy, have been established. With traditional histopathological features definition of high-risk stage II colon cancer patients is inaccurate. Therefore more objective and robust markers for prediction of relapse are needed. DNA copy number aberrations have proven to be robust prognostic markers, but have not yet been investigated for this specific group of patients. The aim of the present study was to identify chromosomal aberrations that can predict relapse of tumor in patients with stage II colon cancer.Materials and Methods: DNA was isolated from 40 formaldehyde fixed paraffin embedded stage II colon cancer samples with extensive clinicopathological data. Samples were hybridized using Comparative Genomic Hybridization (CGH) arrays to determine DNA copy number changes and microsatellite stability was determined by PCR. To analyze differences between stage II colon cancer patients with and without relapse of tumor a Wilcoxon rank-sum test was implemented with multiple testing correction.Results: Stage II colon cancers of patients who had relapse of disease showed significantly more losses on chromosomes 4, 5, 15q, 17q and 18q. In the microsatellite stable (MSS) subgroup (n=28), only loss of chromosome 4q22.1–4q35.2 was significantly associated with disease relapse (p &lt; 0.05, FDR &lt; 0.15). No differences in clinicopathological characteristics between patients with and without relapse were observed.Conclusion: In the present series of MSS stage II colon cancer patients losses on 4q22.1–4q35.2 were associated with worse outcome and these genomic alterations may aid in selecting patients for adjuvant therapy.

Deletion of chromosome 4q predicts outcome in stage II colon cancer patients.

Background: Around 30% of all stage II colon cancer patients will relapse and die of their disease. At present no objective parameters to identify high-risk stage II colon cancer patients, who will benefit from adjuvant chemotherapy, have been established. With traditional histopathological features definition of high-risk stage II colon cancer patients is inaccurate. Therefore more objective and robust markers for prediction of relapse are needed. DNA copy number aberrations have proven to be robust prognostic markers, but have not yet been investigated for this specific group of patients. The aim of the present study was to identify chromosomal aberrations that can predict relapse of tumor in patients with stage II colon cancer. Materials and Methods: DNA was isolated from 40 formaldehyde fixed paraffin embedded stage II colon cancer samples with extensive clinicopathological data. Samples were hybridized using Comparative Genomic Hybridization (CGH) arrays to determine DNA copy number changes and microsatellite stability was determined by PCR. To analyze differences between stage II colon cancer patients with and without relapse of tumor a Wilcoxon rank-sum test was implemented with multiple testing correction. Results: Stage II colon cancers of patients who had relapse of disease showed significantly more losses on chromosomes 4, 5, 15q, 17q and 18q. In the microsatellite stable (MSS) subgroup (n=28), only loss of chromosome 4q22.1–4q35.2 was significantly associated with disease relapse (p < 0.05, FDR < 0.15). No differences in clinicopathological characteristics between patients with and without relapse were observed. Conclusion: In the present series of MSS stage II colon cancer patients losses on 4q22.1–4q35.2 were associated with worse outcome and these genomic alterations may aid in selecting patients for adjuvant therapy.

Genome-Wide DNA Methylation Profiles of Breast Tumors Reveal Loci Associated with Relapse Risk.

Abstract Background:Breast cancer prognosis is used in determining the course of adjuvant therapy for patients. Clinical prognostic indices like the Nottingham Prognostic Index have poor specificity, overestimate the risk of disease recurrence and necessitate more specific and robust prognostic markers. Prognostic gene expression markers are already in clinical use and show improved decision support. Methylation of CpG islands, an important regulator of gene expression, is reported to be disregulated in tumors, thus making methylation markers an important alternative to gene expression markers. We present the results of a genome-wide study that explored loci whose methylation status was significantly associated with recurrence risk.Methods:We used 108 frozen primary breast cancer specimens with ten year follow-up and extensive clinical data including histopathological measurements to identify potential epigenetic markers associated with recurrence risk. Using a previously validated array based method (Kamalakaran et. al., Nucleic Acids Research, 2009) we performed genome-wide measurements of differential CpG island methylation covering over 150,000 loci. We evaluated each locus for its ability to stratify patients into good or poor prognosis groups depending on its methylation status. Statistical significance was established using permutation analysis with appropriate multiple testing corrections. Prognostic markers independent of histopathological factors (ER, PR, HER2, tumor size, grade, node status, age) were identified using multivariate Cox regression analysis.Results:The methylation status of several loci proximal to genes significantly stratified samples independent of other clinical variables. Demethylation of several loci were associated with poor prognosis including ADAMTS4 (Hazard Ratio = 17.5, p-value&amp;lt;&amp;lt;0.001), a metalloproteinase previously implicated in the progression of glioma; DNA Topoisomerase I (HR = 3.81; 95% CI = 1.953-7.462; p&amp;lt;&amp;lt;0.001), implicated in chemotherapy resistance; and JMJD2C (HR = 3.7; 95% CI = 1.828-7.519; p&amp;lt;&amp;lt;0.001), which was found to be frequently amplified in esophageal cancers. The methylation of several loci also had significant association with poor prognosis, such as several members in the forkhead box family (FOXF1, FOXG1B, FOXJ1, FOXL2) and FHL1 (HR = 4.78; 95% CI = 2.38-9.62; p&amp;lt;&amp;lt;0.001). We selected several loci to form an ensemble classifier with statistically significant performance on our dataset. We show that this classifier achieved much higher specificity when compared to the Nottingham Prognostic Index, while maintaining high sensitivity.Discussion:Our retrospective study of genome-wide DNA methylation in breast cancer has identified several novel markers for prognosis. We found methylation deregulation of CpG islands proximal to genes implicated in metastasis and chemotherapy resistance is associated with poor prognosis. Furthermore, the potential for clinical benefit of these markers is their ability to jointly identify significantly larger number of low-risk patients compared to the Nottingham Prognostic Index. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4046.

MicroRNA Classifiers for Predicting Prognosis of Squamous Cell Lung Cancer

Non-small cell lung cancer (NSCLC), which is comprised mainly of adenocarcinoma and squamous cell carcinoma (SCC), is the cause of 80% of all lung cancer deaths in the United States. NSCLC is also associated with a high rate of relapse after clinical treatment and, therefore, requires robust prognostic markers to better manage therapy options. The aim of this study was to identify microRNA (miRNA) expression profiles in SCC of the lung that would better predict prognosis. Total RNA from 61 SCC samples and 10 matched normal lung samples was processed for small RNA species and profiled on MirVana miRNA Bioarrays (version 2, Ambion). We identified 15 miRNAs that were differentially expressed between normal lung and SCC, including members of the miR-17-92 cluster and its paralogues. We also identified miRNAs, including miR-155 and let-7, which had previously been shown to have prognostic value in adenocarcinoma. Based on cross-fold validation analyses, miR-146b alone was found to have the strongest prediction accuracy for stratifying prognostic groups at approximately 78%. The miRNA signatures were superior in predicting overall survival than a previously described 50-gene prognostic signature. Whereas there was no overlap between the mRNAs targeted by the prognostic miRNAs and the 50-gene expression signature, there was a significant overlap in the corresponding biological pathways, including fibroblast growth factor and interleukin-6 signaling. Our data indicate that miRNAs may have greater clinical utility in predicting the prognosis of patients with squamous cell lung carcinomas than mRNA-based signatures.

Methods for Gene Expression Profiling in Clinical Trials of Adjuvant Breast Cancer Therapy

Although endocrine therapy is highly effective in the treatment of endocrine receptor-positive breast cancer, chemotherapy has been shown to provide clinical benefit when added to tamoxifen. However, baseline risk after tamoxifen treatment is so low, especially in patients who are axillary node negative, that significant overtreatment will result if chemotherapy is given to every patient. Robust prognostic and predictive markers need to be developed to identify those at high risk of treatment failure. Although comprehensive gene expression profiling methods do offer promise, they require fresh or frozen tumor samples. To take advantage of existing archived tissue blocks with clinical follow-up collected from finished clinical trials, such as National Surgical Adjuvant Breast and Bowel Project trials B-20 and B-14, technologies that allow interrogation of archived blocks for gene expression profiling need to be realized. Recent developments in gene expression profiling technologies are discussed with their implications in clinical management of endocrine receptor-positive breast cancer.