Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile-0

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile"</p><p>http://www.molecular-cancer.com/content/7/1/6</p><p>Molecular Cancer 2008;7():6-6.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2253555.</p><p></p>d blue blocks). Each tumor sample was compared to its matched normal blood sample, and regions of DNA copy number gain (red lines) and copy number loss (green lines) were plotted along each chromosome. Datasets from only GeneChip50K Hind arrays were used

Urinary Signatures of Renal Cell Carcinoma Investigated by Peptidomic Approaches

<div><p>Renal Cell Carcinoma (RCC) is typically asymptomatic and surgery usually increases patient's lifespan only for early stage tumours. Moreover, solid renal masses cannot be confidently differentiated from RCC. Therefore, markers to distinguish malignant kidney tumours and for their detection are needed. Two different peptide signatures were obtained by a MALDI-TOF profiling approach based on urine pre-purification by C8 magnetic beads. One cluster of 12 signals could differentiate malignant tumours (n = 137) from benign renal masses and controls (n = 153) with sensitivity of 76% and specificity of 87% in the validation set. A second cluster of 12 signals distinguished clear cell RCC (n = 118) from controls (n = 137) with sensitivity and specificity values of 84% and 91%, respectively. Most of the peptide signals used in the two models were observed at higher abundance in patient urines and could be identified as fragments of proteins involved in tumour pathogenesis and progression. Among them: the Meprin 1α with a pro-angiogenic activity, the Probable G-protein coupled receptor 162, belonging to the GPCRs family and known to be associated with several key functions in cancer, the Osteopontin that strongly correlates to tumour stages and invasiveness, the Phosphorylase b kinase regulatory subunit alpha and the SeCreted and TransMembrane protein 1.</p></div

Performances of the cluster of twelve signals to discriminate ccRCC patients from controls (False = Controls; True = ccRCC) with <i>k-fold</i> = 10 cross-validation (A) and of the model, originated in the training phase using about 60% of the data, in validation test using the other about 40% of the studied subjects (B).

<p>Spec.  =  Specificity; Sens.  =  Sensitivity; pred.  =  Prediction; Class precision: a  =  Negative Predictive Value and b  =  Positive Predictive Value. Precision  =  Relative number of correctly classified examples among all examples classified as positive i.e. precision  =  (Positives Correctly Classified)/(Total Predicted Positives). Note that the Total Predicted Positives is the sum of True Positives and False Positives. This is the same as the Negative Predictive Value.</p><p>True True  =  True positive; true False  =  True negative.</p><p>Performances of the cluster of twelve signals to discriminate ccRCC patients from controls (False  =  Controls; True  =  ccRCC) with <i>k-fold</i>  =  10 cross-validation (A) and of the model, originated in the training phase using about 60% of the data, in validation test using the other about 40% of the studied subjects (B).</p

Urinary relative concentration (ccRCC/ctrl) and p-value of the twelve ions included in the model able to distinguish controls from ccRCC.

<p>n.s.  =  not statistically different.</p><p>Urinary relative concentration (ccRCC/ctrl) and p-value of the twelve ions included in the model able to distinguish controls from ccRCC.</p

Identification of seven MALDI signals included in the discriminant clusters.

<p>The assignment was performed through an accurate mass alignment with peptides identified by nLC-ESI MS/MS from C8-MB enriched urine samples. Mascot peptide score (pep_score), molecular weight of the related intact protein or protein isoform (MW), possible hypothetical modification predicted by Mascot (PTM) and the relative abundances of each peptide (p < 0.05) in ccRCC (n = 118) <i>vs</i> controls (n = 137), and/or in malignant tumours (n = 137) and benign renal masses plus healthy subjects (n = 153) have been reported.</p><p>↑  =  over-represented; ↓  =  under-represented; n.s.  =  not statistically different; LM  =  linear mode; RM  =  reflector mode.</p><p>Identification of seven MALDI signals included in the discriminant clusters.</p

Patients clinical characteristics according to the 2009 TNM (tumour-node metastasis) system classification.

<p>*  =  benign renal masses</p><p>** = 5 malignant subtypes and 3 benign renal masses</p><p>Patients clinical characteristics according to the 2009 TNM (tumour-node metastasis) system classification.</p

Urinary relative concentration (malignant/benign+ctrl) and p-value of the twelve ions included in the model able to distinguish benign renal masses or controls from malignant kidney tumours.

<p>n.s.  =  not statistically different.</p><p>Urinary relative concentration (malignant/benign+ctrl) and p-value of the twelve ions included in the model able to distinguish benign renal masses or controls from malignant kidney tumours.</p