Risk Assessment for Venous Thromboembolism in Chemotherapy-Treated Ambulatory Cancer Patients: A Machine Learning Approach

OBJECTIVE: To design a precision medicine approach aimed at exploiting significant patterns in data, in order to produce venous thromboembolism (VTE) risk predictors for cancer outpatients that might be of advantage over the currently recommended model (Khorana score). DESIGN: Multiple kernel learning (MKL) based on support vector machines and random optimization (RO) models were used to produce VTE risk predictors (referred to as machine learning [ML]-RO) yielding the best classification performance over a training (3-fold cross-validation) and testing set. RESULTS: Attributes of the patient data set ( n = 1179) were clustered into 9 groups according to clinical significance. Our analysis produced 6 ML-RO models in the training set, which yielded better likelihood ratios (LRs) than baseline models. Of interest, the most significant LRs were observed in 2 ML-RO approaches not including the Khorana score (ML-RO-2: positive likelihood ratio [+LR] = 1.68, negative likelihood ratio [-LR] = 0.24; ML-RO-3: +LR = 1.64, -LR = 0.37). The enhanced performance of ML-RO approaches over the Khorana score was further confirmed by the analysis of the areas under the Precision-Recall curve (AUCPR), and the approaches were superior in the ML-RO approaches (best performances: ML-RO-2: AUCPR = 0.212; ML-RO-3-K: AUCPR = 0.146) compared with the Khorana score (AUCPR = 0.096). Of interest, the best-fitting model was ML-RO-2, in which blood lipids and body mass index/performance status retained the strongest weights, with a weaker association with tumor site/stage and drugs. CONCLUSIONS: Although the monocentric validation of the presented predictors might represent a limitation, these results demonstrate that a model based on MKL and RO may represent a novel methodological approach to derive VTE risk classifiers. Moreover, this study highlights the advantages of optimizing the relative importance of groups of clinical attributes in the selection of VTE risk predictors

Effect of ingestion of dark chocolates with similar lipid composition and different cocoa content on antioxidant and lipid status in healthy humans

The association between in vitro antioxidant capacity of dark chocolates with different cocoa percentage and the in vivo response on antioxidant status was investigated. In a randomized crossover design, 15 healthy volunteer consumed 100 g of high antioxidants dark chocolate (HADC) or dark chocolate (DC). In vitro, HADC displayed a higher Total Antioxidant Capacity (TAC) than DC. In vivo, plasma TAC significantly peaked 2 h after ingestion of both chocolates. TAC levels went back to zero 5 h after DC ingestion whilst levels remained significantly higher for HADC. HADC induced a significantly higher urinary TAC in the 5-12 h interval time than DC. No change was detected in urinary excretion of F2-isoprostanes. Plasma thiols and triacylglycerol (TG) levels significantly increased for both chocolate with a peak at 2 h remaining significantly higher for DC after 5 h respect to HADC. Results provide evidence of a direct association between antioxidant content of chocolate and the extent of in vivo response on plasma antioxidant capacity. (C) 2011 Elsevier Ltd. All rights reserved

Ensuring sample quality for biomarker discovery studies - Use of ict tools to trace biosample life-cycle

The growing demand of personalized medicine marked the transition from an empirical medicine to a molecular one, aimed at predicting safer and more effective medical treatment for every patient, while minimizing adverse effects. This passage has emphasized the importance of biomarker discovery studies, and has led sample availability to assume a crucial role in biomedical research. Accordingly, a great interest in Biological Bank science has grown concomitantly. In biobanks, biological material and its accompanying data are collected, handled and stored in accordance with standard operating procedures (SOPs) and existing legislation. Sample quality is ensured by adherence to SOPs and sample whole life-cycle can be recorded by innovative tracking systems employing information technology (IT) tools for monitoring storage conditions and characterization of vast amount of data. All the above will ensure proper sample exchangeability among research facilities and will represent the starting point of all future personalized medicine-based clinical trials

Association between serum carcinoembryonic antigen and endothelial cell adhesion molecules in colorectal cancer

OBJECTIVES: To analyse the behaviour of pre-surgical serum levels of soluble (s)E-selectin and vascular cell adhesion molecule (sVCAM) in patients with colorectal cancer, and to evaluate their possible correlation with carcinoembryonic antigen (CEA), pro-inflammatory cytokines and clinicopathological features with respect to their prognostic value in predicting metastatic disease. METHODS: Pre-surgical serum levels of sE-selectin, sVCAM, interleukin-6 (IL-6), IL-1beta, tumour necrosis factor-alpha (TNF-alpha) and CEA were measured in 194 patients with colorectal adenocarcinoma, 40 patients with benign colorectal diseases and 59 healthy subjects. RESULTS: sE-selectin, sVCAM, TNF-alpha and IL-6 levels were significantly higher in patients with colorectal cancer compared to either healthy subjects or patients with benign disease. Positive rates of sE-selectin, sVCAM and TNF-alpha levels were significantly associated with Dukes' stage D colorectal cancer, and all three variables were independently associated to the presence of distant metastases. Positive sE-selectin, sVCAM and TNF-alpha levels were significantly associated to CEA. TNF-alpha and CEA levels were independently related to the presence of positive levels of sE-selectin and/or sVCAM. CONCLUSIONS: Our findings suggest that the host inflammatory response to cancer cells, and/or their released products (i.e. CEA), might be responsible (via cytokine release) for the elevation in circulating adhesion molecules in patients with colorectal cancer

Clinical utility of plasma KRAS, NRAS and BRAF mutational analysis with real time PCR in metastatic colorectal cancer patients -The importance of tissue/plasma discordant cases

Background: Tumor tissue (T) mutational analysis represents the standard for metastatic colorectal cancer (mCRC); however, circulating tumor DNA (ctDNA) detected by liquid biopsy in plasma (PL) can better represent tumor heterogeneity. Methods: mCRC patients undergoing standard first-line chemotherapy with known T-KRAS/NRAS/BRAF status were enrolled in the present prospective study. PL mutations were assessed within 2 weeks before chemotherapy start with real time PCR and correlated with T status and Progression free survival (PFS). Clinical and biochemical variables including also total number of tumor lesions (TNL) and the sum of maximum diameter (SMD) of all lesions were assessed as potential predictors of T/PL discordance. RESULTS: Among 45 enrolled patients, all BRAF mutations were concordant between T and PL and there were 20% of patients RAS discordant: 9% wild type in T and mutated in PL and 11% mutated in T and wild type in PL. T mutations were significantly associated to median PFS (mPFS of 4.5, 8.3 and 22.9 months for T-BRAF mutated, T-RAS mutated, and T-wild type patients, respectively, p for trend 0.00014). PL mutations further refined prognosis: RAS wild type in T and mutated in PL had significantly shorter PFS than concordant RAS wild type in T and PL: mPFS 9.6 vs. 23.3 months, respectively, p = 0.02. Patients RAS mutated in T and wild type in PL had longer PFS than concordant RAS mutated in T and PL: 24.4 vs. 7.8 months, respectively, p = 0.008. At a multivariate cox regression analysis for PFS, PL mutations were independent prognostic factor superior to T analysis (HR 0.13, p = 0.0008). At multivariate logistic regression analysis TNL and SMD were significant predictors of discordant cases. Conclusions: PL mutational analysis allows a better prognostication than T analysis alone and could help in mCRC treatment management

BRCA1 and BRCA2 mutations in central and southern Italian patients

INTRODUCTION: Germline BRCA1 and BRCA2 mutations account for most hereditary breast/ovarian cancers and are associated with male breast cancer. Furthermore, constitutional mutations in these genes may occur in breast/ovarian cancer patients that do not meet stringent criteria of autosomal-dominant predisposition. The relevance of BRCA1 and BRCA2 mutations in such patients is still debated. OBJECTIVES: We sought to determine the impact of BRCA1 and BRCA2 mutations in a population of patients from central and southern Italy. We analyzed the BRCA1 and BRCA2 coding regions in 136 unrelated probands: 117 females with breast/ovarian cancer and 19 males with breast cancer. This population of patients was mostly representative of cases who are at risk for hereditary susceptibility, but who do not meet stringent criteria of autosomal-dominant predisposition. METHODS: Probands, subclassified as follows, were consecutively recruited depending on informed consent from patients attending breast cancer clinics in Rome and Naples. Selection criteria for females were as follows: breast cancer with breast cancer family history [one to two first-/second-degree relative(s), n = 55]; breast cancer diagnosed before age 40 years (no breast/ovarian cancer family history, n = 28); bilateral breast cancer (regardless of age and family history, n =10); breast cancer associated with gastrointestinal, pancreatic or uterine cancers [synchronous/metachronous or in first-degree relative(s), n = 9]; breast or ovarian cancer with family history of breast-ovarian/ovarian cancer (at least 1 first-/ second-degree relative, n = 10); and ovarian cancer with no breast/ovarian cancer family history (n = 5). Males with breast cancer were recruited regardless of age and family history. BRCA1 exon 11 and BRCA2 exons 10 and 11 were screened by PTT. Coding BRCA1 exons 2, 3, 5-10 and 12-24 and BRCA2 exons 2-9 and 12-27 were screened by SSCP. Primers are listed in Table 1. In 27 cases, analyzed by PTT along the entire BRCA1 coding sequence, BRCA1 SSCP analysis was limited to exons 2, 5, 20 and 24. Mutations were verified by sequence analysis on two independent blood samples. RESULTS: Deleterious germline BRCA1/BRCA2 mutations were detected in 11 out of 136 cases (8%). Only three BRCA2 mutations were novel. One BRCA2 mutation recurred in two unrelated probands. Table 2 shows the mutations and data concerning carriers and their families. Table 3 shows correlations between BRCA1/BRCA2 mutations and sex, age at disease diagnosis and familial clustering of breast/ovarian cancer in the total patient population. Table 4 shows the proportions of BRCA1 and BRCA2 mutations in females with site-specific breast and breast-ovarian/ovarian cancer. Table 5 shows the frequency of BRCA1/BRCA2 mutations in males. BRCA1 and BRCA2 mutations, respectively, accounted for four out of 68 (6%) and one out of 68 (1%) cases diagnosed before age 50 years, and for one out of 68 (1%) and five out of 68 (7%) cases diagnosed after age 50 years. BRCA1 mutations were found in five out of 117 females (4%) and in none of 19 males (0%), and BRCA2 mutations were found in four out of 117 females (3%) and in two out of 19 males (10%). The proportions of BRCA1 and BRCA2 mutations coincided in site-specific female breast cancers (four out of 102; ie 4% each). BRCA1 and BRCA2 equally contributed to female breast cancers, with no familial clustering in those diagnosed before age 40 years (one out of 28; 4% each), and to female breast cancers, all ages, with familial clustering in one to two relatives (three out of 55; ie 5% each). In the latter subset of cases, BRCA1 mostly accounted for tumours diagnosed before age 40 years (two out of eight; 25%), and BRCA2 for tumours diagnosed after age 50 years (three out of 34; 9%). Regardless of family history, the respective contributions of BRCA1 and BRCA2 to site-specific female breast cancers diagnosed before age 40 years were 8% (three out of 36) and 3% (one out of 36). One BRCA1 mutation was detected among the 15 female probands from breast-ovarian/ovarian cancer families (7%). Among male breast cancers, BRCA2 mutations were identified in one out of five (20%) cases with family history and in one out of 14 (7%) apparently sporadic cases. No BRCA1 or BRCA2 mutations were found in female probands with nonfamilial bilateral breast cancer (10 cases) or in those with breast cancer associated with gastrointestinal, pancreatic or uterine cancers, synchronous/metachronous or in first-degree relative(s) (nine cases). These cases were all diagnosed after age 40 years. DISCUSSION: Our results indicate a lack of relevant founder effects for BRCA1- and BRCA2-related disease in the sample of patients studied, which is consistent with other Italian studies and with ethnical and historical data. Overall, the contribution of BRCA1 and BRCA2 to breast/ovarian cancer in Italian patients appears to be less significant than in patients from communities with founder mutations. The present study is in agreement with direct estimates on other outbred populations, indicating that 7-10% of all female breast cancers that occur in patients aged under 40 years are due to BRCA1/BRCA2. We found that BRCA1 and BRCA2 equally contributed to site-specific breast cancers who had one/two breast cancer-affected first-/second-degree relative(s) or who were diagnosed within age 40 years in the absence of family history. This is consistent with recent data that indicated that the respective frequencies of BRCA1 and BRCA2 mutations are comparable in early onset breast cancer. Considering the total population of patients analyzed here, however, BRCA1 and BRCA2 mutations were mostly found in cases with disease diagnosis before and after age 50 years, respectively. Moreover, in cases with familial clustering of site-specific breast cancer, BRCA1 mostly accounted for tumours diagnosed before age 40 years, and BRCA2 for tumours diagnosed after age 50 years. This is in agreement with a trend, which has been observed in other populations, for the proportion of cases with BRCA2 mutations to increase, and the proportion with mutations in BRCA1 to decrease, as the age at cancer onset increases. As in other studies, the frequency of BRCA1/BRCA2 mutations taken together was lower than the estimated frequencies at comparable ages for all susceptibility alleles derived from the Contraceptive and Steroid Hormones (CASH) study. The discrepancy between direct data deriving from BRCA1/BRCA2 mutational analysis and CASH estimates could be due to several factors, including contribution of gene(s) other than BRCA1/BRCA2, differences between populations and relative insensitivity of mutational screening. Only BRCA1 mutations were found in breast/ovarian and site-specific ovarian cancer families. BRCA2, but not BRCA1 mutations were found in the male breast cancers. The overall proportion of males with BRCA2 mutations was high when compared with data from other studies on outbred populations, but was low compared with data from populations with founder effects. The present results should be regarded as an approximation, because the following types of mutation are predicted to escape detection by the screening strategy used: mutations in noncoding regions; missense mutations within BRCA1 exon 11 and BRCA2 exons 10 and 11; large gene deletions; and mutations within the first and last 180 nucleotides of the amplicons analyzed by PTT

Plasma Cystatin C correlates with plasma NfL levels and predicts disease progression in Parkinson's disease

INTRODUCTION: Previous studies reported increased plasma levels of Cystatin C (Cys-C) in Parkinson's disease (PD) and claimed for a possible association with disease severity and progression. The aim of this study was to evaluate plasma Cys-C in PD and healthy controls (HC) and test its association with markers of peripheral inflammation, neurodegeneration and clinical progression in a longitudinal study. METHODS: Plasma Cys-C, high-sensitive C-reactive protein (hsCRP), interleukin 6 (IL-6) and Neurofilament Light Chain (NfL) were assessed at the baseline in 71 consecutive non-demented PD and 69 HC. PD patients underwent an extensive motor and cognitive assessment at baseline and after 2 years of follow-up. The association of Cys-C with disease severity was evaluated in a multilinear model adjusted for the effect of age, sex, disease duration and peripheral inflammation. RESULTS: Cys-C levels appeared to be higher in PD compared to controls and correlated with the plasma neuronal marker NfL (r = 0.204, p = 0.046). In longitudinal analyses, PD patients with higher Cys-C levels exhibited faster motor progression at two years of follow-up independently from the peripheral inflammatory profile. CONCLUSIONS: Cys-C was associated with higher NfL levels and a remarkably faster motor progression in PD independently from peripheral inflammation. Further studies are needed in order to understand the mechanisms underpinning the association of Cys-C with higher neuronal damage markers in neurodegenerative diseases