Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters.

Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward's minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward's and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository.

Development and external validation of a prognostic nomogram for metastatic uveal melanoma.

BACKGROUND: Approximately 50% of patients with uveal melanoma (UM) will develop metastatic disease, usually involving the liver. The outcome of metastatic UM (mUM) is generally poor and no standard therapy has been established. Additionally, clinicians lack a validated prognostic tool to evaluate these patients. The aim of this work was to develop a reliable prognostic nomogram for clinicians. PATIENTS AND METHODS: Two cohorts of mUM patients, from Veneto Oncology Institute (IOV) (N=152) and Mayo Clinic (MC) (N=102), were analyzed to develop and externally validate, a prognostic nomogram. RESULTS: The median survival of mUM was 17.2 months in the IOV cohort and 19.7 in the MC cohort. Percentage of liver involvement (HR 1.6), elevated levels of serum LDH (HR 1.6), and a WHO performance status=1 (HR 1.5) or 2-3 (HR 4.6) were associated with worse prognosis. Longer disease-free interval from diagnosis of UM to that of mUM conferred a survival advantage (HR 0.9). The nomogram had a concordance probability of 0.75 (SE .006) in the development dataset (IOV), and 0.80 (SE .009) in the external validation (MC). Nomogram predictions were well calibrated. CONCLUSIONS: The nomogram, which includes percentage of liver involvement, LDH levels, WHO performance status and disease free-interval accurately predicts the prognosis of mUM and could be useful for decision-making and risk stratification for clinical trials.

A retrospective analysis of 141 patients with liver metastases from uveal melanoma: a two-cohort study comparing transarterial chemoembolization with CPT-11 charged microbeads and historical treatments.

We retrospectively evaluated the benefit of transarterial chemoembolization with CPT-11 charged microbeads (TACE) in 58 of 141 uveal melanoma patients with liver metastases. This was a retrospective analysis of a prospectively maintained database ranging from September 1990 to April 2014. Statistical analyses adjusting for possible confounding effects of extent of liver metastases were carried out using the Cox regression model under the verified hypothesis of proportional hazards. Among 141 patients with liver metastases, 58 were treated with TACE as first-line therapy and 36 were dead at the time of the analysis; 83 patients received other first-line treatments (deaths=83). The treatment with TACE conferred a survival advantage (median 16.5 vs. 12.2 months, respectively); when the two cohorts were analyzed comparing the two groups according to the percentage of liver involvement, there was significant evidence that patients with worse hepatic involvement benefited most from the treatment (liver metastases=20-50%: hazard ratio=0.50, P=0.048 and liver metastases ≥50%: hazard ratio=0.17, P=0.009). Liver function tests (transaminases and γ-glutamyl-transpeptidase) and age were higher in the historic group, and LDH tended to show higher values. There were no high-grade toxicities with TACE. TACE seems to be a tolerable regimen that confers an improvement in the survival of uveal melanoma patients with liver metastases. Confirmation of the clinical efficacy of TACE is recommended in a phase III trial, possibly with the inclusion of a targeted therapy such as a MEK inhibitor.

Dephosphorylation of gamma H2A by Glc7/protein phosphatase 1 promotes recovery from inhibition of DNA replication.

Replication fork stalling caused by deoxynucleotide depletion triggers Rad53 phosphorylation and subsequent checkpoint activation, which in turn play a crucial role in maintaining functional DNA replication forks. How cells regulate checkpoint deactivation after inhibition of DNA replication is poorly understood. Here, we show that the budding yeast protein phosphatase Glc7/protein phosphatase 1 (PP1) promotes disappearance of phosphorylated Rad53 and recovery from replication fork stalling caused by the deoxynucleoside triphosphate (dNTP) synthesis inhibitor hydroxyurea (HU). Glc7 is also required for recovery from a double-strand break-induced checkpoint, while it is dispensable for checkpoint inactivation during methylmethane sulfonate exposure, which instead requires the protein phosphatases Pph3, Ptc2, and Ptc3. Furthermore, Glc7 counteracts in vivo histone H2A phosphorylation on serine 129 (gamma H2A) and dephosphorylates gamma H2A in vitro. Finally, the replication recovery defects of HU-treated glc7 mutants are partially rescued by Rad53 inactivation or lack of gamma H2A formation, and the latter also counteracts hyperphosphorylated Rad53 accumulation. We therefore propose that Glc7 activity promotes recovery from replication fork stalling caused by dNTP depletion and that gamma H2A dephosphorylation is a critical Glc7 function in this process.