Epigenetic Control of Adamantinomatous Craniopharyngiomas.

Introduction: Studies addressing the methylation pattern in adamantinomatous craniopharyngioma (ACP) are lacking.

Objective: To identify methylation signatures in ACPs regarding clinical presentation and outcome.

Methods: Clinical and pathology data were collected from 35 patients with ACP (54% male; 18.

Integrating Methylome and Transcriptome Signatures Expands the Molecular Classification of the Pituitary Tumors.

Objective: To explore pituitary tumors by methylome and transcriptome signatures in a heterogeneous ethnic population.

Methods: In this retrospective cross-sectional study, clinicopathological features, methylome, and transcriptome were evaluated in pituitary tumors from 77 patients (61% women, age 12-72 years) followed due to functioning (FPT: GH-secreting n = 18, ACTH-secreting n = 14) and nonfunctioning pituitary tumors (NFPT, n = 45) at Ribeirao Preto Medical School, University of São Paulo.

Results: Unsupervised hierarchical clustering analysis (UHCA) of methylome (n = 77) and transcriptome (n = 65 out of 77) revealed 3 clusters each: one enriched by FPT, one by NFPT, and a third by ACTH-secreting and NFPT.

DNA methylation is a comprehensive marker for pediatric adrenocortical tumors.

Children diagnosed with pediatric adrenocortical tumors (pACT) have variable outcomes, and, to date, the disease lacks robust prognostic biomarkers. The prognostic potential of tumor methylation has been demonstrated in several cancers. We aimed to evaluate the pACT methylation profile and its association with disease presentation and survival.

A proteomic study of myeloproliferative neoplasms using reverse-phase protein arrays.

Myeloproliferative neoplasms polycythemia vera (PV), essential thrombocythaemia (ET) and primary myelofibrosis constitute a group of haematological diseases. The comprehensive assessment of signaling pathway activation in blood cells may aid the understanding of MPN pathophysiology. Thus, levels of post-translational protein modifications and total protein expression were determined in MPN patients and control leukocytes by using reverse-phase protein arrays (RPPA).

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.

SIFTER-T: a scalable and optimized framework for the SIFTER phylogenomic method of probabilistic protein domain annotation.

Statistical Inference of Function Through Evolutionary Relationships (SIFTER) is a powerful computational platform for probabilistic protein domain annotation. Nevertheless, SIFTER is not widely used, likely due to usability and scalability issues. Here we present SIFTER-T (SIFTER Throughput-optimized), a substantial improvement over SIFTER's original proof-of-principle implementation.