The integration of large biological and clinical datasets towards the understanding of human disease

As the cost of high-throughput techniques reduces, and new more powerful equipment is designed, more highly-dimensional biological data will be available – and a lot of data is already in the public domain. The aim of this thesis is to investigate three case studies with interesting opportunities for the integration of large molecular datasets, corresponding clinical data, and publicly available data. Genome-wide DNA methylation was studied with respect to hypertension. Genomic location data was used both to group individual methylation sites into meaningful functional groups such as promoter regions, and to report the results in a genomic context. Genome-wide SNP data was used to help rule out potential false positives where SNPs interfere with detection of DNA methylation. Left ventricular hypertrophy is an intermediate cardiovascular phenotype associated with the development of heart failure. This phenotype was studied as a continuous variable – left ventricular mass index (LVMI) – using multiple sample types, in the context of a large cohort, using datasets with different classes of biomolecules and varying genomic coverage. Two alternative analysis approaches were compared, and a linear model was generated showing that a signature of molecular and clinical markers in combination best describes LVMI. A multi-omics respiratory dataset was investigated, which includes high-throughput data for mRNA, miRNA, proteins, and metabolites and has measurements in two relevant sample types. Test statistics were performed on all datasets, identifying molecules dysregulated with asthma, COPD, and smoking. An asthma molecular interaction network was created with the significant molecules, and the links between them were formed using a variety of public data. Comparisons were made between asthma and COPD, and between asthma in smokers and non-smokers. Correlations with cell type counts may indicate cell type of origin in samples with multiple cell types like induced sputum

Mechanisms and Novel Therapeutic Approaches for Gynecologic Cancer

This book—entitled “Mechanisms and Novel Therapeutic Approaches for Gynecologic Cancer”—was edited as a Special Issue of Biomedicines, focusing on basic research such as genomics, epigenomics, and proteomics, as well as clinical research in the field of gynecologic oncology. The number of patients with gynecological cancer has been increasing worldwide due to its high lethality and lack of early detection tools and effective therapeutic interventions. In this regard, basic research on its pathophysiology and novel molecular targeting intervention is required to improve the prognosis of gynecologic cancer. This book contains 13 papers, including 8 original research papers and 5 reviews focusing on the basic research of gynecologic oncology. The reader can learn about state-of-the-art research and obtain extensive knowledge of the current advances in the field of gynecologic oncology. It is my hope that this book contributes towards the progress of gynecologic oncology

Extracellular vesicles from induced neurons trigger epigenetic silencing of a brain neurotransmitter.

Introduction: Antithrombin (AT) is a glycoprotein involved in the regulation of blood coagulation. It belongs to the family of serine-protease inhibitors and acts as the most important antagonist of different clot- ting factors. Two types of inherited AT deficiency can be distinguished: Type I (quantitative deficit), and Type II (qualitative deficit). The latter is characterized by an impaired inhibitory activity related to dysfunc- tional domains of the protein. Three Type II subtypes can be defined: Type IIa (reactive site defect), Type IIb (heparin binding site defect) and Type IIc (pleiotropic defect). This classification has clinical importance since these subtypes have a different thrombotic risk. No functional routine diagnostic assay, however, can be assumed to detect all forms of Type II deficiencies since false-negative results may hamper the diagnosis. Methods: We analysed the biochemical/biophysical association of ATT to EVs. We separated EVs from plasma of healthy or Type II affected patients or from cultured hepatocytes through differential ultracentrifu- gation followed by sucrose density gradient and/or immunoprecipitation. We next combined dot blot ana- lysis, WB, 2D electrophoresis and enzymatic assays to reveal the nature of ATT association to EVs. Results: We evidenced that ATT is associated to the external leaflet of EVs. We also found that specific ATT isoforms are enriched in EV preparations in respect to total plasma and that those isoforms are selectively associated to EVs when comparing healthy or ATT type II deficient patients. Summary/Conclusion: ATT selective association pat- tern to EVs might be related either to mutations in the primary sequence of the protein or alterations in the glycosylation process, hence experiments are ongoing to reveal the nature of this phenomenon. Our findings suggest that analysis of ATT enriched in EV prepara- tions might be useful to gain insights into the patho- genesis and be of support in the diagnostic algorithm of ATT deficiency. Funding: This work acknowledges FFABR (Fondo finanziamento attività Base di ricerca from MIUR, Ministry of Education, Universities and Research, Italy) for financial support

PRELIMINARY FINDINGS OF A POTENZIATED PIEZOSURGERGICAL DEVICE AT THE RABBIT SKULL

The number of available ultrasonic osteotomes has remarkably increased. In vitro and in vivo studies have revealed differences between conventional osteotomes, such as rotating or sawing devices, and ultrasound-supported osteotomes (Piezosurgery®) regarding the micromorphology and roughness values of osteotomized bone surfaces. Objective: the present study compares the micro-morphologies and roughness values of osteotomized bone surfaces after the application of rotating and sawing devices, Piezosurgery Medical® and Piezosurgery Medical New Generation Powerful Handpiece. Methods: Fresh, standard-sized bony samples were taken from a rabbit skull using the following osteotomes: rotating and sawing devices, Piezosurgery Medical® and a Piezosurgery Medical New Generation Powerful Handpiece. The required duration of time for each osteotomy was recorded. Micromorphologies and roughness values to characterize the bone surfaces following the different osteotomy methods were described. The prepared surfaces were examined via light microscopy, environmental surface electron microscopy (ESEM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM) and atomic force microscopy. The selective cutting of mineralized tissues while preserving adjacent soft tissue (dura mater and nervous tissue) was studied. Bone necrosis of the osteotomy sites and the vitality of the osteocytes near the sectional plane were investigated, as well as the proportion of apoptosis or cell degeneration. Results and Conclusions: The potential positive effects on bone healing and reossification associated with different devices were evaluated and the comparative analysis among the different devices used was performed, in order to determine the best osteotomes to be employed during cranio-facial surgery