INNOVATIVE BIOSTATISTICAL AND BIOINFORMATIC APPROACHES IN THE ANALYSIS OF BREAST CANCER: COMPETING RISK SURVIVAL ANALYSIS THROUGH PSEUDO-VALUES AND COMPREHENSIVE EVALUATION OF METHODS FOR THE TUMOR MICROENVIRONMENT DISSECTION AVAILABLE AT THE PRESENT DAY.

Since my personal original background was quite distant from the statistical bioinformatic approaches for data analysis, having a master degree in Sanitary Biotechnology and Molecular Medicine, my PhD fellowship was spent in building my skills in this field while studying and trying to contribute to the development of biostatistical and bioinformatic approaches to be applied in clinic, with a special focus on oncology, in the optic to contribute to the field of personalized medicine. Personalized medicine is indeed the ultimate goal for life sciences, particularly for oncology, and, in my opinion, a key aspect of the future wellness of humanity. Personalized medicine is the idea of developing the ability to identify the best therapeutic strategy for each unique person and its efficacy relies on having accurate diagnostic tests that identify patients who can benefit from targeted therapies. A striking example consists in the determination of the overexpression of the human epidermal growth factor receptor type 2 (HER2) in the routinely diagnosis of Breast Cancer (BC). HER2 is indeed associated with a worse prognosis but also predicts a better response to the medication trastuzumab; a test for HER2 was approved along with the drug (as a \u201ccompanion diagnostic\u201d) so that clinicians can better target patients' treatment. My thesis is composed by the description of the two projects that have mainly characterized my fellowship. Both projects rely on breast cancer (BC) and the objective of understanding the effects of chronic low inflammation, which has been studied in my projects as the leucocyte infiltration and the body mass index. The focus on BC derives from a practical aspect and an epidemiological aspect. The practical aspect consists on the fact that my group is part of a European research group, led by Christine Desmedt from Belgium, which allowed me to obtain unique data and to interact with experts of BC and bioinformatics from different countries. The epidemiological aspect is represented by the fact that breast cancer is actually a hot topic, being the second most common cancer worldwide and the first among women, but still open to investigations, since the complexity and variability of BC, reflected both at histopathological and molecular level, have proven challenging to classify and therefore to effectively treat to the present day. The first project presented, the tumor microenvironment (TME) dissection project, occupied the first part of my fellowship and was focused on the managing of an enormous quantity of data in order to compare different tools and approaches used to analyze breast cancer. This project consisted in a big European collaboration which tried to establish the reliability of bioinformatic tools in retrieving the TME composition by analyzing bulk transcriptome and methylome and comparing the obtained results to standard approaches, as the pathologist evaluation, and emerging methods, as digital image analysis. This project led to the preparation of a paper, which is currently under submission, under the supervision of Christine Desmedt, the leader of this breast cancer research group, and Elia Biganzoli, my supervisor and member of the cited group. The second project presented, the competing risk analysis through pseudo-values project, which characterized the third year of my PhD, is more focused on the statistical aspects of clinical data analysis and represent the arrival point of my studies of statistical methodology. The project consisted in the exploration of a forefront approach to the analysis of survival data based on pseudo-values, which has the desirable feature to generate measures with a clear and direct interpretation at a clinical level, becoming an invaluable tool for clinical decision making. This project represents a first step in a longer-term project that will led to the preparation of several papers in the future

80/20 Principle: Application in Manufacturing Companies

Responding to the request of a company in pushing the income statement in profit, the authors of this article propose to apply to the products contribution margin the 80/20 principl

Oral sucrosomial iron is as effective as intravenous ferric carboxy‐maltose in treating anemia in patients with ulcerative colitis

Anemia is a frequent complication of ulcerative colitis, and is frequently caused by iron deficiency. Oral iron supplementation displays high rates of gastrointestinal adverse effects. However, the formulation of sucrosomial iron (SI) has shown higher tolerability. We performed a prospective study to compare the effectiveness and tolerability of oral SI and intravenous ferric carboxy‐maltose (FCM) in patients with ulcerative colitis in remission and mild‐to‐moderate anemia. Patients were randomized 1:1 to receive 60 mg/day for 8 weeks and then 30 mg/day for 4 weeks of oral SI or intravenous 1000 mg of FCM at baseline. Hemoglobin and serum levels of iron and ferritin were assessed after 4, 8, and 12 weeks from baseline. Hemoglobin and serum iron increased in both groups after 4 weeks of therapy, and remained stable during follow up, without significant treatment or treatment‐by‐time interactions (p = 0.25 and p = 0.46 for hemoglobin, respectively; p = 0.25 and p = 0.26 for iron, respectively). Serum ferritin did not increase over time during SI supplementation, while it increased in patients treated with FCM (treatment effect, p = 0.0004; treatment‐bytime interaction effect, p = 0.0002). Overall, this study showed that SI and FCM displayed similar effectiveness and tolerability for treatment of mild‐to‐moderate anemia in patients with ulcerative colitis under remission

Comprehensive evaluation of methodology to assess abundance of immune infiltrates in breast cancer

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Raising children on a vegan diet: Parents’ opinion on problems in everyday life

A growing number of Italian families are adopting a vegan diet (VD) for their offspring from infancy for various reasons, with health benefits and ethics being the most common reasons. Barriers to effective communication with primary care pediatricians (PCPs) are perceived by many parents and, depending on the actors involved and the environment, a VD may affect social interactions in everyday life. A national cross‐sectional survey was conducted between July and September 2020. Parents of children following a VD completed an online questionnaire. Data from 176 Italian parents were collected. About 72% (71.8%) of the children included in this study had been on a VD since weaning. Parents did not inform their primary care pediatricians (PCP) about the VD in 36.2% of the cases. In 70.8% of the cases, PCPs were perceived as skeptical or against a VD. About 70% (71.2%) of the parents relied on medical dietitians, and 28.2% on nutritionists/dietitians for dietary counseling. Parents administered an individual B12 supplement in 87.2% of the cases. To the best of our knowledge, this survey is the first which explores the relationship between vegan parents and their PCPs, the parental management of their children’s diet and problems regarding the implementation of a VD in everyday life

Between GERD and NERD: the relevance of weakly acidic reflux

Nonerosive reflux disease (NERD) is a common condition and the most frequent phenotype of gastroesophageal reflux disease (GERD). NERD is extremely heterogeneous and includes patients with negative endoscopy but abnormal esophageal acid exposure and/or positive reflux-symptom association analysis (hypersensitive esophagus). This segregation is only possible owing to the use of impedance-pH monitoring. Indeed, weakly acidic reflux represents one of the most common causes of refractory symptoms in patients evaluated off antisecretory therapy and, more importantly, during antisecretory drug treatment. Patients with heartburn who do not have any type of reflux underlying their symptoms (functional heartburn) must be excluded from the category of GERD. The drawbacks of impedance-pH are mainly due to the day-to-day variability of the test and the fact that the accuracy of the symptom-reflux correlation scores is often far from perfect. Some histopathological characteristics, such as dilated intercellular spaces, can be helpful in distinguishing patients with NERD through esophageal biopsies. Patients with NERD in whom acid is the main pathogenetic factor respond successfully to proton pump inhibitor therapy, while those with hypersensitive esophagus to weakly acidic reflux could be treated with reflux inhibitors or surgery, although further controlled studies are required

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays.

Microarray-based gene expression profiling is well suited for parallel quantitative analysis of large numbers of RNAs, but its application to cancer biopsies, particularly formalin-fixed, paraffin-embedded (FFPE) archived tissues, is limited by the poor quality of the RNA recovered. This represents a serious drawback, as FFPE tumor tissue banks are available with clinical and prognostic annotations, which could be exploited for molecular profiling studies, provided that reliable analytical technologies are found. We applied and evaluated here a microarray-based cDNA-mediated annealing, selection, extension and ligation (DASL) assay for analysis of 502 mRNAs in highly degraded total RNA extracted from cultured cells or FFPE breast cancer (MT) biopsies. The study included quantitative and qualitative comparison of data obtained by analysis of the same RNAs with genome-wide oligonucleotide microarrays vs DASL arrays and, by DASL, before and after extensive in vitro RNA fragmentation. The DASL-based expression profiling assay applied to RNA extracted from MCF-7 cells, before or after 24 h stimulation with a mitogenic dose of 17b-estradiol, consistently allowed to detect hormone-induced gene expression changes following extensive RNA degradation in vitro. Comparable results where obtained with tumor RNA extracted from FFPE MT biopsies (6 to 19 years old). The method proved itself sensitive, reproducible and accurate, when compared to results obtained by microarray analysis of RNA extracted from snap-frozen tissue of the same tumor

Three-Dimensional Iron Oxide Nanoparticle-Based Contrast-Enhanced Magnetic Resonance Imaging for Characterization of Cerebral Arteriogenesis in the Mouse Neocortex

Purpose: Subsurface blood vessels in the cerebral cortex have been identified as a bottleneck in cerebral perfusion with the potential for collateral remodeling. However, valid techniques for non-invasive, longitudinal characterization of neocortical microvessels are still lacking. In this study, we validated contrast-enhanced magnetic resonance imaging (CE-MRI) for in vivo characterization of vascular changes in a model of spontaneous collateral outgrowth following chronic cerebral hypoperfusion. Methods: C57BL/6J mice were randomly assigned to unilateral internal carotid artery occlusion or sham surgery and after 21 days, CE-MRI based on T2*-weighted imaging was performed using ultra-small superparamagnetic iron oxide nanoparticles to obtain subtraction angiographies and steady-state cerebral blood volume (ss-CBV) maps. First pass dynamic susceptibility contrast MRI (DSC-MRI) was performed for internal validation of ss-CBV. Further validation at the histological level was provided by ex vivo serial two-photon tomography (STP). Results: Qualitatively, an increase in vessel density was observed on CE-MRI subtraction angiographies following occlusion; however, a quantitative vessel tracing analysis was prone to errors in our model. Measurements of ss-CBV reliably identified an increase in cortical vasculature, validated by DSC-MRI and STP. Conclusion: Iron oxide nanoparticle-based ss-CBV serves as a robust, non-invasive imaging surrogate marker for neocortical vessels, with the potential to reduce and refine preclinical models targeting the development and outgrowth of cerebral collateralization

Genome-wide activity of unliganded estrogen receptor-\u3b1\ua0 in breast cancer cells

Estrogen receptor-\u3b1 (ER\u3b1) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ER\u3b1 has functions that are independent of ligands. In the present work, we investigated the binding of ER\u3b1 to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ER\u3b1 binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ER\u3b1 binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ER\u3b1 in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulatedmRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ER\u3b1 down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ER\u3b1 binding sites. Finally, we found that FOXA1 and AP2\u3b3 binding to several sites is decreased upon ER\u3b1 silencing, suggesting that unliganded ER\u3b1 participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cell

Influence of the serotonin transporter 5HTTLPR polymorphism on symptom severity in irritable bowel syndrome

5HTTLPR polymorphism of serotonin transporter yields short (S) and long (L) alleles. SS and LS genotypes are associated with reduced expression of serotonin transporter. This cross-sectional study investigated the association of 5HTTLPR with symptom severity of irritable bowel syndrome (IBS). Patients with IBS (Rome III) and healthy controls were included. Genomic DNA was extracted from saliva, and 5HTTLPR alleles were assessed by polymerase chain reaction. IBS symptom severity was evaluated by means of IBS-SSS questionnaire. Two hundreds and four IBS patients (159 females; mean age: 39.6±12.3 years; 106 with constipation: C-IBS; 98 with diarrhea: D-IBS) and 200 healthy controls (154 females; mean age: 40.4±15.8 years) were enrolled. The overall IBS-SSS value was higher in LS/SS than LL patients (319.0±71.5 versus 283.8±62.3; P = 0.0006). LS/SS patients had also higher values of abdominal pain (59.7±21.0 versus 51.0±18.8; P = 0.020) and bowel dissatisfaction (80.1±23.9 versus 70.5±22.8; P = 0.035). The overall IBS-SSS values in C-IBS and D-IBS patients were 317.2±68.3 and 296.1±71.4, respectively (P = 0.192), with significantly higher values for abdominal distension (65.0±24.4 versus 51.4±24.8; P = 0.0006), but not for bowel dissatisfaction (80.5±21.7 versus 72.9±25.7; P = 0.138). Frequencies of 5HTTLPR genotypes did not differ significantly when comparing IBS patients (overall or upon stratification in C-IBS and D-IBS) with healthy controls. In conclusion, the LS and SS genotypes are significantly correlated with IBS symptom severity, although their possible direct causal role remains to be proven. In addition, the present findings do not support an association of 5HTTLPR with IBS or its clinical presentation in terms of bowel habit predominance