Copy number variation analysis implicates novel pathways in patients with oculo-auriculo-vertebral-spectrum and congenital heart defects.

Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder of craniofacial morphogenesis. Its etiology is unclear, but assumed to be complex and heterogeneous, with contribution of both genetic and environmental factors. We assessed the occurrence of copy number variants (CNVs) in a cohort of 19 unrelated OAVS individuals with congenital heart defect. Chromosomal microarray analysis identified pathogenic CNVs in 2/19 (10.5%) individuals, and CNVs classified as variants of uncertain significance in 7/19 (36.9%) individuals. Remarkably, two subjects had small intragenic CNVs involving DACH1 and DACH2, two paralogs coding for key components of the PAX-SIX-EYA-DACH network, a transcriptional regulatory pathway controlling developmental processes relevant to OAVS and causally associated with syndromes characterized by craniofacial involvement. Moreover, a third patient showed a large duplication encompassing DMBX1/OTX3, encoding a transcriptional repressor of OTX2, another transcription factor functionally connected to the DACH-EYA-PAX network. Among the other relevant CNVs, a deletion encompassing HSD17B6, a gene connected with the retinoic acid signaling pathway, whose dysregulation has been implicated in craniofacial malformations, was also identified. Our findings suggest that CNVs affecting gene dosage likely contribute to the genetic heterogeneity of OAVS, and implicate the PAX-SIX-EYA-DACH network as novel pathway involved in the etiology of this developmental trait.

Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS).

Oculo-auriculo-vertebral-spectrum (OAVS; OMIM 164210) is a rare disorder originating from abnormal development of the first and second branchial arch. The clinical phenotype is extremely heterogeneous with ear anomalies, hemifacial microsomia, ocular defects, and vertebral malformations being the main features. MYT1, AMIGO2, and ZYG11B gene variants were reported in a few OAVS patients, but the etiology remains largely unknown. A multifactorial origin has been proposed, including the involvement of environmental and epigenetic mechanisms. To identify the epigenetic mechanisms contributing to OAVS, we evaluated the DNA-methylation profiles of 41 OAVS unrelated affected individuals by using a genome-wide microarray-based methylation approach. The analysis was first carried out comparing OAVS patients with controls at the group level. It revealed a moderate epigenetic variation in a large number of genes implicated in basic chromatin dynamics such as DNA packaging and protein-DNA organization. The alternative analysis in individual profiles based on the searching for Stochastic Epigenetic Variants (SEV) identified an increased number of SEVs in OAVS patients compared to controls. Although no recurrent deregulated enriched regions were found, isolated patients harboring suggestive epigenetic deregulations were identified. The recognition of a different DNA methylation pattern in the OAVS cohort and the identification of isolated patients with suggestive epigenetic variations provide consistent evidence for the contribution of epigenetic mechanisms to the etiology of this complex and heterogeneous disorder.

Genetics and Genomics of Breast Cancer: update and translational perspectives.

In the recent years the rapid scientific innovation in the evaluation of the individual's genome have allowed the identification of variants associated with the onset, treatment and prognosis of various pathologies including cancer, and with a potential impact in the assessment of therapy responses. Despite the analysis and interpretation of genomic information is considered incomplete, in many cases the identification of specific genomic profile has allowed the stratification of subgroups of patients characterized by a better response to drug therapies. Individual genome analysis has changed profoundly the diagnostic and therapeutic approach of breast cancer in the last 15 years by identifying selective molecular lesions that drive the development of neoplasms, showing that each tumor has its own genomic signature, with some specific features and some features common to several sub-types. Several personalized therapies have been (and still are being) developed showing a remarkable efficacy in the treatment of breast cancer.

Identification of a novel RUNX2 gene mutation and early diagnosis of CCD in a cleidocranial dysplasia suspected Iranian family.

This research resulted in the identification and submission of a novel RUNX2 gene mutation in the affected members of the studied pedigree. Mutation screening is an effective method for the early diagnosis of CCD in the affected individuals.

Emergency department boarding: a descriptive analysis and measurement of impact on outcomes.

OBJECTIVES: Delays in transfer of admitted patients boarded in the emergency department (ED) to an inpatient bed is a major driver of ED overcrowding. We sought to identify explanatory factors behind ED boarding as well as the impact of boarding on total inpatient length of stay (IP LOS) and inpatient mortality. METHODS: We conducted a retrospective single-centre observational study during the period between January 1 and December 31, 2015 at a very high volume community hospital. All patients admitted from the ED to Medicine, Pediatrics, Surgery, and Critical Care were identified. The mean ED LOS and boarding time as well as patient-specific and institutional factors that were independently associated with prolonged ED LOS (≥24 hours) and prolonged boarding time (≥12 hours) were identified. Mean inpatient length of stay (IP LOS) and the odds of inpatient mortality were calculated for those patients with prolonged ED wait times. RESULTS: There were 13,872 unique admissions during the study period. Patients admitted to the Medicine service exhibited significantly higher ED wait times than other services. Within Medicine patients, there was a statistically significant greater odds of prolonged ED wait times for patients who were older, had a greater comorbidity burden, and required more specialized inpatient care. Medicine patients with prolonged boarding times also experienced a mean of 0.9 days longer IP LOS even after adjusting for confounders. CONCLUSION: Within our cohort, older, sicker patients and those patients requiring more resource-intensive inpatient care had the longest ED wait times. These prolonged wait times are associated with significantly increased IP LOS.

Galectin-3: One Molecule for an Alphabet of Diseases, from A to Z.

Galectin-3 (Gal-3) regulates basic cellular functions such as cell-cell and cell-matrix interactions, growth, proliferation, differentiation, and inflammation. It is not surprising, therefore, that this protein is involved in the pathogenesis of many relevant human diseases, including cancer, fibrosis, chronic inflammation and scarring affecting many different tissues. The papers published in the literature have progressively increased in number during the last decades, testifying the great interest given to this protein by numerous researchers involved in many different clinical contexts. Considering the crucial role exerted by Gal-3 in many different clinical conditions, Gal-3 is emerging as a new diagnostic, prognostic biomarker and as a new promising therapeutic target. The current review aims to extensively examine the studies published so far on the role of Gal-3 in all the clinical conditions and diseases, listed in alphabetical order, where it was analyzed.

Comparative analysis of diagnostic performance, feasibility and cost of different test-methods for thyroid nodules with indeterminate cytology.

Since it is impossible to recognize malignancy at fine needle aspiration (FNA) cytology in indeterminate thyroid nodules, surgery is recommended for all of them. However, cancer rate at final histology is <30%. Many different test-methods have been proposed to increase diagnostic accuracy in such lesions, including Galectin-3-ICC (GAL-3-ICC), BRAF mutation analysis (BRAF), Gene Expression Classifier (GEC) alone and GEC+BRAF, mutation/fusion (M/F) panel, alone, M/F panel+miRNA GEC, and M/F panel by next generation sequencing (NGS), FDG-PET/CT, MIBI-Scan and TSHR mRNA blood assay.We performed systematic reviews and meta-analyses to compare their features, feasibility, diagnostic performance and cost. GEC, GEC+BRAF, M/F panel+miRNA GEC and M/F panel by NGS were the best in ruling-out malignancy (sensitivity = 90%, 89%, 89% and 90% respectively). BRAF and M/F panel alone and by NGS were the best in ruling-in malignancy (specificity = 100%, 93% and 93%). The M/F by NGS showed the highest accuracy (92%) and BRAF the highest diagnostic odds ratio (DOR) (247). GAL-3-ICC performed well as rule-out (sensitivity = 83%) and rule-in test (specificity = 85%), with good accuracy (84%) and high DOR (27) and is one of the cheapest (113 USD) and easiest one to be performed in different clinical settings.In conclusion, the more accurate molecular-based test-methods are still expensive and restricted to few, highly specialized and centralized laboratories. GAL-3-ICC, although limited by some false negatives, represents the most suitable screening test-method to be applied on a large-scale basis in the diagnostic algorithm of indeterminate thyroid lesions.

Combined clinical and ultrasound follow-up assists in malignancy detection in Galectin-3 negative Thy-3 thyroid nodules.

The use of galectin-3 ThyroTest in the preoperative evaluation of cytologically indeterminate (Thy-3) thyroid nodules has been largely validated by retrospective and prospective multicentre studies. Here we report the results of galectin-3 ThyroTest routinely applied in the management of Thy-3 nodules in combination with clinical and ultrasonography (US) examination, in which galectin-3 positive nodules were directly referred to surgery whereas galectin-3 negative lesions were considered for clinical and US long-term follow-up. A cohort of 331 patients, bearing 340 thyroid Thy-3 nodules, was enrolled and subjected to galectin-3 expression analysis. A total of 256 galectin-3 negative nodules were directed to periodical clinical and US examination, while 84 galectin-3 positive cases were referred to surgery. Excluding 63 dropout patients plus 15 patients that were operated because of clinical reasons the remaining 176 galectin-3 negative nodules were followed with clinical and US examination for an average period of 31 months. During the follow-up, the volume of galectin-3 negative nodules was unchanged in 85 cases (48 %), reduced in 47 (27 %), and increased in 44 (25 %). Based on combined clinical features and US follow-up results, a total of 36 out of 191 galectin-3 negative nodules (19 %) were referred to surgery, with a final histological finding of 28 benign lesions, three follicular tumor of uncertain malignant potential (FT-UMP), and five malignant lesions, corresponding to a 7 % false negative rate. In the group of 84 galectin-3 positive nodules, we detected 65 thyroid cancers with a prevalence of 77 %, 12 FT-UMPs, and 7 false positive lesions, corresponding to a 4 % false positive rate. A total of 150 patients were not operated and are still under clinical and US monitoring while surgery was performed in 118 patients with a final 70 thyroid cancers diagnosed, corresponding to a 59 % prevalence of malignancy detected at surgery and to a 26 % prevalence of malignancy among the entire Thy-3 nodule population. Galectin-3 ThyroTest is an easy and cheap diagnostic procedure that integrates conventional fine-needle-aspiration cytology, reduces the number of unnecessary thyroidectomies and increases the rate of malignancy at surgery. Clinical and US follow-up of galectin-3 negative lesions allows to further reduce false negative cases.

Investigation of VOCs associated with different characteristics of breast cancer cells.

The efficacy of breath volatile organic compounds (VOCs) analysis for the screening of patients bearing breast cancer lesions has been demonstrated by using gas chromatography and artificial olfactory systems. On the other hand, in-vitro studies suggest that VOCs detection could also give important indications regarding molecular and tumorigenic characteristics of tumor cells. Aim of this study was to analyze VOCs in the headspace of breast cancer cell lines in order to ascertain the potentiality of VOCs signatures in giving information about these cells and set-up a new sensor system able to detect breast tumor-associated VOCs. We identified by Gas Chromatography-Mass Spectrometry analysis a VOCs signature that discriminates breast cancer cells for: i) transformed condition; ii) cell doubling time (CDT); iii) Estrogen and Progesterone Receptors (ER, PgR) expression, and HER2 overexpression. Moreover, the signals obtained from a temperature modulated metal oxide semiconductor gas sensor can be classified in order to recognize VOCs signatures associated with breast cancer cells, CDT and ER expression. Our results demonstrate that VOCs analysis could give clinically relevant information about proliferative and molecular features of breast cancer cells and pose the basis for the optimization of a low-cost diagnostic device to be used for tumors characterization.

A novel method based on learning automata for automatic lesion detection in breast magnetic resonance imaging.

Breast cancer continues to be a significant public health problem in the world. Early detection is the key for improving breast cancer prognosis. In this way, magnetic resonance imaging (MRI) is emerging as a powerful tool for the detection of breast cancer. Breast MRI presently has two major challenges. First, its specificity is relatively poor, and it detects many false positives (FPs). Second, the method involves acquiring several high-resolution image volumes before, during, and after the injection of a contrast agent. The large volume of data makes the task of interpretation by the radiologist both complex and time-consuming. These challenges have led to the development of the computer-aided detection systems to improve the efficiency and accuracy of the interpretation process. Detection of suspicious regions of interests (ROIs) is a critical preprocessing step in dynamic contrast-enhanced (DCE)-MRI data evaluation. In this regard, this paper introduces a new automatic method to detect the suspicious ROIs for breast DCE-MRI based on region growing. The results indicate that the proposed method is thoroughly able to identify suspicious regions (accuracy of 75.39 ± 3.37 on PIDER breast MRI dataset). Furthermore, the FP per image in this method is averagely 7.92, which shows considerable improvement comparing to other methods like ROI hunter.

Association between total duration of breastfeeding and iron deficiency.

OBJECTIVE: To determine whether there is an association between the total breastfeeding duration and iron stores, iron deficiency, and iron deficiency anemia in healthy urban children. METHODS: A cross-sectional study of healthy children, aged 1 to 6 years, seen for primary health care between December 2008 and July 2011 was conducted through the TARGet Kids! practice-based research network. Univariate and adjusted regression analyses were used to evaluate an association between total breastfeeding duration and serum ferritin, iron deficiency, and iron deficiency anemia. RESULTS: Included were 1647 healthy children (median age 36 months) with survey, anthropometric, and laboratory data. An association was found between increasing duration of breastfeeding and lower serum ferritin (P = .0015). Adjusted logistic regression analysis revealed the odds of iron deficiency increased by 4.8% (95% confidence interval: 2%-8%) for each additional month of breastfeeding. Exploratory analysis suggested an increasing cumulative probability of iron deficiency with longer total breastfeeding duration with an adjusted odds ratio of 1.71 (95% confidence interval: 1.05-2.79) for iron deficiency in children breastfed over versus under 12 months of age. The relationship between total breastfeeding duration and iron deficiency anemia did not meet statistical significance. CONCLUSIONS: Increased total breastfeeding duration is associated with decreased iron stores, a clinically important association warranting additional investigation.

Hyperproliferation in nasal polyposis tissues is not associated with somatic genomic instability.

BACKGROUND: Nasal polyps (NPs) are abnormal lesions that arise from any portion of the nasal mucosa or paranasal sinuses within the nasal cavities. They are characterized by the formation of inflammatory swellings of unstable respiratory mucosa, which protrude into the nasal cavity. The causes and the pathogenesis of NP development are not well understood. The current and principal hypothesis is that NPs result from allergy and inflammation, which cause an unstable respiratory mucosa with increased epithelial cell proliferation and epithelial morphologic changes. OBJECTIVE: To understand if epithelial cell hyperproliferation can lead to acquired genomic instability and if nasal polyposis is a consequence of acquired chromosomal alterations in hyperproliferative nasal epithelia. MATERIALS AND METHODS: To test this hypothesis and to perform a survey of chromosomal aberrations in nasal polyps, we applied array comparative genome hybridization (aCGH; 1 Mb resolution, made of 2464 bacterial artificial chromosome (BAC), P1 derived artificial chromosome (PAC), and P1 clones spanning the whole human genome) to deoxyribonucleic acid (DNA) obtained from the NPs of nine patients. The patients recruited in this study had been analyzed for Ki-67 expression using the MIB-1 antibody as a marker of proliferation and were chosen to represent a wide range of hyperproliferative status. RESULTS: After data analysis, no chromosomal aberrations were detected by aCGH. CONCLUSIONS: Our data do not support the hypothesis that nasal polyposis is a consequence of acquired chromosomal alterations in hyperproliferative nasal epithelia.