Environmental Genomics: A Tale of Two Fishes

The influence of the environment on two congeneric fishes, Gillichthys mirabilis and Gillichthys seta, that live in the Gulf of California at temperatures of 10-25 degrees C, and up to 42-44 degrees C, respectively, was addressed by analyzing their genomes. Compared with G. mirabilis, G. seta showed some striking features. Substitution rates in the mitochondrial genes were found to be extremely fast, in fact faster than in noncoding control regions (D-loops), from which a divergence time of less than 0.66-0.75 Mya could be estimated. In the nuclear genome, 1) both AT --> GC/GC --> AT and transversion: transition ratios in coding sequences (CDSs) were relatively high; moreover, the ratios of nonsynonymous/synonymous changes (Ka/Ks) suggested that some genes were under positive selection; 2) DNA methylation showed a very significant decrease; and 3) a GC-rich minisatellite underwent a 4-fold amplification in the gene-rich regions. All these observations clearly indicate that the environment (temperature and the accompanying hypoxia) can rapidly mold the nuclear as well as the mitochondrial genome. The stabilization of gene-rich regions by the amplification of the GC-rich minisatellite and by the GC increase in nuclear CDSs is of special interest because it provides a model for the formation of the GC-rich and gene-rich isochores of the genomes of mammals and birds

RELATIONSHIP BETWEEN POLYMORPHISMS OF TAS2R38 BITTER TASTE RECEPTOR AND CHRONIC UPPER AIRWAY INFECTIONS

1Department of Neuroscience, ENT Section, “Federico II” University of Naples, Italy 2Department of Translational Medical Sciences, European Laboratory for Food Induced Diseases, Napoli, Italy The presence of taste receptors in extra-oral tissues may suggest additional roles apart from taste perception. Recently, an increasing number of reports demonstrated that the bitter taste G-protein coupled receptors family T2R, expressed in ciliated epithelial cells of the respiratory tract, are able to detect bacterial products and to stimulate innate immune defense against pathogens. Most microbial agents, secretes chemical signals known as quorum-sensing molecules that regulate the expression of genes involved in biofilm formation, virulence and other vital processes for microorganisms. Among the quorum-sensing molecules, the AHLs produced by P. aeruginosa, activate the receptor for bitter T2R38 expressed in ciliated epithelial cells of the respiratory tract, whereas mutants of P. aeruginosa lacking the AHL are not able to activate it. The activation of the receptor results in an increase of the Ca2+ flow and the ciliary beat frequency, as well as stimulating the production of NO which acts as a bactericide against the pathogen. The Caucasian population express three common polymorphisms (Pro49Ala, Ala262Val, Val296Ile) for TAS2R38 that lead to two major haplotypes PAV and AVI. The expression of either haplotype gives respectively 2 forms of receptors ̶ functional or non-functional ̶ i.e. unable to respond to specific agonists such phenylthiocarbamide and propylthiouracil (PROP). The two haplotypes PAV and AVI segregate into two major phenotypic classes: the "functional", sensitive to bitter, are homo- or heterozygous for the allele PAV, the "non-functional", are homozygous for the allele AVI. The genetic variations of the receptor TAS2R38 that affect sensitivity to bitter taste can help determine individual differences in susceptibility to bacterial infections of the respiratory tract allowing to plan a “target therapy”. Cellular cultures from homozygous PAV/PAV individuals showed a more effective NO production, mucociliary clearance and bactericide effect than cultures from AVI/PAV or AVI/AVI individuals. As a consequence it is reasonable to assume that patients with genotype AVI/PAV or AVI/AVI are at greater risk of contracting infections from gram-negative, compared with homozygous PAV. Some authors have studied the correlation between genotype and microbiological results TAS2R38 tissue of respiratory mucosa. The result of this analysis proved to be very interesting, because it showed a significant difference in the frequency of non-functional (AVI) than functional (PAV) among patients whose cultures were positive for Gram-negative bacteria, including P. aeruginosa. The aim of the study was to characterize phenotypically the sensitivity to PROP and the receptor polymorphisms of TAS2R38, in patients with chronic or recurrent infections of the upper respiratory tract to identify high risk patients. The identification of high-risk individuals would allow to draw up protocols for specific follow-up and appropriate “target therapy”

Head and Neck squamocellular carcinomas: E-cadherin and Keratin 5 as biomolecular markers

E- Cadherin is a transmembranar protein that plays an important role in the cellular adhesion and insure the connection of the tissue cells; it is present in the epithelial cells and its aberrant expression is correlated with different kinds of head and neck squamocellular carcinoma. Keratin 5 (K5) is present in the basal layer of a stratified squamous keratinized and non keratinized epithe-lium. The purpose of the present study was to identify the expression particularities of E-cadherin and Keratin 5 in rapport with the localization and the differentiation of various head and neck squamocellular carcinomas (larynx, pharynx, hard palate, tongue, submandibular, lip, gingival sulcus, nasal pyramid, maxillary, zygomatic). Immunoreactions for E-cadherin in the tumoral cells were examined according to the this score: 0 (0% positive cells), 1 (30%). The presence of maximum score (value 3) of E-cadherin was found in well-differentiated squamocellular carcinomas of laryngeal, tongue, lip, nasal pyramid, zygomatic area origin. A lower value of the score was present in the less differentiated histopathological type. The role of E-cadherin in the squamocellular carcinomas is far from being clarified. It seems that the trials to estimate a prognosis in this clinical entity should include a combination between the molecular markers, the histopathological data and clinical parameters. K5 expression was observed in all squamocellular carcinomas included in the present study with scores between 1 and 3. For well and moderately differentiated histopathological types, a maximum score of 3 was recorded for all of the cases, not including the laryngeal area, which presented a score of 2. The following scores were identified in the regions of the poorly differentiated carcinomas: Jaw, 3; gingival sulcus, 2; and tongue and submandibular area, 1. The present study confirms the role of K5 in the definition of the differentiation of squamocellular carcinoma of head and neck revealing a differential expression depending on the anatomic site of the primary tumor. These observations may aid with an improved stratification of head and neck squamocellular carcinoma, thus improving the diagnosis and treatment strategies for this type of cancer

The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions

We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1 to 3 hours at 37°C; (ii) this induced apoptosis (possibly because of oxygen deprivation), as shown by the electrophoretic nucleosomal ladder produced by DNA preparations; (iii) low molecular-weight DNA fragments (∼200 bp) were cloned, sequenced, and shown to derive predominantly from genes and surrounding 100 kb regions; (iv) a few hundred cuts were produced, very often involving the same chromosomal sites; (v) at comparable DNA degradation levels, micrococcal nuclease (MNase) also showed a general preference for genes and surrounding regions, but MNase cuts were located at sites that were quite distinct from, and less specific than, those cut by apoptosis. In conclusion, the approach presented here, which is the mildest and least intrusive approach, identifies a preferred accessibility landscape in interphase chromatin

Therapeutic homology-independent targeted integration in retina and liver

Challenges to the widespread application of gene therapy with adeno-associated viral (AAV) vectors include dominant conditions due to gain-of-function mutations which require allele-specific knockout, as well as long-term transgene expression from proliferating tissues, which is hampered by AAV DNA episomal status. To overcome these challenges, we used CRISPR/Cas9-mediated homology-independent targeted integration (HITI) in retina and liver as paradigmatic target tissues. We show that AAV-HITI targets photoreceptors of both mouse and pig retina, and this results in significant improvements to retinal morphology and function in mice with autosomal dominant retinitis pigmentosa. In addition, we show that neonatal systemic AAV-HITI delivery achieves stable liver transgene expression and phenotypic improvement in a mouse model of a severe lysosomal storage disease. We also show that HITI applications predominantly result in on-target editing. These results lay the groundwork for the application of AAV-HITI for the treatment of diseases affecting various organs

Clinical features and outcomes of elderly hospitalised patients with chronic obstructive pulmonary disease, heart failure or both

Background and objective: Chronic obstructive pulmonary disease (COPD) and heart failure (HF) mutually increase the risk of being present in the same patient, especially if older. Whether or not this coexistence may be associated with a worse prognosis is debated. Therefore, employing data derived from the REPOSI register, we evaluated the clinical features and outcomes in a population of elderly patients admitted to internal medicine wards and having COPD, HF or COPD + HF. Methods: We measured socio-demographic and anthropometric characteristics, severity and prevalence of comorbidities, clinical and laboratory features during hospitalization, mood disorders, functional independence, drug prescriptions and discharge destination. The primary study outcome was the risk of death. Results: We considered 2,343 elderly hospitalized patients (median age 81 years), of whom 1,154 (49%) had COPD, 813 (35%) HF, and 376 (16%) COPD + HF. Patients with COPD + HF had different characteristics than those with COPD or HF, such as a higher prevalence of previous hospitalizations, comorbidities (especially chronic kidney disease), higher respiratory rate at admission and number of prescribed drugs. Patients with COPD + HF (hazard ratio HR 1.74, 95% confidence intervals CI 1.16-2.61) and patients with dementia (HR 1.75, 95% CI 1.06-2.90) had a higher risk of death at one year. The Kaplan-Meier curves showed a higher mortality risk in the group of patients with COPD + HF for all causes (p = 0.010), respiratory causes (p = 0.006), cardiovascular causes (p = 0.046) and respiratory plus cardiovascular causes (p = 0.009). Conclusion: In this real-life cohort of hospitalized elderly patients, the coexistence of COPD and HF significantly worsened prognosis at one year. This finding may help to better define the care needs of this population

Serum Albumin Is Inversely Associated With Portal Vein Thrombosis in Cirrhosis

We analyzed whether serum albumin is independently associated with portal vein thrombosis (PVT) in liver cirrhosis (LC) and if a biologic plausibility exists. This study was divided into three parts. In part 1 (retrospective analysis), 753 consecutive patients with LC with ultrasound-detected PVT were retrospectively analyzed. In part 2, 112 patients with LC and 56 matched controls were entered in the cross-sectional study. In part 3, 5 patients with cirrhosis were entered in the in vivo study and 4 healthy subjects (HSs) were entered in the in vitro study to explore if albumin may affect platelet activation by modulating oxidative stress. In the 753 patients with LC, the prevalence of PVT was 16.7%; logistic analysis showed that only age (odds ratio [OR], 1.024; P = 0.012) and serum albumin (OR, -0.422; P = 0.0001) significantly predicted patients with PVT. Analyzing the 112 patients with LC and controls, soluble clusters of differentiation (CD)40-ligand (P = 0.0238), soluble Nox2-derived peptide (sNox2-dp; P < 0.0001), and urinary excretion of isoprostanes (P = 0.0078) were higher in patients with LC. In LC, albumin was correlated with sCD4OL (Spearman's rank correlation coefficient [r(s)], -0.33; P < 0.001), sNox2-dp (r(s), -0.57; P < 0.0001), and urinary excretion of isoprostanes (r(s), -0.48; P < 0.0001) levels. The in vivo study showed a progressive decrease in platelet aggregation, sNox2-dp, and urinary 8-iso prostaglandin F2 alpha-III formation 2 hours and 3 days after albumin infusion. Finally, platelet aggregation, sNox2-dp, and isoprostane formation significantly decreased in platelets from HSs incubated with scalar concentrations of albumin. Conclusion: Low serum albumin in LC is associated with PVT, suggesting that albumin could be a modulator of the hemostatic system through interference with mechanisms regulating platelet activation

Antidiabetic Drug Prescription Pattern in Hospitalized Older Patients with Diabetes

Objective: To describe the prescription pattern of antidiabetic and cardiovascular drugs in a cohort of hospitalized older patients with diabetes. Methods: Patients with diabetes aged 65 years or older hospitalized in internal medicine and/or geriatric wards throughout Italy and enrolled in the REPOSI (REgistro POliterapuie SIMI—Società Italiana di Medicina Interna) registry from 2010 to 2019 and discharged alive were included. Results: Among 1703 patients with diabetes, 1433 (84.2%) were on treatment with at least one antidiabetic drug at hospital admission, mainly prescribed as monotherapy with insulin (28.3%) or metformin (19.2%). The proportion of treated patients decreased at discharge (N = 1309, 76.9%), with a significant reduction over time. Among those prescribed, the proportion of those with insulin alone increased over time (p = 0.0066), while the proportion of those prescribed sulfonylureas decreased (p < 0.0001). Among patients receiving antidiabetic therapy at discharge, 1063 (81.2%) were also prescribed cardiovascular drugs, mainly with an antihypertensive drug alone or in combination (N = 777, 73.1%). Conclusion: The management of older patients with diabetes in a hospital setting is often sub-optimal, as shown by the increasing trend in insulin at discharge, even if an overall improvement has been highlighted by the prevalent decrease in sulfonylureas prescription

The “Diabetes Comorbidome”: A Different Way for Health Professionals to Approach the Comorbidity Burden of Diabetes

(1) Background: The disease burden related to diabetes is increasing greatly, particularly in older subjects. A more comprehensive approach towards the assessment and management of diabetes’ comorbidities is necessary. The aim of this study was to implement our previous data identifying and representing the prevalence of the comorbidities, their association with mortality, and the strength of their relationship in hospitalized elderly patients with diabetes, developing, at the same time, a new graphic representation model of the comorbidome called “Diabetes Comorbidome”. (2) Methods: Data were collected from the RePoSi register. Comorbidities, socio-demographic data, severity and comorbidity indexes (Cumulative Illness rating Scale CIRS-SI and CIRS-CI), and functional status (Barthel Index), were recorded. Mortality rates were assessed in hospital and 3 and 12 months after discharge. (3) Results: Of the 4714 hospitalized elderly patients, 1378 had diabetes. The comorbidities distribution showed that arterial hypertension (57.1%), ischemic heart disease (31.4%), chronic renal failure (28.8%), atrial fibrillation (25.6%), and COPD (22.7%), were the more frequent in subjects with diabetes. The graphic comorbidome showed that the strongest predictors of death at in hospital and at the 3-month follow-up were dementia and cancer. At the 1-year follow-up, cancer was the first comorbidity independently associated with mortality. (4) Conclusions: The “Diabetes Comorbidome” represents the perfect instrument for determining the prevalence of comorbidities and the strength of their relationship with risk of death, as well as the need for an effective treatment for improving clinical outcomes