Cell type specific long non-coding RNA targets identified by integrative analysis of single-cell and bulk colorectal cancer transcriptomes.

Long non-coding RNAs (lncRNAs) represent an emerging class of genes which play significant and diverse roles in human cancers. Nevertheless, the functional repertoires of lncRNAs in cancer cell subtypes remains unknown since most studies are focused on protein coding genes. Here, we explored the contribution of lncRNAs in Colorectal Cancer (CRC) heterogeneity. We analyzed 49'436 single-cells from 29 CRC patients and showed that lncRNAs are significantly more cell type specific compared to protein-coding genes. We identified 996 lncRNAs strongly enriched in epithelial cells. Among these, 98 were found to be differentially expressed in tumor samples compared to normal controls, when integrating 270 bulk CRC profiles. We validated the upregulation of two of them (CASC19 and LINC00460) in CRC cell lines and showed their involvement in CRC proliferation by CRISPR-Cas9 knock down experiments. This study highlights a list of novel RNA targets for potential CRC therapeutics, substantiated through experimental validation.

Effect of biodegradable polymers upon grazing activity of the sea urchin Paracentrotus lividus (Lmk) revealed by morphological, histological and molecular analyses.

In the last years biodegradable polymers (BPs) were largely used as real opportunity to solve plastic pollution. Otherwise, their wide use in commercial products, such as packaging sector, is causing a new pollution alarm, mainly because few data reported about their behaviour in the environment and toxicity on marine organisms. Our previous results showed that embryos of the sea urchin Paracentrotus lividus (Lmk) exposed to poly(ε-caprolactone) (PCL), poly(3-hydroxybutyrate) (PHB) and poly(lactic acid) (PLA) showed delay of their development and morphological malformations, also affecting at the molecular levels the expression of several genes involved in different functional responses. In the present work for the first time, we tested the effects of five microplastics (MPs) obtained from BPs such as PBS, poly(butylene succinate), PBSA, poly(butylene succinate-co-butylene adipate), PCL, PHB and PLA, upon grazing activity of the sea urchin revealed by: i. histological analysis seeing at the gonadic tissues; ii. morphological analysis of the deriving embryos; iii. molecular analyses on these embryos to detect variations of the gene expression of eighty-seven genes involved in stress response, detoxification, skeletogenesis, differentiation and development. All these results will help in understanding how MP accumulated inside various organs in the adult sea urchins, and more in general in marine invertebrates, could represent risks for the marine environment.

Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates.

A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such 'cis-lncRNAs' are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistor's simple and conservative statistical models are compatible with functionally defined target gene maps generated by existing and future technologies. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Known cis-lncRNAs are correctly identified, including XIST, LINC00240 and UMLILO, and predictions are consistent across analysis methods, perturbation types and independent experiments. We detect cis-activity in a minority of lncRNAs, primarily involving activators over repressors. Cis-lncRNAs are detected by both RNA interference and antisense oligonucleotide perturbations. Mechanistically, cis-lncRNA transcripts are observed to physically associate with their target genes and are weakly enriched with enhancer elements. In summary, TransCistor establishes a quantitative foundation for cis-lncRNAs, opening a path to elucidating their molecular mechanisms and biological significance.

De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816).

The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.

Preliminary Results of a Double-Blind Randomized Controlled Trial Evaluating the Cardiometabolic Effects of Levothyroxine and Liothyronine Compared to Levothyroxine with Placebo in Athyreotic Low-Risk Thyroid Cancer Patients.

Background: Evidence is needed on the risks and benefits of combination therapy with levothyroxine (LT4)+liothyronine (LT3) for the treatment of hypothyroidism. Objective and Methods: We performed a randomized, double-blind placebo-controlled study to assess the effects of LT4+LT3 therapy versus LT4+placebo in a homogeneous group of athyreotic patients, without cardiovascular risk factors during long-term replacement monotherapy with LT4. The primary objective of the study was to assess the effects of combination LT4+LT3 therapy on heart rate, cardiac rhythm, and sensitive cardiovascular parameters of cardiac morphology and function by means of electrocardiography and Doppler echocardiography. The secondary objective of the study was to evaluate patient compliance, tolerability, and potential adverse events. Results: Thirty-eight patients with postsurgical hypothyroidism satisfying the inclusion criteria were selected from a group of 300 patients with low-risk thyroid cancer followed for a routine follow-up; they were randomized to receive LT4+LT3 or LT4+placebo. Twenty-four patients were evaluated after 1 year of treatment. All clinical and laboratory parameters were compared with the results obtained from 50 healthy euthyroid volunteers without comorbidities, matched for gender, age, physical activity, and lifestyle. Participants and clinicians remained blinded to the treatment allocation. After 1 year of combination therapy, a significant improvement in the diastolic function, evidenced by a significant reduction in the E/e' ratio (p = 0.046) and its positive trend over time, was observed in the LT4+LT3 group versus the LT4+placebo group. In addition, the univariate analyses showed a significant relationship between free triiodothyronine (fT3) levels (in pg/mL) with Δ of variation of the E/e' ratio in the LT4+LT3 group (standardized ß coefficient = 0.603 [confidence interval: 0.001-1.248], p = 0.050) after combination therapy. No adverse events including tachycardia, arrhythmias, atrial fibrillation, or other important events occurred between the first administration and the end of the study. Conclusions: In this preliminary report, combination treatment with LT4+LT3 induced favorable changes in cardiovascular parameters of diastolic function without any adverse cardiovascular events. Trial Registration: EUDRACT number: 2017-001261-25.

Right Ventricular Myocardial Involvement in Anderson-Fabry Disease at Diagnosis: Evaluation with Three-Dimensional Strain Imaging.

Background: Right ventricular (RV) involvement in Anderson-Fabry disease (AFD) is well known in the advanced stages of the disease RV hypertrophies, but little is known about the early involvement. The aim of our study was to assess RV function in AFD patients at diagnosis. Methods: A total of 23 AFD patients and 15 controls comparable for age and sex were recruited. A complete 2D standard echo with 3D volumetric and strain analysis of RV was performed. Results: Two patient populations, comparable for clinical baseline characteristics were considered. RV free wall thickness was significantly increased in the AFD group. No significant differences in standard RV indices (TAPSE, transverse diameter, tissue Doppler velocities of the lateral tricuspid annulus) were found. A 3D volumetric analysis showed reduced RV ejection fraction and lower values of longitudinal septal, free wall and global longitudinal strain (GLS) in AFD patients. RV free wall thickness significantly correlated with both free wall RV LS and RV GLS. In multiple linear regression analysis, RV free wall thickness was independently associated with RV GLS even after correction for age and heart rate. Conclusions: In AFD patients, 3D echocardiography allows for the identification of early subclinical functional impairment of RV. RV dysfunction is independently associated with RV hypertrophy.

Tumour mutations in long noncoding RNAs enhance cell fitness.

Long noncoding RNAs (lncRNAs) are linked to cancer via pathogenic changes in their expression levels. Yet, it remains unclear whether lncRNAs can also impact tumour cell fitness via function-altering somatic "driver" mutations. To search for such driver-lncRNAs, we here perform a genome-wide analysis of fitness-altering single nucleotide variants (SNVs) across a cohort of 2583 primary and 3527 metastatic tumours. The resulting 54 mutated and positively-selected lncRNAs are significantly enriched for previously-reported cancer genes and a range of clinical and genomic features. A number of these lncRNAs promote tumour cell proliferation when overexpressed in in vitro models. Our results also highlight a dense SNV hotspot in the widely-studied NEAT1 oncogene. To directly evaluate the functional significance of NEAT1 SNVs, we use in cellulo mutagenesis to introduce tumour-like mutations in the gene and observe a significant and reproducible increase in cell fitness, both in vitro and in a mouse model. Mechanistic studies reveal that SNVs remodel the NEAT1 ribonucleoprotein and boost subnuclear paraspeckles. In summary, this work demonstrates the utility of driver analysis for mapping cancer-promoting lncRNAs, and provides experimental evidence that somatic mutations can act through lncRNAs to enhance pathological cancer cell fitness.

Speckle tracking echocardiography in early disease stages: a therapy modifier?

Echocardiography has been included as a first-line tool in several international guidelines for the management of patients with various cardiac diseases. Beyond diagnosis, echocardiographic examination helps in characterizing the severity of the condition since the very first stages. In particular, the application of second-level techniques, speckle tracking echocardiography in particular, can also reveal a subclinical dysfunction, while the standard parameters are in the normality range. The present review describes the potentialities of advanced echocardiography in different settings, including arterial hypertension, atrial fibrillation, diastolic dysfunction, and oncological patients, thus opening up potential starting points for its application as a clinical routine changer.

SARS-CoV-2 Lysate Stimulation Impairs the Release of Platelet-like Particles and Megakaryopoiesis in the MEG-01 Cell Line.

SARS-CoV-2 infection causes a considerable inflammatory response coupled with impaired platelet reactivity, which can lead to platelet disorders recognized as negative prognostic factors in COVID-19 patients. The virus may cause thrombocytopenia or thrombocytosis during the different disease stages by destroying or activating platelets and influencing platelet production. While it is known that several viruses can impair megakaryopoiesis by generating an improper production and activation of platelets, the potential involvement of SARS-CoV-2 in affecting megakaryopoiesis is poorly understood. To this purpose, we explored, in vitro, the impact of SARS-CoV-2 stimulation in the MEG-01 cell line, a human megakaryoblastic leukemia cell line, considering its spontaneous capacity of releasing platelet-like particles (PLPs). We interrogated the effect of heat-inactivated SARS-CoV-2 lysate in the release of PLPs and activation from MEG-01, the signaling pathway influenced by SARS-CoV-2, and the functional effect on macrophagic skewing. The results highlight the potential influence of SARS-CoV-2 in the early stages of megakaryopoiesis by enhancing the production and activation of platelets, very likely due to the impairment of STATs signaling and AMPK activity. Overall, these findings provide new insight into the role of SARS-CoV-2 in affecting megakaryocyte-platelet compartment, possibly unlocking another avenue by which SARS-CoV-2 moves.

The "Bald Disease" of the Sea Urchin Paracentrotus lividus: Pathogenicity, Molecular Identification of the Causative Agent and Therapeutic Approach.

In recent decades, various species of Mediterranean sea urchins, including Paracentrotus lividus, have been subject to widespread seasonal episodes of mass mortality whose causative agents are still unclear. In particular, P. lividus is subject to late winter events of mortality, due to a disease manifested by a massive loss of spines and the presence of greenish amorphous material on the tests (i.e., the sea urchin skeleton consisting of spongeous calcite). Documented mortality events show a seasonal epidemic diffusion and might produce economic losses also in aquaculture facilities, besides the environmental constraints to its diffusion. We collected individuals showing conspicuous lesions on the body surface and reared them in recirculated aquaria. Samples of external mucous were collected along with coelomic liquids and cultured to isolate bacterial and fungal strains, further submitted to molecular identification through the amplification of prokaryotic 16S rDNA. In addition, pools of infected sea urchins were reared in recirculated tanks after short baths in a formulated therapeutic compound and their survival rates were compared to non-treated individuals for variable periods. Here, we aimed at a redescription of the etiopathogenetic nature of the parasites and tested the efficacy of a possible treatment, to be proposed for aquaculture purposes.

Bioactive Molecules from Marine Diatoms and Their Value for the Nutraceutical Industry.

The search for novel sources of nutrients is among the basic goals for achievement of sustainable progress. In this context, microalgae are relevant organisms, being rich in high-value compounds and able to grow in open ponds or photobioreactors, thus enabling profitable exploitation of aquatic resources. Microalgae, a huge taxon containing photosynthetic microorganisms living in freshwater, as well as in brackish and marine waters, typically unicellular and eukaryotic, include green algae (Chlorophyceae), red algae (Rhodophyceae), brown algae (Phaeophyceae) and diatoms (Bacillariophyceae). In recent decades, diatoms have been considered the most sustainable sources of nutrients for humans with respect to other microalgae. This review focuses on studies exploring their bio-pharmacological activities when relevant for human disease prevention and/or treatment. In addition, we considered diatoms and their extracts (or purified compounds) when relevant for specific nutraceutical applications.

Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis.

The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.

Bedside Ultrasound for Hemodynamic Monitoring in Cardiac Intensive Care Unit.

Thanks to the advances in medical therapy and assist devices, the management of patients hospitalized in cardiac intensive care unit (CICU) is becoming increasingly challenging. In fact, Patients in the cardiac intensive care unit are frequently characterized by dynamic and variable diseases, which may evolve into several clinical phenotypes based on underlying etiology and its complexity. Therefore, the use of noninvasive tools in order to provide a personalized approach to these patients, according to their phenotype, may help to optimize the therapeutic strategies towards the underlying etiology. Echocardiography is the most reliable and feasible bedside method to assess cardiac function repeatedly, assisting clinicians not only in characterizing hemodynamic disorders, but also in helping to guide interventions and monitor response to therapies. Beyond basic echocardiographic parameters, its application has been expanded with the introduction of new tools such as lung ultrasound (LUS), the Venous Excess UltraSound (VexUS) grading system, and the assessment of pulmonary hypertension, which is fundamental to guide oxygen therapy. The aim of this review is to provide an overview on the current knowledge about the pathophysiology and echocardiographic evaluation of perfusion and congestion in patients in CICU, and to provide practical indications for the use of echocardiography across clinical phenotypes and new applications in CICU.

Gene Expression Detects the Factors Influencing the Reproductive Success and the Survival Rates of Paracentrotus lividus Offspring.

The increase in the demand for Paracentrotus lividus roe, a food delicacy, causes increased pressure on its wild stocks. In this scenario, aquaculture facilities will mitigate the effects of anthropogenic pressures on the wild stocks of P. lividus. Consequently, experimental studies should be conducted to enhance techniques to improve efficient aquaculture practices for these animals. Here, we for the first time performed molecular investigations on cultured sea urchins. We aimed at understanding if maternal influences may significantly impact the life of future offspring, and how the culture conditions may impact the development and growth of cultured specimens. Our findings demonstrate that the outcomes of in vitro fertilization of P. lividus are influenced by maternal influences, but these effects are largely determined by culture conditions. In fact, twenty-three genes involved in the response to stress and skeletogenesis, whose expressions were measured by Real Time qPCR, were differently expressed in sea urchins cultured in two experimental conditions, and the results were largely modified in offspring deriving from two groups of females. The findings herein reported will be critical to develop protocols for the larval culture of the most common sea urchin, both for research and industrial production purposes for mass production.

Non-Invasive Assessment of Right Ventricle to Arterial Coupling for Prognosis Stratification of Fibrotic Interstitial Lung Diseases.

Background: The coupling of the right ventricle (RV) to the pulmonary circulation is an indicator of RV performance that can be non-invasively estimated by echocardiography. There are no data about its use in patients affected by fibrotic interstitial lung diseases (f-ILD). Methods: Fifty f-ILD patients, including 27 cases with idiopathic pulmonary fibrosis (IPF) (M = 37; mean age 67 ± 7 years), were studied with standard and speckle-tracking echocardiography and compared with 30 age-matched healthy volunteers. The mean patient follow-up was 70 ± 4 months. Results: Fibrotic ILD patients had a larger right ventricle (RV) and worse diastolic function because the RV global longitudinal strain (GLS) was significantly lower and the systolic pulmonary artery pressure (sPAP) estimates were higher in comparison with those of controls. Conversely, tricuspid annular systolic excursion (TAPSE) did not differ between controls and patients. Median values of TAPSE/sPAP and RV GLS/sPAP were significantly reduced in f-ILD patients (p < 0.0001). Patients with an RV GLS/sPAP below the median value had a shorter survival time (61 vs. 74 months, p = 0.01); this parameter was an independent predictor of a worse outcome. Conclusion: Low estimates of RV GLS/sPAP are predictive of worse outcomes in f-ILD patients. RV coupling seems to be a promising surrogate biomarker of RV performance to discriminate the patient phenotype with significant management and prognosis implications.

Bioactive Compounds from Marine Sponges and Algae: Effects on Cancer Cell Metabolome and Chemical Structures.

Metabolomics represent the set of small organic molecules generally called metabolites, which are located within cells, tissues or organisms. This new "omic" technology, together with other similar technologies (genomics, transcriptomics and proteomics) is becoming a widely used tool in cancer research, aiming at the understanding of global biology systems in their physiologic or altered conditions. Cancer is among the most alarming human diseases and it causes a considerable number of deaths each year. Cancer research is one of the most important fields in life sciences. In fact, several scientific advances have been made in recent years, aiming to illuminate the metabolism of cancer cells, which is different from that of healthy cells, as suggested by Otto Warburg in the 1950s. Studies on sponges and algae revealed that these organisms are the main sources of the marine bioactive compounds involved in drug discovery for cancer treatment and prevention. In this review, we analyzed these two promising groups of marine organisms to focus on new metabolomics approaches for the study of metabolic changes in cancer cell lines treated with chemical extracts from sponges and algae, and for the classification of the chemical structures of bioactive compounds that may potentially prove useful for specific biotechnological applications.

Impact of Age and Heart Rate on Strain-Derived Myocardial Work in a Population of Healthy Subjects.

Background: The influence of age and gender on strain-imaging-derived myocardial work (MW) was recently investigated in healthy subjects. No information is available on the impact of heart rate (HR) on MW. Methods: 177 healthy subjects (47% men, mean age 42 years) underwent an echo-Doppler exam, including quantification of global longitudinal strain (GLS). Cuff blood pressure was used as a surrogate of left ventricular peak pressure to estimate global work index (GWI), global constructive work (GCW), global wasted work (GWW) and global work efficiency (GWE). Statistical analyses were performed according to age and HR tertiles. Results: GWW was higher in the third HR tertile, i.e., ≥74 bpm (74.7 ± 33.6 mmHg %) than in the first HR tertile (<66 bpm) (61.0 ± 32.5 mmHg %) (p < 0.02). In the pooled population, by adjusting for systolic blood pressure, GLS, E/e' ratio and left atrial volume index, age was independently associated with GCW (ß = 0.748) and GWI (ß = 0.685) (both p < 0.0001) and HR with GWW (ß = 0.212, p = 0.006) and GWE (ß = −0.204, p = 0.007). Conclusions: In healthy subjects age shows a mild influence on GCW. HR exerts an independent negative impact on GWW and GWE: the higher HR the greater wasted work and lower myocardial efficiency.

Gender Differences Associated with the Prognostic Value of BPIFB4 in COVID-19 Patients: A Single-Center Preliminary Study.

In the ongoing global COVID-19 pandemic, male sex is a risk factor for severe disease and death, and the reasons for these clinical discrepancies are largely unknown. The aim of this work is to study the influence of sex on the course of infection and the differences in prognostic markers between genders in COVID-19 patients. Our cohort consisted of 64 adult patients (n = 34 men and n = 30 women) with PCR-proven SARS-CoV-2 infection. Further, a group of patients was characterized by a different severity degree (n = 8 high- and n = 8 low-grade individuals for both male and female patients). As expected, the serum concentrations of LDH, fibrinogen, CRP, and leucocyte count in men were significantly higher than in females. When serum concentrations of the inflammatory cytokines, including IL-6, IL-2, IP-10 and IL-4 and chemokines like MCP-1, were measured with multiplex ELISA, no significant differences between male and female patients were found. In COVID-19 patients, we recently attributed a new prognostic value to BPIFB4, a natural defensin against dysregulation of the immune responses. Here, we clarify that BPIFB4 is inversely related to the disease degree in men but not in women. Indeed, higher levels of BPIFB4 characterized low-grade male patients compared to high-grade ones. On the contrary, no significant difference was reported between low-grade female patients and high-grade ones. In conclusion, the identification of BPIFB4 as a biomarker of mild/moderate disease and its sex-specific activity would open an interesting field for research to underpin gender-related susceptibility to the disease.

Organic extract of Geodia cydonium induces cell cycle block in human mesothelioma cells.

The serious side effects caused by chemotherapeutics and the development of cancer chemoresistance represent the most significant limitations in the treatment of cancer. Some alternative approaches have been developed in recent years, which are based on natural compounds, and have allowed important advances in cancer therapeutics. During the last 50 years, sponges have been considered a promising source of natural products from the marine environment, representing ~30% of all marine natural products. Among sponges, the Mediterranean species Geodia cydonium represents a potential source of these type of products with considerable biotechnological interest as pharmaceutical agents. The present study demonstrated the antiproliferative effect of an organic G. cydonium extract (GEOCYDO) against three human mesothelioma cell lines, MSTO-211H (MSTO), NCI-H2452 (NCI) and Ist-Mes2 (Mes2), which differ in their sensitivity (MSTO and NCI) and resistance (Mes2) to standard combined treatment with cisplatin and piroxicam. To this aim, the activity of the extract was evaluated by analyzing its effects on cell viability, cancer properties and cell cycle progression by means of colony formation assay, cell cycle analysis and protein expression analysis. The results revealed, in mesothelioma, this extract was able to reduce self-renewal, cell migration and it could induce cell cycle arrest in G0/G1 stage, thus blocking cell proliferation. In conclusion, to the best of our knowledge, the present results indicated for the first time that GEOCYDO can contain active compounds able to affect cell proliferation in mesothelioma, suggesting that it could be considered as a potential novel drug source for cancer treatment.