From Neuronal Differentiation of iPSCs to 3D Neural Organoids: Modeling of Neurodegenerative Diseases

In the last decade, the finding that somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) leads to a great improvement of research involving the use of differentiated stem cells as model of diseases. In the field of neurodegeneration, iPSC technology allowed to culture in vitro all the types of patient-specific neurons, not only helping the discovery of diseases’ etiopathology but also testing new drugs with a personalized medicine approach. Moreover, iPSCs can be combined with the 3D bioprinting technology, allowing physiological cell-to-cell interactions, given by a combination of several biomaterials, scaffolds, and cells. This technology combines bioplotter and biomaterials which can encapsulate several types of cells, e.g., iPSCs or differentiated neurons, to develop an innovative cellular model. iPSCs and 3D cell cultures’ technologies represent the first step to obtain a more reliable model, like an organoid to facilitate neurodegenerative diseases’ investigation

Both selective and neutral processes drive GC content evolution in the human genome

<p>Abstract</p> <p>Background</p> <p>Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait.</p> <p>Results</p> <p>Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Yet, a distinct contribution to GC content evolution is accounted for by a selective process. Accordingly, we searched for independent evidences that GC content distribution does not conform to neutral expectations. Indeed, after correcting for possible biases, we show that intron GC content and size display isochore-specific correlations.</p> <p>Conclusion</p> <p>We consider that the more parsimonious explanation for our results is that GC content is subjected to the action of both weak selection and BGC in the human genome with features such as nucleosome positioning or chromatin conformation possibly representing the final target of selective processes. This view might reconcile previous contrasting findings and add some theoretical background to recent evidences suggesting that GC content domains display different behaviors with respect to highly regulated biological processes such as developmentally-stage related gene expression and programmed replication timing during neural stem cell differentiation.</p

A complex selection signature at the human AVPR1B gene

<p>Abstract</p> <p>Background</p> <p>The vasopressin receptor type 1b (<it>AVPR1B</it>) is mainly expressed by pituitary corticotropes and it mediates the stimulatory effects of AVP on ACTH release; common <it>AVPR1B </it>haplotypes have been involved in mood and anxiety disorders in humans, while rodents lacking a functional receptor gene display behavioral defects and altered stress responses.</p> <p>Results</p> <p>Here we have analyzed the two exons of the gene and the data we present suggest that <it>AVPR1B </it>has been subjected to natural selection in humans. In particular, analysis of exon 2 strongly suggests the action of balancing selection in African populations and Europeans: the region displays high nucleotide diversity, an excess of intermediate-frequency alleles, a higher level of within-species diversity compared to interspecific divergence and a genealogy with common haplotypes separated by deep branches. This relatively unambiguous situation coexists with unusual features across exon 1, raising the possibility that a nonsynonymous variant (Gly191Arg) in this region has been subjected to directional selection.</p> <p>Conclusion</p> <p>Although the underlying selective pressure(s) remains to be identified, we consider this to be among the first documented examples of a gene involved in mood disorders and subjected to natural selection in humans; this observation might add support to the long-debated idea that depression/low mood might have played an adaptive role during human evolution.</p

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs

Altered immune system in frailty: Genetics and diet may influence inflammation.

Frailty is a complex geriatric syndrome associated with biological vulnerability to stressors and decreased physiological reserve. Its etiology and pathogenesis are not completely understood, although various causes and complex pathways have been proposed. Immune system alterations (immunosenescence and "InflammAging") have been suggested to contribute to frailty, but a precise causative role of such alterations remains to be determined. Genetic studies support the suggestion of immune system involvement in frailty: genetic variants in genes involved in immune system function have been associated with the syndrome. Interestingly, nutritional status, through its effects on cellular metabolism, may also influence the immune system, i.e. hormone and cytokine (mainly adipocytokine) levels, and immune cell populations and function, increasing inflammation and contributing to frailty. This review aims to discuss the role of immune system alterations in frailty, analyzing the role of genetic factors in frailty onset and the impact of diet on inflammation and, in turn, on frailty

HuD regulates SOD1 expression during oxidative stress in differentiated neuroblastoma cells and sporadic ALS motor cortex.

The neuronal RNA-binding protein (RBP) HuD plays an important role in brain development, synaptic plasticity and neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's (AD). Bioinformatics analysis of the human SOD1 mRNA 3' untranslated region (3'UTR) demonstrated the presence of HuD binding adenine-uridine (AU)-rich instability-conferring elements (AREs). Using differentiated SH-SY5Y cells along with brain tissues from sporadic amyotrophic lateral sclerosis (sALS) patients, we assessed HuD-dependent regulation of SOD1 mRNA. In vitro binding and mRNA decay assays demonstrate that HuD specifically binds to SOD1 ARE motifs promoting mRNA stabilization. In SH-SY5Y cells, overexpression of full-length HuD increased SOD1 mRNA and protein levels while a dominant negative form of the RBP downregulated its expression. HuD regulation of SOD1 mRNA was also found to be oxidative stress (OS)-dependent, as shown by the increased HuD binding and upregulation of this mRNA after H2O2 exposure. This treatment also induced a shift in alternative polyadenylation (APA) site usage in SOD1 3'UTR, increasing the levels of a long variant bearing HuD binding sites. The requirement of HuD for SOD1 upregulation during oxidative damage was validated using a specific siRNA that downregulated HuD protein levels to 36% and prevented upregulation of SOD1 and 91 additional genes. In the motor cortex from sALS patients, we found increases in SOD1 and HuD mRNAs and proteins, accompanied by greater HuD binding to this mRNA as confirmed by RNA-immunoprecipitation (RIP) assays. Altogether, our results suggest a role of HuD in the post-transcriptional regulation of SOD1 expression during ALS pathogenesis

Six Drivers to Face the XXI Century Challenges and Build the New Healthcare System: "La Salute in Movimento" Manifesto

: The aging of the population, the burden of chronic diseases, possible new pandemics are among the challenges for healthcare in the XXI century. To face them, technological innovations and the national recovery and resilience plan within the European Union can represent opportunities to implement changes and renovate the current healthcare system in Italy, in an effort to guarantee equal access to health services. Considering such scenario, a panel of Italian experts gathered in a multidisciplinary Think Tank to discuss possible design of concepts at the basis of a new healthcare system. These ideas were summarized in a manifesto with six drivers for change: vision, governance, competence, intelligence, humanity and relationship. Each driver was linked to an action to actively move toward a new healthcare system based on trust between science, citizens and institutions

The Relationship Between Blue-Fundus Autofluorescence and Optical Coherence Tomography in Eyes With Lamellar Macular Holes

PURPOSE. The purpose of this study was to evaluate the relationship between blue-fundus autofluorescence (B-FAF) and optical coherence tomography (OCT) in eyes with lamellar macular holes (LMHs). METHODS. this was a multicenter, observational case series. Ninety-two eyes with LMH associated with the standard epiretinal membrane (ERM) or lamellar hole-associated epiretinal proliferation (LHEP) were evaluated. The eyes must also present an area of increased autofluorescence on B-FAF. RESULTS. The ERM-alone group and the LHEP group differed with respect to the following variables: logarithm of the minimum angle of resolution best-corrected visual acuity (0.13 +/- 0.13 vs. 0.25 +/- 0.17;P < 0.001), central foveal thickness (218.74 +/- 52.4 mu m vs. 187.28 +/- 50.29 mu m;P = 0.008), FAF diameter (400.78 +/- 189.36 mu m vs. 503.37 +/- 214.25 mu m;P = 0.014), outer plexiform layer (OPL) diameter (382.10 +/- 157.34 mu m vs. 550.79 +/- 228.05 mu m;P = 0.0001), and disruption of external limiting membrane and ellipsoid zone, which was noted in only 1 and 3 eyes with ERM alone, respectively, and in 18 and 23 eyes with LHEP, respectively (P < 0.0001 for both observations). No difference was found for diameters measured at the level of the inner limiting membrane and schisis/cavitation. In both the ERM-alone group and the LHEP group, a strong correlation was found between the diameters measured on B-FAF and diameters measured at the OPL level on OCT images (P < 0.0001 for both groups). CONCLUSIONS. In eyes with LMHs, a strong correlation exists between the diameters of the holes measured with B-FAF and those measured at the OPL level with OCT. This may indicate that the loss or displacement of retinal cells containing macular pigment at the OPL level, specifically photoreceptors and/or Muller cells, is involved in this vitreomaculopathy