RNA-based strategies for cancer therapy: in silico design and evaluation of ASOs for targeted exon skipping

Precision medicine in oncology has made significant progress in recent years by approving drugs that target specific genetic mutations. However, many cancer driver genes remain challenging to pharmacologically target ("undruggable"). To tackle this issue, RNA-based methods like antisense oligonucleotides (ASOs) that induce targeted exon skipping (ES) could provide a promising alternative. In this work, a comprehensive computational procedure is presented, focused on the development of ES-based cancer treatments. The procedure aims to produce specific protein variants, including inactive oncogenes and partially restored tumor suppressors. This novel computational procedure encompasses target-exon selection, in silico prediction of ES products, and identification of the best candidate ASOs for further experimental validation. The method was effectively employed on extensively mutated cancer genes, prioritized according to their suitability for ES-based interventions. Notable genes, such as NRAS and VHL, exhibited potential for this therapeutic approach, as specific target exons were identified and optimal ASO sequences were devised to induce their skipping. To the best of our knowledge, this is the first computational procedure that encompasses all necessary steps for designing ASO sequences tailored for targeted ES, contributing with a versatile and innovative approach to addressing the challenges posed by undruggable cancer driver genes and beyond

An orthotopic xenograft model of human nonseminomatous germ cell tumour

We have established the first example of an orthotopic xenograft model of human nonseminomatous germ cell tumour (NSGCT). This reproducible model exhibits many clinically relevant features including metastases to the retroperitoneal lymph nodes and lungs, making it an ideal tool for research into the development and progression of testicular germ cell tumours. © 2001 Cancer Research Campaign http://www.bjcancer.co

Hygienic and dietetic guidelines for implant-supported full-arch immediate loading prostheses

Introduction: Proper oral hygiene and diet are important considerations for success in implant prosthodontics. However, detailed hygienic and dietetic guidelines for patients rehabilitated with implant-supported, immediate loading prostheses are lacking in the literature. Methods: The authors have developed a dietary and hygienic protocol for patients rehabilitated with implant-supported, full-arch, immediate loading prostheses in order to avoid occlusal overloads during osseointegration and optimize healing. Results: The dietary and hygienic guidelines provided in this paper emphasize the importance of maintaining proper oral hygiene and diet to support osseointegration and soft tissue healing during postsurgery healing periods. Conclusions: The protocol presented has been an effective instrument to obtain and maintain osseointegration in patients rehabilitated with full-arch, immediate loading prostheses

Diagnosis of right bundle branch block: a concordance study

Bundle branch block; ConcordanceBloqueig de branca; ConcordançaBloqueo de rama; ConcordanciaBACKGROUND: Right bundle branch block is one of the most common electrocardiographic abnormalities. Most cases of right bundle branch block are detected in asymptomatic patients in primary care, so a correct interpretation of electrocardiograms (ECGs) at this level is necessary. The objective of this research is to determine the degree of concordance in the diagnosis of incomplete and complete right bundle branch block between four primary care researchers and a cardiologist. METHODS: The research design is a retrospective cohort study of patients over 18 years of ages of patients over 18 years of ages who underwent an ECG for any reason and were diagnosed with right bundle branch block by their physician. The physicians participating, 4 primary care researchers and a cardiologist were specialized in interpreting electrocardiographic records. The diagnosis of incomplete and complete right bundle branch block was recorded and other secondary variables were analysed. In case of diagnostic discordance between the researchers, the ECGs were reviewed by an expert cardiologist, who interpreted them, established the diagnosis and analysed the possible causes for the discrepancy. RESULTS: We studied 160 patients diagnosed with right bundle branch block by their general practise. The patients had a mean age of 64.8 years and 54% of them were men. The concordance in the diagnosis of incomplete right bundle branch block showed a Fleiss' kappa index (k) of 0.71 among the five researchers and of 0.85 among only the primary care researchers. The k for complete right bundle branch block was 0.93 among the five researchers and 0.96 among only the primary care researchers. CONCLUSION: The interobserver agreement in the diagnosis of right bundle branch block performed by physicians specialized in ECG interpretation (primary care physicians and a cardiologist) was very good. The variability was greater for the diagnosis of incomplete right bundle branch block

Temporal dynamics of soil fungal communities after partial and total clear-cutting in a managed Pinus sylvestris stand

Forest management aimed to maximize timber production might impact soil fungi, especially those symbiotically associated to tree roots. In this study, we analyse the temporal dynamics of soil fungi along five sampling years after tree removal in a managed Pinus sylvestris stand in northern Spain, where timber production is combined with regular mushroom harvesting. Two management methods were tested: total and partial clear-cutting leaving retention trees for seedling regeneration. Undisturbed, uncut plots were also included in the experiment as a control treatment. The whole fungal community (phylotypes and ecological guilds) were analysed by high-throughput Illumina MiSeq sequencing of fungal ITS1 amplicons. We hypothesized that (1) ectomycorrhizal fungal communities will decrease after both clear-cutting treatments with a concurrent increase in the abundance of saprotrophs, (2) the abundance and diversity of the ectomycorrhizal guild will be more preserved in partially clear-cut than in total clear-cut plots, and (3) the overall fungal diversity will decrease in the cut plots leading to major losses of ectomycorrhizal species. Our results show that soil fungal composition changed across the five years after clear-cutting by decreasing ectomycorrhizal fungi and increasing saprotrophs. However, these changes did not significantly affect fungal diversity and there were taxa-specific responses to tree harvest treatments. Boletus edulis, the most abundant ectomycorrhizal species fruiting in the study area and a valuable local non-forest resource, was negatively affected by either clear-cutting treatments. Soil fungal community composition in partially clear-cut areas was not different from that of total clear-cut areas. Our results indicate a strong effect of tree harvest on the relative abundance of ectomycorrhizal fungi along the first years after clear-cutting. However, levels of fungal diversity were comparable to the undisturbed forest, thus suggesting a potential further recovery of ectomycorrhizal fungi through the colonization of the regenerated seedlings.info:eu-repo/semantics/acceptedVersio

Nanocomposite MFI-alumina and FAU-alumina Membranes: Synthesis, Characterization and Application to Paraffin Separation and CO2 Capture

Rouleau, L. Pirngruber, G. Guillou, F. Barrere-Tricca, C. Omegna, A. Valtchev, V. Pera-Titus, M. Miachon, S. Dalmon, J. A.International audienceIn this work, we report the preparation of thermally and mechanically resistant high-surface (24-cm2) nanocomposite MFI-alumina and FAUalumina membranes by pore-plugging synthesis inside the macropores of α-alumina multilayered tubular supports. The MFI membranes were prepared from a clear solution precursor mixture being able to easily penetrate into the pores of the support. The MFI membranes were evaluated in the separation of n-/i-butane mixtures. The synthesis reliability was improved by mild stirring. The most selective MFI membranes were obtained for supports with mean pore sizes of 0.2 and 0.8 μm. The MFI effective thickness could be reduced to less than 10 μm by impregnating the support with water prior to synthesis and by diluting the synthesis mixture. The best MFI membrane offered an excellent tradeoff between selectivity and permeance at 448 K, with separation factors for equimolar n-butane/i-butane mixtures up to 18 and n-butane mixture permeances as high as 0.7 μmol$\cdot$s-1$\cdot$m-2$\cdot$Pa-1.Furthermore, a novel nanocomposite FAU membrane architecture has been obtained by an original synthesis route including in situ seeding using a cold gel-like precursor mixture, followed by growth of the FAU material by hydrothermal synthesis in two steps using a clear solution of low viscosity. This new membrane showed interesting performance in the separation of an equimolar CO2/N2 mixture at 323 K, with CO2/N2 separation factors and mixture CO2 permeances up to 12 and 0.4 μmol$\cdot$s-1$\cdot$m-2$\cdot$Pa-1,respectively

Neurological assessment of newborns with spinal muscular atrophy identified through neonatal screening

The possibility to identify patients with spinal muscular atrophy through neonatal screenings has highlighted the need for clinical assessments that may systematically evaluate the possible presence of early neurological signs. The aim of this study was to use the Hammersmith Neonatal Neurological Examination (HNNE) and a module specifically designed for floppy infants to assess the possible variability of neurological findings in infants identified through neonatal screening. The infants included in this study were identified as part of a pilot study exploring neonatal screening in two Italian regions. A neurological examination was performed using the HNNE and an additional module developed for the assessment of floppy infants. Seventeen infants were identified through the screening. One patient had 1 SMN2 copy, 9 had 2 copies, 3 had 3, and 4 had more than 3 copies. Nine of the 17 infants (53%) had completely normal results on both scales, 3 had minimal signs, and the other 5 had more obvious clinical signs. The number of SMN2 copies was related to the presence of abnormal neurological signs (p = 0.036) but two SMN2 copies were associated with variable clinical signs as they were found in some infants with respectively normal examination or obvious severe early signs. Conclusions: Our results suggest that the combination of both scales increases the possibility to detect neonatal neurological signs and to define different early patterns of involvement also identifying paucisymptomatic patients.What is Known:• The use of new therapeutic options in presymptomatic SMA patients leads to a dramatic reduction of the onset and severity of the diesease.• The already existing tools commonly used in Type I SMA (HINE and CHOP-intend) may not be suitable to identify minor neurological signs in the neonatal period.What is New:• Combining the HNNE and the floppy infant module, we were able to identify early neurological signs in SMA infants identified through newborn screening and may help to predict the individual therapeutic outcome of these patients.• Iinfants with 2 SMN2 copies identified through the screening had a more variable neonatal examination compared to those with three or more copies, in agreement with similar findings in older infants

Sex chromosome positions in human interphase nuclei as studied by in situ hybridization with chromosome specific DNA probes

Two cloned repetitive DNA probes, pXBR and CY1, which bind preferentially to specific regions of the human X and Y chromosome, respectively, were used to study the distribution of the sex chromosomes in human lymphocyte nuclei by in situ hybridization experiments. Our data indicate a large variability of the distances between the sex chromosomes in male and female interphase nuclei. However, the mean distance observed between the X and Y chromosome was significantly smaller than the mean distance observed between the two X-chromosomes. The distribution of distances determined experimentally is compared with three model distributions of distances, and the question of a non-random distribution of sex chromosomes is discussed. Mathematical details of these model distributions are provided in an Appendix to this paper. In the case of a human translocation chromosome (XqterXp22.2::Yq11Y qter) contained in the Chinese hamster x human hybrid cell line 445 x 393, the binding sites of pXBR and CY1 were found close to each other in most interphase nuclei. These data demonstrate the potential use of chromosome-specific repetitive DNA probes to study the problem of interphase chromosome topography

Genome-wide identification of direct HBx genomic targets

Background: The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modulate histone post-translational modifications and to regulate viral cccDNA transcription and cellular gene expression. Aiming to identify genes and non-coding RNAs (ncRNAs) directly targeted by HBx, we performed a chromatin immunoprecipitation sequencing (ChIP-Seq) to analyse HBV recruitment on host cell chromatin in cells replicating HBV. Results: ChIP-Seq high throughput sequencing of HBx-bound fragments was used to obtain a high-resolution, unbiased, mapping of HBx binding sites across the genome in HBV replicating cells. Protein-coding genes and ncRNAs involved in cell metabolism, chromatin dynamics and cancer were enriched among HBx targets together with genes/ncRNAs known to modulate HBV replication. The direct transcriptional activation of genes/miRNAs that potentiate endocytosis (Ras-related in brain (RAB) GTPase family) and autophagy (autophagy related (ATG) genes, beclin-1, miR-33a) and the transcriptional repression of microRNAs (miR-138, miR-224, miR-576, miR-596) that directly target the HBV pgRNA and would inhibit HBV replication, contribute to HBx-mediated increase of HBV replication. Conclusions: Our ChIP-Seq analysis of HBx genome wide chromatin recruitment defined the repertoire of genes and ncRNAs directly targeted by HBx and led to the identification of new mechanisms by which HBx positively regulates cccDNA transcription and HBV replication