Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of ...lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified ≈2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown.
A number of microRNAs have been shown to regulate skeletal muscle development and differentiation. MicroRNA-222 is downregulated during myogenic differentiation and its overexpression leads to ...alteration of muscle differentiation process and specialized structures. By using RNA-induced silencing complex (RISC) pulldown followed by RNA sequencing, combined with in silico microRNA target prediction, we have identified two new targets of microRNA-222 involved in the regulation of myogenic differentiation, Ahnak and Rbm24. Specifically, the RNA-binding protein Rbm24 is a major regulator of muscle-specific alternative splicing and its downregulation by microRNA-222 results in defective exon inclusion impairing the production of muscle-specific isoforms of Coro6, Fxr1 and NACA transcripts. Reconstitution of normal levels of Rbm24 in cells overexpressing microRNA-222 rescues muscle-specific splicing. In conclusion, we have identified a new function of microRNA-222 leading to alteration of myogenic differentiation at the level of alternative splicing, and we provide evidence that this effect is mediated by Rbm24 protein.
Multiple Sclerosis (MS) is caused by a still unknown interplay between genetic and environmental factors. Epigenetics, including DNA methylation, represents a model for environmental factors to ...influence MS risk.
Twenty-six affected and 26 unaffected relatives from 8 MS multiplex families were analysed in a multicentric Italian study using MeDIP-Seq, followed by technical validation and biological replication in two additional families of differentially methylated regions (DMRs) using SeqCap Epi Choice Enrichment kit (Roche®).
Associations from MeDIP-Seq across families were combined with aggregation statistics, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypo-methylated regions, which point to NTM and BAI3 genes, and to 2 hyper-methylated regions in PIK3R1 and CAPN13.
These 4 novel regions contain genes of potential interest that need to be tested in larger cohorts of patients.
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•The 233 genetic loci associated with MS explain less than 40% of disease heritability, leaving a role to epigenetics in disease risk•We compared whole-genome methylation profiles in whole blood of affected and unaffected relatives of 8 multiplex MS families•We used MeDIP-seq and technical and biological replication in 2 additional families using a custom panel•Due to the heterogeneity of results in families, we adopted a method which leveraged consistency of signal across families•Filtering criteria lead to 2 hypo- and 2 hyper-methylated DMRs which relate to NTM, BAI3, PIK3R1 and CAPN13 genes•Replication of these signals is needed in additional cohort of MS patients
Limited amounts of reactive oxygen species are necessary for cell survival and signaling, but their excess causes oxidative stress. H(2)O(2) and other reactive oxygen species are formed as byproducts ...of several metabolic pathways, possibly including oxidative protein folding in the endoplasmic reticulum. B- to plasma-cell differentiation is characterized by a massive expansion of the endoplasmic reticulum, finalized to sustain abundant immunoglobulin (Ig) synthesis and secretion. The increased production of disulfide-rich Ig might cause oxidative stress that could serve signaling roles in the differentiation and lifespan control of antibody-secreting cells. Here we show that terminal B-cell differentiation entails redox stress, NF-E2-related factor-2 (Nrf2) activation, and reshaping of the antioxidant responses. However, plasma-cell differentiation was not dramatically impaired in peroxiredoxin (Prx)1-, 2-, 3-, and 4-, glutathione peroxidase 1-, and Nrf2-knockout splenocytes, suggesting redundancy and robustness in antioxidant systems. Endoplasmic reticulum (ER)-resident Prx4 increases dramatically during differentiation. In its absence, IgM secretion was not significantly affected, but more high-molecular-weight covalent complexes accumulated intracellularly. Our results suggest that the early intracellular production of H(2)O(2) facilitates B-cell proliferation and reveal a role for the Nrf2 pathway in the differentiation and function of IgM-secreting cells.
Gaia Data Release 3 Babusiaux, C.; Fabricius, C.; Khanna, S. ...
Astronomy and astrophysics (Berlin),
06/2023, Letnik:
674
Journal Article
Recenzirano
Odprti dostop
Context.
The third
Gaia
data release (DR3) provides a wealth of new data products. The early part of the release,
Gaia
EDR3, already provided the astrometric and photometric data for nearly two ...billion sources. The full release now adds improved parameters compared to
Gaia
DR2 for radial velocities, astrophysical parameters, variability information, light curves, and orbits for Solar System objects. The improvements are in terms of the number of sources, the variety of parameter information, precision, and accuracy. For the first time,
Gaia
DR3 also provides a sample of spectrophotometry and spectra obtained with the Radial Velocity Spectrometer, binary star solutions, and a characterisation of extragalactic object candidates.
Aims.
Before the publication of the catalogue, these data have undergone a dedicated transversal validation process. The aim of this paper is to highlight limitations of the data that were found during this process and to provide recommendations for the usage of the catalogue.
Methods.
The validation was obtained through a statistical analysis of the data, a confirmation of the internal consistency of different products, and a comparison of the values to external data or models.
Results.
Gaia
DR3 is a new major step forward in terms of the number, diversity, precision, and accuracy of the
Gaia
products. As always in such a large and complex catalogue, however, issues and limitations have also been found. Detailed examples of the scientific quality of the
Gaia
DR3 release can be found in the accompanying data-processing papers as well as in the performance verification papers. Here we focus only on the caveats that the user should be aware of to scientifically exploit the data.
Abstract
Background
BACE1-antisense RNA (BACE1-AS) is a lncRNA antisense to the Beta-Secretase-1 (BACE1) gene encoding a key enzyme in the production of the β-amyloid peptide, associated to ...Alzheimer's disease (AD). In a previous study1, we showed that the BACE1-AS/BACE1 axis is activated in heart failure (HF) patients, leading to β-amyloid accumulation in failing hearts. Accordingly, BACE1-AS expression in different cultured cardiac cell types induced the expression of BACE1 and β-amyloid that, in turn, triggered apoptosis. The mechanisms underlying BACE1-AS action are not yet fully elucidated. Indeed, current models based on miRNA “sponging” or “masking” inducing BACE1 post-transcriptional stabilization may not recapitulate all BACE1-AS functions.
Purpose
Our aim is to investigate the molecular mechanisms regulated by BACE1-AS in heart failure disease.
Methods
BACE1-AS-pull-down, followed by RNA-Seq, was used to identify RNAs interacting with BACE1-AS in AC16 cardiomyocytes. Moreover, accessible chromatin sites induced by BACE1-AS overexpression were assayed by ATAC-Seq.
Results
BACE1-AS pull-down identified 698 BACE1-AS interacting RNAs. Among these enriched transcripts, 69 were mapping to genomic enhancer regions that have been found to be hypo-methylated in AD brains2. After qPCR validation of the interactions identified by RNA-seq, the modulation of SEMA4D, ABCG1, GFRA2 and RIMBP2, which were under the control of a subset of these enhancers, was assayed upon BACE1-AS overexpression in cardiomyocytes. It was found that their expression was induced, supporting the functional interaction between BACE1-AS and the identified enhancer loci.
To gain further insight into BACE1-AS function in cardiomyocytes, accessible chromatin sites induced by BACE1-AS overexpression were assayed by ATAC-Seq. Interestingly, 17 regions identified by this approach overlapped with enhancers that are hypo-methylated in AD brains. One of the accessible chromatin sites was the locus encompassing RNF214/BACE1/BACE1-AS that maps to active enhancer marks, indicating that BACE1-AS may regulate the expression of BACE1 transcriptionally.
Conclusion
Collectively, these data suggest BACE1-AS as a node of shared disease-mechanisms between heart failure and AD.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Italian Ministry of Health
We attempt to identify the plasma membrane transporter involved in the uptake of 5'-deoxy-5-fluorouridine (5'-DFUR), an intermediate metabolite of capecitabine. This novel oral fluoropyrimidine is ...used in cancer treatments and is a direct precursor of the cytostatic agent 5'-fluorouracil. We also examine the role of the transporter in 5'-DFUR cytotoxicity. The human concentrative nucleoside transporter (hCNT1) was cloned from human fetal liver and expressed in Xenopus laevis oocytes. The two-electrode voltage-clamp technique was used to demonstrate that 5'-DFUR, but not capecitabine or 5'-FU, is an hCNT1 substrate. Then, hCNT1 was heterologously expressed in the mammalian cell line Chinese hamster ovary-K1. Functional expression was demonstrated by monitoring transport of radiolabeled substrates and by using a monospecific polyclonal antibody generated against the transporter. hCNT1-expressing cells were more sensitive to 5'-DFUR than vector-transfected or wild-type cells. The sensitivity of the three cell types to other agents such as cisplatin or 5'-FU was identical. In conclusion, this study shows that 1) the pharmacological profile of a nucleoside transporter can be determined by an electrophysiological approach; 2) the hCNT1 transporter is involved in 5'-DFUR uptake; and 3) hCNT1 expression may increase cell sensitivity to 5'-DFUR treatment. This study also reports for the first time the generation of an antibody against hCNT1, which may be useful in the elucidation of the relationship between hCNT1 expression and tumor response to capecitabine treatment.
Concentrative nucleoside transporter (CNT) 1, CNT3, equilibrative nucleoside transporter (ENT) 1, and, to a lesser extent, ENT2, appear to be the transporters responsible for ...2',2'-difluorodeoxycytidine (gemcitabine; Gemzar) uptake into cells. Gemcitabine is used currently in the treatment of pancreatic cancer, but the role of specific nucleoside carrier proteins in gemcitabine cytotoxicity has not been elucidated. Indeed, it is not known which nucleoside transporters are expressed in human pancreas.
In this study we have used four cell lines pancreatic neoplasia (NP)9, NP18, NP29, and NP31 derived from human pancreatic adenocarcinomas to monitor the pattern of nucleoside transporter expression, and we have heterologously expressed the high-affinity gemcitabine transporter human orthologue (h) CNT1 to monitor its role in drug responsiveness.
All of the cell lines take up gemcitabine mostly via the hENT1 transporter, which is expressed at high levels. Reverse transcription-PCR analysis of the other four cloned plasma membrane transporter mRNAs revealed very different expression patterns among NP cell lines, with apparent selective loss or decrease of hCNT mRNAs. NP cells transiently express hCNT1-type Na(+)-dependent nucleoside transport activity at low/medium cell density but not in confluent cultures. Cells expressing hCNT1 in a more constitutive manner were cloned after stable transfection of hCNT1. Despite high constitutive hENT1 activity, this increased sensitivity to gemcitabine.
In summary, human pancreatic adenocarcinoma cells overexpress hENT1, although they retain the ability to express a functional hCNT1 transporter, an isoform that confers sensitivity to gemcitabine.
Recent evidence indicates that hematopoietic stem and progenitor cells (HSPCs) can serve as vehicles for therapeutic molecular delivery to the brain by contributing to the turnover of resident ...myeloid cell populations. However, such engraftment needs to be fast and efficient to exert its therapeutic potential for diseases affecting the central nervous system. Moreover, the nature of the cells reconstituted after transplantation and whether they could comprise bona fide microglia remain to be assessed. We demonstrate that transplantation of HSPCs in the cerebral lateral ventricles provides rapid engraftment of morphologically, antigenically, and transcriptionally dependable microglia-like cells. We show that the cells comprised within the hematopoietic stem cell compartment and enriched early progenitor fractions generate this microglia-like population when injected in the brain ventricles in the absence of engraftment in the bone marrow. This delivery route has therapeutic relevance because it increases the delivery of therapeutic molecules to the brain, as shown in a humanized animal model of a prototypical lysosomal storage disease affecting the central nervous system.
To evalúate the mechanisms involved in macrophage proliferation and activation, we studied the regulation of the nucleoside transport systems. In murine bone marrow‐derived macrophages, the ...nucleo‐sides required for DNA and RNA synthesis are recruited from the extracellular medium. M‐CSF induced macrophage proliferation and DNA and RNA synthesis, whereas interferon γ (IFN‐γ) led to activation, blocked proliferation, and induced only RNA synthesis. Macrophages express at least the concentrative systems N1 and N2 (CNT2 and CNT1 genes, respectively) and the equilibrative systems es and ei (ENT1 and ENT2 genes, respectively). Incubation with M‐CSF only up‐regulated the equilibrative system es. Inhibition of this transport system blocked M‐CSF‐dependent proliferation. Treatment with IFN‐γ only induced the concentrative N1 and N2 systems. IFN‐γ also down‐regulated the increased expression of the es equilibrative system induced by M‐CSF. Thus, macrophage proliferation and activation require selective regulation of nucleoside transporters and may respond to specific requirements for DNA and RNA synthesis. This report also shows that the nucleo‐side transporters are critical for macrophage proliferation and activation.
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