Closing the circle : current state and perspectives of circular RNA databases

Circular RNAs (circRNAs) are covalently closed RNA molecules that have been linked to various diseases, including cancer. However, a precise function and working mechanism are lacking for the larger majority. Following many different experimental and computational approaches to identify circRNAs, multiple circRNA databases were developed as well. Unfortunately, there are several major issues with the current circRNA databases, which substantially hamper progression in the field. First, as the overlap in content is limited, a true reference set of circRNAs is lacking. This results from the low abundance and highly specific expression of circRNAs, and varying sequencing methods, data-analysis pipelines, and circRNA detection tools. A second major issue is the use of ambiguous nomenclature. Thus, redundant or even conflicting names for circRNAs across different databases contribute to the reproducibility crisis. Third, circRNA databases, in essence, rely on the position of the circRNA back-splice junction, whereas alternative splicing could result in circRNAs with different length and sequence. To uniquely identify a circRNA molecule, the full circular sequence is required. Fourth, circRNA databases annotate circRNAs' microRNA binding and protein-coding potential, but these annotations are generally based on presumed circRNA sequences. Finally, several databases are not regularly updated, contain incomplete data or suffer from connectivity issues. In this review, we present a comprehensive overview of the current circRNA databases and their content, features, and usability. In addition to discussing the current issues regarding circRNA databases, we come with important suggestions to streamline further research in this growing field

Clonal Haematopoiesis and Risk of Chronic Liver Disease

Chronic liver disease is a major public health burden worldwide1. Although different aetiologies and mechanisms of liver injury exist, progression of chronic liver disease follows a common pathway of liver inflammation, injury and fibrosis2. Here we examined the association between clonal haematopoiesis of indeterminate potential (CHIP) and chronic liver disease in 214,563 individuals from 4 independent cohorts with whole-exome sequencing data (Framingham Heart Study, Atherosclerosis Risk in Communities Study, UK Biobank and Mass General Brigham Biobank). CHIP was associated with an increased risk of prevalent and incident chronic liver disease (odds ratio = 2.01, 95% confidence interval (95% CI) [1.46, 2.79]; P \u3c 0.001). Individuals with CHIP were more likely to demonstrate liver inflammation and fibrosis detectable by magnetic resonance imaging compared to those without CHIP (odds ratio = 1.74, 95% CI [1.16, 2.60]; P = 0.007). to assess potential causality, Mendelian randomization analyses showed that genetic predisposition to CHIP was associated with a greater risk of chronic liver disease (odds ratio = 2.37, 95% CI [1.57, 3.6]; P \u3c 0.001). In a dietary model of non-alcoholic steatohepatitis, mice transplanted with Tet2-deficient haematopoietic cells demonstrated more severe liver inflammation and fibrosis. These effects were mediated by the NLRP3 inflammasome and increased levels of expression of downstream inflammatory cytokines in Tet2-deficient macrophages. In summary, clonal haematopoiesis is associated with an elevated risk of liver inflammation and chronic liver disease progression through an aberrant inflammatory response

Is Vasomotion in Cerebral Arteries Impaired in Alzheimer’s Disease?

A substantial body of evidence supports the hypothesis of a vascular component in the pathogenesis of Alzheimer’s disease (AD). Cerebral hypoperfusion and blood-brain barrier dysfunction have been indicated as key elements of this pathway. Cerebral amyloid angiopathy (CAA) is a cerebrovascular disorder, frequent in AD, characterized by the accumulation of amyloid-β (Aβ) peptide in cerebral blood vessel walls. CAA is associated with loss of vascular integrity, resulting in impaired regulation of cerebral circulation, and increased susceptibility to cerebral ischemia, microhemorrhages, and white matter damage. Vasomotion— the spontaneous rhythmic modulation of arterial diameter, typically observed in arteries/arterioles in various vascular beds including the brain— is thought to participate in tissue perfusion and oxygen delivery regulation. Vasomotion is impaired in adverse conditions such as hypoperfusion and hypoxia. The perivascular and glymphatic pathways of Aβ clearance are thought to be driven by the systolic pulse. Vasomotion produces diameter changes of comparable amplitude, however at lower rates, and could contribute to these mechanisms of Aβ clearance. In spite of potential clinical interest, studies addressing cerebral vasomotion in the context of AD/CAA are limited. This study reviews the current literature on vasomotion, and hypothesizes potential paths implicating impaired cerebral vasomotion in AD/CAA. Aβ and oxidative stress cause vascular tone dysregulation through direct effects on vascular cells, and indirect effects mediated by impaired neurovascular coupling. Vascular tone dysregulation is further aggravated by cholinergic deficit and results in depressed cerebrovascular reactivity and (possibly) impaired vasomotion, aggravating regional hypoperfusion and promoting further Aβ and oxidative stress accumulation

Arsenic impact in the xero-halophyte plant species Atriplex atacamensis Phil. at the seedling stage

Arsenic (As) is a toxic metalloid ubiquitously present in the environment and which threaten human health in numerous areas in the world. Atriplex atacamensis, is an endemic xero-halophyte plant species of Northern Chile found close to the Atacama Desert where arsenic contamination frequently occurs mainly due to mine waste and volcanic sediments. This region is also characterized by high salinity. The global aim of our study is to analyze the physiological behavior of A. atacamensis exposed to toxic doses of As in order to quantify its level of resistance and to decipher its mechanisms of tolerance to this toxic element. A field analysis confirmed the presence of high As doses in the soil and in the water collected from Rio Loa in North Chile. Experiments were then performed in nutrient solution on seedlings issued from seeds collected on mature plants and confirmed that young seedlings were able to cope with high As doses (up to 1000 µM). Both As(V) and As(III) were detected within plant tissues. Addition of NaCl increased As translocation from the root to the shoot and the proportion of endogenous As(V) comparatively to As(III). In contrast, phosphate deficiency reduced As translocation. Arsenic did not induce any water stress at the plant level and As was not excreted by the leaf trichomes. Beside osmoprotectant (proline, glycinebetaine), polyamines may also afford protection in response to As toxicity. External As(III) was more toxic than As(V) at both the whole plant and cell levels. As content in the roots (up 5000 µg.g-1) were at least 10 times higher than in old leaves and approximately 50 times higher than in young leaves. The root As accumulation and cell wall sequestration appeared to be efficient strategies for As resistance. Oversynthesis of phytochelatin plays a key role in plant protection against accumulated As. Atriplex atacamensis is considered as a promising tool for the phytomanagement of As-contaminated areas in arid regions.(SC - Sciences) -- UCL, 201

Signaling pathways involved in the pathophysiological responses of vascular smooth muscle cells during cerebral amyloid angiopathy and post-angioplasty restenosis

L'angiopathie amyloïde cérébrale (AAC) est caractérisée par des dépôts amyloïdes au sein des parois cérébrovasculaires, associés à des altérations vasculaires et des troubles cognitifs. L'inflammation étant un processus délétère au cours de l'AAC, je me suis intéressée à l'effet inflammatoire sur les cellules musculaires lisses (CML) vasculaires du peptide amyloïde principalement accumulé au sein des parois artérielles, le peptide A 1-40. Cette étude met en évidence que le peptide A 1-40 n'induit pas directement de réponse inflammatoire de la part des CML, mais les sensibilise aux stimuli pro-inflammatoires. Aussi, cette sensibilisation cellulaire résulte d'une pré-activation des voies PI3K/Akt et NF- B, insuffisante à elle-seule pour induire une réponse inflammatoire. Dans une seconde partie de ma thèse, je me suis intéressée aux mécanismes moléculaires impliqués dans la migration des CML au cours de la re-sténose post-angioplastie. Lorsque l'athérosclérose conduit à une sténose artérielle, l'angioplastie est l'opération chirurgicale rétablissant le flux sanguin. Cependant, dans les 6 mois postopératoires, 10 à 20% des patients présentent une re-sténose post-angioplastie. Un des principaux facteurs impliqué dans ce processus est la migration des CML de la paroi vers la lumière artérielle. Dans ce contexte, j'ai pu démontrer que la re-sténose post-angioplastie chez le rat est dépendante du niveau d'expression de l'adénylyl cyclase 8 (AC8). Dans cette étude, nous avons également montré que l'expression de l'AC8 induit la migration des CML et l'activation de la métalloprotéinase matricielle-2, en stimulant les voies Epac2/Rap1 et PI3K/Akt.Cerebral amyloid angiopathy (CAA) is defined by amyloid deposits within cerebral vasculature associated with vascular damages and cognitive impairment. As inflammation is a deleterious event during CAA, I explored the inflammatory effect in vascular smooth muscle cells (VSMC) of the amyloid peptide which is mainly accumulated in arterial wall, the peptide A1-40. This study evidenced that A1-40 does not directly induce inflammatory response of VSMC but sensitizes these cells to pro-inflammatory stimuli. Furthermore, this sensitization results from a pre-activation of PI3K/Akt and NF-B pathways, insufficient alone to induce inflammatory response.In the second part of my thesis, I studied the molecular mechanisms involved in VSMC migration occurring in post-angioplasty restenosis. When atherosclerosis leads to arterial stenosis, angioplasty is the surgery practiced to restore blood flow. However, during the 6 month post-surgery, 10 to 20% of patients display post-angioplasty restenosis. One of the main components of this event is the migration of VSMC from the wall to arterial lumen. In this context, I demonstrated that the severity of rat post-angioplasty restenosis is dependent to the level of adenylyl cyclase 8 (AC8) expression. In this study, we have also shown that AC8 expression promotes VSMC migration and matrix metalloproteinase-2 activation through Epac2/Rap1 and PI3K/Akt pathways