RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can ...post-transcriptionally repress thousands of genes. Using reporter constructs, we observed that degradation of mRNAs bearing sites imperfectly complementary to the endogenous let-7 miRNA is considerably stronger in human HEK293 than HeLa cells. The degradation did not result from the Ago2-mediated endonucleolytic cleavage but it was Dicer- and Ago2-dependent. We used this feature of HEK293 to address the size of a pool of transcripts regulated by RNA silencing in a single cell type. We generated HEK293 cell lines depleted of Dicer or individual Ago proteins. The cell lines were used for microarray analyses to obtain a comprehensive picture of RNA silencing. The 3'-untranslated region sequences of a few hundred transcripts that were commonly up-regulated upon Ago2 and Dicer knock-downs showed a significant enrichment of putative miRNA-binding sites. The up-regulation upon Ago2 and Dicer knock-downs was moderate and we found no evidence, at the mRNA level, for activation of silenced genes. Taken together, our data suggest that, independent of the effect on translation, miRNAs affect levels of a few hundred mRNAs in HEK293 cells.
Abstract Background Circulating microRNAs (miRNAs) emerge as potential heart failure biomarkers. We aimed to identify associations between acute heart failure (AHF)-specific circulating miRNAs and ...well-known heart failure biomarkers. Methods Associations between 16 biomarkers predictive for 180 day mortality and the levels of 12 AHF-specific miRNAs were determined in 100 hospitalized AHF patients, at baseline and 48 hours. Patients were divided in 4 pre-defined groups, based on clinical parameters during hospitalization. Correlation analyses between miRNAs and biomarkers were performed and complemented by miRNA target prediction and pathway analysis. Results No significant correlations were found at hospital admission. However, after 48 hours, 7 miRNAs were significantly negatively correlated to biomarkers indicative for a worse clinical outcome in the patient group with the most unfavorable in-hospital course (n = 21); miR-16-5p was correlated to C-reactive protein (R =-0.66, p-value = 0.0027), miR-106a-5p to creatinine (R =-0.68, p-value = 0.002), miR-223-3p to growth differentiation factor 15 (R =-0.69, p-value = 0.0015), miR-652-3p to soluble ST-2 (R =-0.77, p-value < 0.001), miR-199a-3p to procalcitonin (R =-0.72, p-value < 0.001) and galectin-3 (R =-0.73, p-value < 0.001) and miR-18a-5p to procalcitonin (R =-0.68, p-value = 0.002). MiRNA target prediction and pathway analysis identified several pathways related to cardiac diseases, which could be linked to some of the miRNA-biomarker correlations. Conclusions The majority of correlations between circulating AHF-specific miRNAs were related to biomarkers predictive for a worse clinical outcome in a subgroup of worsening heart failure patients at 48 hours of hospitalization. The selective findings suggest a time-dependent effect of circulating miRNAs and highlight the susceptibility to individual patient characteristics influencing potential relations between miRNAs and biomarkers.
Biomarkers play an important role in heart failure. They provide us information about the mechanisms involved in specific types of heart failure and can identify patients at higher risk. Although the ...majority of biomarker studies in heart failure focus on their prognostic value, the clinical applicability of prognostication in heart failure needs to be established. However, biomarkers can be used for many other purposes. For example, they can help us with the diagnosis of heart failure, and they can be used to select our therapy, leading to personalized tailored therapy. Finally, when biomarkers are causally involved in the disease process, they can even become targets for therapy. The present paper reviews the established and potential value of the novel heart failure biomarkers, mid-regional atrial natriuretic peptide, soluble ST2, growth differentiation factor 15, galectin-3, renal tubular damage markers, and microRNAs. Their potential clinical value will be discussed and compared with the reference markers, the natriuretic peptides.
Aims
Our aim was to identify circulating microRNAs (miRNAs) associated with acute heart failure (AHF).
Methods and results
Plasma miRNA profiling included 137 patients with AHF from 3 different ...cohorts, 20 with chronic heart failure (CHF), 8 with acute exacerbation of COPD, and 41 healthy controls. Levels of circulating miRNAs were measured using quantitative reverse transcription–polymerase chain reaction (qRT–PCR). Plasma levels of miRNAs in patients with AHF were decreased compared with CHF patients or healthy subjects, whereas no significant changes were observed between acute COPD patients and controls. Fifteen miRNAs found in the discovery phase to differ most significantly between healthy controls and patients with AHF were further investigated in an extended cohort of 100 AHF patients at admission and a separate cohort of 18 AHF patients at different time points. Out of these 15 miRNAs, 12 could be confirmed in an additional AHF validation cohort and 7 passed the Bonferroni correction threshold (miR‐18a‐5p, miR‐26b‐5p, miR‐27a‐3p, miR‐30e‐5p, miR‐106a‐5p, miR‐199a‐3p, and miR‐652‐3p, all P < 0.00005). A further drop in miRNA levels within 48 h after AHF admission was associated with an increased risk of 180‐day mortality in a subset of the identified miRNAs.
Conclusions
Declining levels of circulating miRNAs were associated with increasing acuity of heart failure. Early in‐hospital decreasing miRNA levels were predictive for mortality in a subset of miRNAs in patients with AHF. The discovered miRNA panel may serve as a launch‐pad for molecular pathway studies to identify new pharmacological targets and miRNA‐based therapies.
ABSTRACT Background Deregulation of microRNAs (miRNAs) may be involved in the pathogenesis of heart failure (HF) and renal disease. Our aim is to describe miRNA levels related to early worsening ...renal function in acute HF patients. Method and results We studied the association between 12 circulating miRNAs and Worsening Renal Function (WRF; defined as an increase in the serum creatinine level of 0.3 mg per deciliter or more from admission to day 3), absolute change in creatinine and Neutrophil Gelatinase Associated Lipocalin (NGAL) from admission to day 3 in 98 patients hospitalized for acute HF. At baseline, circulating levels of all miRNAs were lower in patients with WRF, with statistically significant decreased levels of miR-199a-3p, miR-423-3p, and miR-let-7i-5p ( p -value < 0.05). The increase in creatinine during the first 3 days of hospitalization was significantly associated with lower levels of miR-199a-3p, miR-27a-3p, miR-652-3p, miR-423-5p, and miR-let-7i-5p, while the increase in NGAL was significantly associated with lower levels of miR-18a-5p, miR-106a-5p, miR-223-3p, miR-199a-3p and miR-423-3p. MiR-199a-3p was the strongest predictor of WRF, with an Odds Ratio of 1.48 (1.061–2.065; p -value = 0.021) and a C-index of 0.701. Conclusions Our results show that the levels of circulating miRNAs at hospital admission for acute HF were consistently lower in patients who developed worsening of renal function. MiR-199a-3p was the best predictor of WRF in these patients.
Proteomics-based clinical studies represent promising resources for the discovery of novel biomarkers or for unraveling molecular mechanisms underlying particular diseases. Here, we present a ...discovery study of hepatocellular carcinoma developed on nonfibrotic liver (nfHCC) that combines complementary quantitative iTRAQ-based proteomics and phosphoproteomics approaches. Using both approaches, we compared a set of 24 samples (18 nfHCC versus six nontumor liver tissue). We identified 43 proteins (67 peptides) differentially expressed and 32 peptides differentially phosphorylated between the experimental groups. The functional analysis of the two data sets pointed toward the deregulation of a protein homeostasis (proteostasis) network including the up-regulation of the Endoplasmic Reticulum (ER) resident HSPA5, HSP90B1, PDIA6, and P4HB and of the cytosolic HSPA1B, HSP90AA1, HSPA9, UBC, CNDP2, TXN, and VCP as well as the increased phosphorylation of the ER resident calnexin at Ser583. Antibody-based validation approaches (immunohistochemistry, immunoblot, Alphascreen®, and AMMP®) on independent nfHCC tumor sets (up to 77 samples) confirmed these observations, thereby indicating a common mechanism occurring in nfHCC tumors. Based on these results we propose that adaptation to proteostasis imbalance in nfHCC tumors might confer selective advantages to those tumors. As such, this model could provide an additional therapeutic opportunity for those tumors arising on normal liver by targeting the tumor proteostasis network. Data are available via ProteomeXchange with identifier PXD001253.
Dans ce chapitre, nous abordons la durabilité des systèmes alimentaires en lien avec l’urbanisation de nos économies. Nous identifions les enjeux d’une alimentation durable à travers, d’une part, les ...liens entre urbanisation, localisation et transport de marchandises et des personnes et, d’autre part, les liens entre les villes et leurs territoires voisins dans une perspective de développement local soutenable et de sécurisation de l’approvisionnement alimentaire pour les citadins. Nous proposons ensuite quelques orientations de recherche autour de deux axes majeurs : (i) les impacts d’une hausse du prix de l’énergie sur la localisation des différentes activités agroalimentaires et, en retour, sur la durabilité des systèmes alimentaires dans un contexte d’urbanisation croissante et (ii) les avantages/inconvénients relatifs (environnementaux, sociaux, économiques, sanitaires, pertes/déchets) de différentes organisations spatiales de systèmes alimentaires (circuits de proximité vs. circuit long notamment) pour nourrir les agglomérations en tenant compte des stratégies des différents acteurs (des producteurs, des distributeurs, des collectivités locales, …).
Dans ce chapitre, nous abordons la durabilité des systèmes alimentaires en lien avec l’urbanisation de nos économies. Nous identifions les enjeux d’une alimentation durable à travers, d’une part, les ...liens entre urbanisation, localisation et transport de marchandises et des personnes et, d’autre part, les liens entre les villes et leurs territoires voisins dans une perspective de développement local soutenable et de sécurisation de l’approvisionnement alimentaire pour les citadins. Nous proposons ensuite quelques orientations de recherche autour de deux axes majeurs : (i) les impacts d’une hausse du prix de l’énergie sur la localisation des différentes activités agroalimentaires et, en retour, sur la durabilité des systèmes alimentaires dans un contexte d’urbanisation croissante et (ii) les avantages/inconvénients relatifs (environnementaux, sociaux, économiques, sanitaires, pertes/déchets) de différentes organisations spatiales de systèmes alimentaires (circuits de proximité vs. circuit long notamment) pour nourrir les agglomérations en tenant compte des stratégies des différents acteurs (des producteurs, des distributeurs, des collectivités locales, …).
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