Molecular Profiling of Decompensated Cirrhosis by a Novel MicroRNA Signature.

Noninvasive staging of decompensated cirrhosis is an unmet clinical need. The aims of this study were to characterize and validate a novel microRNA (miRNA) signature to stage decompensated cirrhosis and predict the portal pressure and systolic cardiac response to nonselective beta-blockers (NSBBs). Serum samples from patients with decompensated cirrhosis (n = 36) and healthy controls (n = 36) were tested for a novel signature of five miRNAs (miR-452-5p, miR-429, miR-885-5p, miR-181b-5p, and miR-122-5p) identified in the secretome of primary human hepatocytes and for three miRNAs (miR-192-5p, miR-34a-5p, and miR-29a-5p) previously discovered as biomarkers of chronic liver disease. All patients had ascites, which was refractory in 18 (50%), and were placed on NSBBs for variceal bleeding prophylaxis. In all patients, serum miRNAs, hepatic venous pressure gradient, and an echocardiogram study were performed before and 1 month after NSBBs. Patients with cirrhosis had lower serum levels of miR-429, miR-885-5p, miR-181b-5p, miR-122-5p, miR-192-5p, and miR-29a-5p (P < 0.05). Baseline serum miR-452-5p and miR-429 levels were lower in NSBB responders (P = 0.006). miR-181b-5p levels were greater in refractory ascites than in diuretic-sensitive ascites (P = 0.008) and correlated with serum creatinine. miR-452-5p and miR-885-5p were inversely correlated with baseline systemic vascular resistance (ρ = -0.46, P = 0.007; and ρ = -0.41, P = 0.01, respectively) and with diminished systolic contractility (ρ = -0.55, P = 0.02; and ρ = -0.55, P = 0.02, respectively) in patients with refractory ascites after NSBBs. Conclusion: Analysis of a miRNA signature in serum discriminates between patients with decompensated cirrhosis who show more severe systemic circulatory dysfunction and compromised systolic function after beta-blockade and those more likely to benefit from NSBBs.

Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model.

Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes.IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples-just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.