Acquisition of epithelial plasticity in human chronic liver disease.

For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.

As the cost of single-cell RNA-seq experiments has decreased, an increasing number of datasets are now available. Combining newly generated and publicly accessible datasets is challenging due to non-biological signals, commonly known as batch effects. Although there are several computational methods available that can remove batch effects, evaluating which method performs best is not straightforward. Here, we present BatchBench (https://github.com/cellgeni/batchbench), a modular and flexible pipeline for comparing batch correction methods for single-cell RNA-seq data. We apply BatchBench to eight methods, highlighting their methodological differences and assess their performance and computational requirements through a compendium of well-studied datasets. This systematic comparison guides users in the choice of batch correction tool, and the pipeline makes it easy to evaluate other datasets.

Untargeted metabolomics in doping control: detection of new markers of testosterone misuse by ultrahigh performance liquid chromatography coupled to high-resolution mass spectrometry.

The use of untargeted metabolomics for the discovery of markers is a promising and virtually unexplored tool in the doping control field. Hybrid quadrupole time-of-flight (QTOF) and hybrid quadrupole Orbitrap (Q Exactive) mass spectrometers, coupled to ultrahigh pressure liquid chromatography, are excellent tools for this purpose. In the present work, QTOF and Q Exactive have been used to look for markers for testosterone cypionate misuse by means of untargeted metabolomics. Two different groups of urine samples were analyzed, collected before and after the intramuscular administration of testosterone cypionate. In order to avoid analyte losses in the sample treatment, samples were just 2-fold diluted with water and directly injected into the chromatographic system. Samples were analyzed in both positive and negative ionization modes. Data from both systems were treated under untargeted metabolomic strategies using XCMS application and multivariate analysis. Results from the two mass spectrometers differed in the number of detected features, but both led to the same potential marker for the particular testosterone ester misuse. The in-depth study of the MS and MS/MS behavior of this marker allowed for the establishment of 1-cyclopentenoylglycine as a feasible structure. The putative structure was confirmed by comparison with synthesized material. This potential marker seems to come from the metabolism of the cypionic acid release after hydrolysis of the administered ester. Its suitability for doping control has been evaluated.

The landscape of expression and alternative splicing variation across human traits.

Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.

The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes.

The advances in high-throughput sequencing (HTS) have enabled the characterisation of biological processes at an unprecedented level of detail; most hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains a main challenge. Although variability in results may be introduced at various stages, e.g., alignment, summarisation or detection of differential expression, one source of variability was systematically omitted: the sequencing design, which propagates through analyses and may introduce an additional layer of technical variation. We illustrate qualitative and quantitative differences arising from splitting samples across lanes on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling and the peaks' properties. At the single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10× data are presented. The observed reduction in the number of unique sequenced fragments limits the level of detail on which the different prediction approaches depend. Furthermore, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias. Subsequently, we observe an overall reduction in sequencing complexity and a distortion in the biological signal across technologies, experimental contexts, organisms and tissues.

Efficacy and safety of direct-acting antiviral agents when combined with secukinumab.

BACKGROUND: The interference in the immune response induced by biological disease-modifying antirheumatic drugs (bDMARDs) increases the risk of reactivation of infections. Treatment of patients with chronic hepatitis C virus (HCV) infection and psoriasis is complex. The efficacy and safety of the new direct-acting antiviral agents (DAA) when combined with bDMARDs remain unknown. CASE REPORT: We present a case of a 44-year-old Caucasian man affected with psoriasis and HCV infection. Throughout the course of the psoriatic disease, this patient received several lines of treatment, including secukinumab, a new type of bDMARD. At the time of commencing secukinumab, new DAA agents (ledipasvir/sofosbuvir) were also initiated. At week 12 post-treatment, hepatitis C viral load was undetectable and the patient remained in remission of psoriasis. CONCLUSION: This case report suggests that secukinumab is a therapeutic option in patients with psoriasis, particularly in those cases with HCV infection where treatment with DAA agents is warranted.

[Clinical and epidemiological study of adult patients with positive blood cultures]. / Estudio clinico y epidemiológico de pacientes adultos con hemocultivo positivo.

A cohort evaluation of the microbiology, epidemiology and outcome of adult patients with positive blood cultures was performed on 336 patients, from July 1997 to March 2000. Data for mortality were obtained from 328 of these patients. The six most common pathogens were Staphylococcus aureus: 81 (23.5%), coagulase negative staphylococci: 50 (14.5%), Escherichia coli: 48 (14.0%), Streptococcus pneumoniae: 30 (8.7%), enterococci: 19 (5.5%) and Pseudomonas aeruginosa: 19 (5.5%). In 169 episodes infections were hospital-acquired and community-acquired in the remaining 159. Main infection foci included the respiratory and urinary tracts. Infection associated mortality was 33.2%; 29.6% of patients received inappropriate empiric antibiotic treatment. Univariate analysis showed that an age of 70 or more years, a systemic inflammatory response syndrome (SIRS) score higher than 2, a polimicrobial episode, certain foci (abdominal, respiratory or unknown), and an inappropriate empiric antibiotic treatment influenced outcome. By multivariate analysis the variables that influenced death by infectious cause were age of 70 or more years, a SIRS score higher than 2, certain foci (abdominal, respiratory or unknown), and an inappropriate empiric antibiotic treatment. SIRS score was useful to predict the positivity of the blood culture. No relation between outcome and presence of underlying disease, isolation of Gram negative microorganism and nosocomial vs. community acquired episode was observed (univariate analysis). In order to improve outcome in bacteremic patients, after performing cultures of blood and other relevant clinical foci, prompt and appropriate antibiotic treatment remains critical. Microbiologic, clinical and epidemiological information results crucial for the management of this critically ill population.

Bioseguridad para el personal de servicios de radiología / Guidelines for biosecurity at the radiologic departament

Los autores presentan un extenso trabajo de actualización detallando las normas de bioseguridad y otros aspectos aplicables en los Servicios de Diagnóstico por Imágenes reparando, en particular, sobre los riesgos vinculados al manejo de pacientes HIV positivos

Estudio clinico y epidemiologico de pacientes adultos con hemocultivo positivO / Clinical and epidemiological study of adult patients with positive blood cultures

A cohort evaluation of the microbiology, epidemiology and outcome of adult patients with positive blood cultures was performed on 336 patients, from July 1997 to March 2000. Data for mortality were obtained from 328 of these patients. The six most common pathogens were Staphylococcus aureus: 81 (23.5 percent), coagulase negative staphylococci: 50 (14.5 percent), Escherichia coli: 48 (14.0 percent), Streptococcus pneumoniae: 30 (8.7 percent), enterococci: 19 (5.5 percent) and Pseudomonas aeruginosa: 19 (5.5 percent). In 169 episodes infections were hospital-acquired and community-acquired in the remaining 159. Main infection foci included the respiratory and urinary tracts. Infection associated mortality was 33.2 percent; 29.6 percent of patients received inappropriate empiric antibiotic treatment. Univariate analysis showed that an age of 70 or more years, a systemic inflammatory response syndrome (SIRS) score higher than 2, a polimicrobial episode, certain foci (abdominal, respiratory or unknown), and an inappropriate empiric antibiotic treatment influenced outcome. By multivariate analysis the variables that influenced death by infectious cause were age of 70 or more years, a SIRS score higher than 2, certain foci (abdominal, respiratory or unknown), and an inappropriate empiric antibiotic treatment. SIRS score was useful to predict the positivity of the blood culture. No relation between outcome and presence of underlying disease, isolation of Gram negative microorganism and nosocomial vs. community acquired episode was observed (univariate analysis). In order to improve outcome in bacteremic patients, after performing cultures of blood and other relevant clinical foci, prompt and appropriate antibiotic treatment remains critical. Microbiologic, clinical and epidemiological information results crucial for the management of this critically ill population. AD - Hospital Municipal de San Isidro, Provincia de Buenos Aires, Capitan Juan de San Martin 1531, 1609 Boulogne, Pcia. Buenos Aires.