Mandatory criteria for the application of variability-based parameters of fluid responsiveness: a prospective study in different groups of ICU patients

BACKGROUND AND OBJECTIVE

Stroke volume variation (SVV) has high sensitivity and specificity in predicting fluid responsiveness. However, sinus rhythm (SR) and controlled mechanical ventilation (CV) are mandatory for their application. Several studies suggest a limited applicability of SVV in intensive care unit (ICU) patients. We hypothesized that the applicability of SVV might be different over time and within certain subgroups of ICU patients. Therefore, we analysed the prevalence of SR and CV in ICU patients during the first 24 h of PiCCO-monitoring (primary endpoint) and during the total ICU stay. We also investigated the applicability of SVV in the subgroups of patients with sepsis, cirrhosis, and acute pancreatitis.

METHODS

The prevalence of SR and CV was documented immediately before 1241 thermodilution measurements in 88 patients.

RESULTS

In all measurements, SVV was applicable in about 24%. However, the applicability of SVV was time-dependent: the prevalence of both SR and CV was higher during the first 24 h compared to measurements thereafter (36.1% vs. 21.9%; P<0.001). Within different subgroups, the applicability during the first 24 h of monitoring ranged between 0% in acute pancreatitis, 25.5% in liver failure, and 48.9% in patients without pancreatitis, liver failure, pneumonia or sepsis.

CONCLUSIONS

The applicability of SVV in a predominantly medical ICU is only about 25%-35%. The prevalence of both mandatory criteria decreases over time during the ICU stay. Furthermore, the applicability is particularly low in patients with acute pancreatitis and liver failure.

Vitamin D Deficiency Is Highly Prevalent in Critically Ill Patients and a Risk Factor for Mortality: A Prospective Observational Study Comparing Noncirrhotic Patients and Patients With Cirrhosis

INTRODUCTION

A 25-hydroxyvitamin D, 25(OH)D, deficiency is common among critically ill patients and correlated with increased mortality. Furthermore, deficiency is associated with advanced liver disease. However, there are no studies available comparing the dimensions and consequences of a 25(OH)D deficiency between patients with and without liver cirrhosis in the setting of intensive care units (ICUs). This study focuses on differences in 25(OH)D status between critically ill noncirrhosis patients and patients with cirrhosis (primary end point), hypothesizing that deficiency and its impact on mortality risk are even more pronounced in patients with cirrhosis.

METHODS

We performed a prospective observational study of 176 patients (noncirrhosis patients, N = 114; patients with cirrhosis, N = 62) with a laboratory assessment of 25(OH)D on ICU admission and survival analyses after 180 days.

RESULTS

On admission, 55% of patients showed a severe deficiency, 25(OH)D <10 ng/mL, and a further 23% moderate deficiency (10-19 ng/mL). The overall median level of 25(OH)D was 8.0 (5.0-18.0) ng/mL (10.5 [6.0-21.3] in noncirrhosis patients vs 7.0 [4.8-10.0] in patients with cirrhosis; P < .001). We found extremely low levels particularly in patients without prior vitamin D supplementation (6.0 [4.0-7.5] in patients with cirrhosis vs 8.0 [5.0-12.0] ng/mL in noncirrhosis patients; P = .004). Vitamin D status correlated inversely with the sequential organ failure assessment, acute and physiology chronic health evaluation, model of end-stage liver disease, and Child-Pugh scores. Survival analyses categorized 25(OH)D levels <10 ng/mL as a high-risk factor for mortality 180 days after admission (hazard ratio [HR]: 2.45, 95% confidence interval [CI] = 1.60-3.70; P < .001). In patients with cirrhosis, a severe deficiency (<10 ng/mL) involved a significantly higher mortality risk than in noncirrhosis patients (HR: 2.30, 95% CI = 1.39-3.82; P = .001). In cases of admission levels ≥10 ng/mL, however, mortality risk was similar between patients with cirrhosis and noncirrhosis patients (HR: 1.08, 95% CI = 0.43-2.73; P = .873).

CONCLUSIONS

Hypovitaminosis D is a highly frequent disorder in critically ill patients admitted to ICU. A severe deficiency with levels <10 ng/mL is a high risk factor for increased mortality, especially in patients with cirrhosis.

Validation of RIFLE, AKIN, and a modified AKIN definition ("backward classification") of acute kidney injury in a general ICU: Analysis of a 1-year period

The aim of this study was to validate Acute Kidney Injury Network (AKIN) and to develop a modified AKIN aimed at an improved classification of patients without baseline creatinine versus Risk, Injury, Failure, Loss of kidney function, and End-stage kidney disease (RIFLE) in general intensive care unit (ICU) patients.We retrospectively analyzed medical records of general ICU patients over a 1-year period. We compared the grading of severity as well as the prediction of mortality and renal replacement therapy by AKIN and RIFLE. Furthermore, a modified AKIN score was evaluated.A total of 321 patients were included. In 87% of cases, the 2 definitions classified patients in the concordant severity group. Higher scores of AKIN and RIFLE were associated with increased ICU- and 28-day mortality. Both definitions provided large receiver operating characteristics (ROC)-area under the curve (AUCs) for the prediction of mortality, which were comparable to the ROC-AUC of unclassified serum creatinine. Modification of the AKIN score with a "backward classification" of baseline creatinine based on its time course resulted in a higher AKIN score in 32 patients.RIFLE and AKIN definitions had a high concordance in staging the severity of acute kidney injury. There was a strong relationship between the stages and need for dialysis, ICU, and 28-day mortality. However, unclassified serum creatinine values were at least comparable. Standardized observation of the creatinine time course allows for "ex-post" AKIN-classification in a substantial number of patients with missing baseline creatinine values.

Increased risk of candidemia in patients with necrotising pancreatitis infected with candida species

BACKGROUND AND OBJECTIVES

Candida infections are frequent in necrotising pancreatitis. Candidemia is associated with very high mortality and its risk due to infected pancreatic necrosis is unknown. So we aimed to assess potential risk factors and the risk of candidemia in necrotising pancreatitis.

METHODS

We retrospectively searched our clinical database for the diagnosis necrotising pancreatitis from 2007 till March 2017 and entered relevant information in a database for statistical analysis.

RESULTS

in total, 136 patients met the inclusion criteria. Candida infected pancreatic necrosis were found in 54 patients and 7 patients developed candidemia. Patients with Candida infected necrosis had a significantly higher in hospital mortality (35.2% versus 13.4%, p = 0.003). The highest mortality was observed in patients with candidemia (57.1% versus 20.2%, p = 0.042). Male gender (OR 0.32, CI 0.13-0.78, p = 0.013) and post-ERCP pancreatitis (OR 4.32, CI 1.01-18.36, p = 0.048) had a significant impact on the risk of Candida infections of pancreatic necrosis. Candidemia was significantly more frequent in patients with Candida infected necrosis (11.1% versus 1.2%, p = 0.016). Candida albicans was the most common species followed by Candida glabrata.

CONCLUSION

Candidemia is a relevant complication of necrotising pancreatitis and associated with high mortality. If patients do not respond to antibiotic therapy empiric antifungal therapy should be discussed.

Gallic acid, a common dietary phenolic protects against high fat diet induced DNA damage

Purpose

Aim of the study was to find out if gallic acid (GA), a common phenolic in plant foods, prevents obesity induced DNA damage which plays a key role in the induction of overweight associated cancer.

Methods

Male and female C57BL6/J mice were fed with a low fat or a high fat diet (HFD). The HFD group received different doses GA (0, 2.6–20 mg/kg b.w./day) in the drinking water for 1 week. Subsequently, alterations of the genetic stability in blood and inner organs were monitored in single cell gel electrophoresis assays. To elucidate the underlying molecular mechanisms: oxidized DNA bases, alterations of the redox status, lipid and glucose metabolism, cytokine levels and hepatic NF-κB activity were monitored.

Results

HFD fed animals had higher body weights; increased DNA damage and oxidation of DNA bases damage were detected in colon, liver and brain but not in blood and white adipose tissue. Furthermore, elevated concentrations of insulin, glucose, triglycerides, MCP-1, TNF-α and NF-κB activity were observed in this group. Small amounts of GA, in the range of human consumption, caused DNA protection and reduced oxidation of DNA bases, as well as biochemical and inflammatory parameters.

Conclusions

Obese animals have increased DNA damage due to oxidation of DNA bases. This effect is probably caused by increased levels of glucose and insulin. The effects of GA can be explained by its hypoglycaemic properties and indicate that the consumption of GA-rich foods prevents adverse health effects in obese individuals.

Electronic supplementary material

The online version of this article (10.1007/s00394-018-1782-2) contains supplementary material, which is available to authorized users.

Large-volume paracentesis effects plasma disappearance rate of indo-cyanine green in critically ill patients with decompensated liver cirrhosis and intraabdominal hypertension

BACKGROUND

Ascites is a major complication of decompensated liver cirrhosis. Intraabdominal hypertension and structural alterations of parenchyma involve decisive changes in hepatosplanchnic blood flow. Clearance of indo-cyanine green (ICG) is mainly dependent on hepatic perfusion and hepatocellular function. As a consequence, plasma disappearance rate of ICG (ICG-PDR) is rated as a useful dynamic parameter of liver function. This study primarily evaluates the impact of large-volume paracentesis (LVP) on ICG-PDR in critically ill patients with decompensated cirrhosis. Additionally, it describes influences on intraabdominal pressure (IAP), abdominal perfusion pressure (APP), hepatic blood flow, hemodynamic and respiratory function.

METHODS

We analyzed LVP in 22 patients with decompensated liver cirrhosis. ICG-PDR was assessed by using noninvasive LiMON technology (Pulsion® Medical Systems; Maquet Getinge Group), and hepatic blood flow was analyzed by color-coded duplex sonography.

RESULTS

Paracentesis of a median volume of 3450 mL ascites evoked significant increases of ICG-PDR from 3.6 (2.8-4.6) to 5.1 (3.9-6.2)%/min (p < 0.001). Concomitantly, we observed a raise in "ICG-Clearance" from 99 (73.5-124.5) to 104 (91-143.5) mL/min/m2 (p = 0.005), while circulating blood volume index was unchanged [2412 (1983-3025) before paracentesis vs. 2409 (1997-2805) mL/m2, p = 0.734]. Sonography revealed a significant impact of paracentesis on hepatic blood flow: Hepatic artery resistance index dropped from 0.74 (0.68-0.75) to 0.68 (0.65-0.71) (p < 0.001) and maximum flow velocity in hepatic vein increased from 24 (17-30) to 30 (22-36) cm/s (p < 0.001). Consistent with previous studies, paracentesis caused significant decreases in IAP from 19.0 (15.0-20.3) to 11.0 (8.8-12.3) mmHg (p < 0.001) and central venous pressure from 22.5 (17.8-29.0) to 17.5 (12.8-24.0) mmHg (p < 0.001) with inverse increases in APP from 63.0 (56.8-69.5) to 71.0 (65.5-78.5) mmHg (p < 0.001). Changes in ICG-PDR were concomitant with changes in IAP (r = - 0.602) and APP (r = 0.576). Moreover, we found a substantial improvement in respiratory function. By contrast, hemodynamic parameters assessed by transpulmonary thermodilution, serum bilirubin and international normalized ratio did not change after paracentesis.

CONCLUSION

Critically ill patients with decompensated cirrhosis and elevated IAP showed dramatically impaired ICG-PDR. Paracentesis evoked an improvement in ICG-PDR in parallel with a decreased IAP and an increased APP, while conventional parameters of liver function did not change. This effect on ICG-PDR is mainly referable to a relief of intraabdominal hypertension and changes in hepatosplanchnic blood flow.

Mean arterial pressure targeted fluid resuscitation may lead to fluid overload: A bleeding-resuscitation animal experiment

Introduction

Fluid resuscitation is the cornerstone of treatment in hemorrhagic shock. Despite increasing doubts, several guidelines recommend to maintain mean arterial pressure (MAP) >65 mmHg as the most frequent indication of fluid therapy. Our aim was to investigate the effects of a MAP-guided management in a bleeding-resuscitation animal experiment.

Materials and methods

After anesthesia and instrumentation (t_bsl) animals were bled till the initial stroke volume index dropped by 50% (t₀). Fluid replacement was performed in 4 equivalent steps (t_1-4) with balanced crystalloid solution to reach the baseline values of MAP. Invasive hemodynamic measurements and blood gas analyses were performed after each step.

Results

Mean arterial pressure dropped from t_bsl to t₀ (114±11 vs 76.9±16.9 mmHg, p<0.001) and returned to baseline by t₄ (101.4±14.4 mmHg). From t_bsl-t₀ stroke volume index (SVI), cardiac index (CI) decreased (SVI: 40±8.6 vs 19.3±3.6 ml/m², p<0.001; CI: 3.4±0.3 vs 1.9±0.3 l/min/m², p<0.001), pulse pressure variation (PPV) increased (13.2±4.3 vs 22.1±4.3%, p<0.001). There was a decrease in oxygen delivery (464±45 vs 246±26.9 ml/min, p<0.001), central venous oxygen saturation (82.8±5.4 vs 53.6±12.1%, p<0.001) and increase in lactate levels (1.6±0.4 vs 3.5±1.6 mmol/l, p<0.005). SVI, CI and PPV returned to their initial values by t₂. To normalize MAP fluid therapy had to be continued till t₄, with the total infused volume of 4.5±0.8 l.

Conclusion

In the current experiment bleeding led to hemorrhagic shock, while MAP remained higher than 65 mmHg. Furthermore, MAP was unable to indicate the normalization of SVI, CI and PPV that resulted in unnecessary fluid administration. Our data give further evidence that MAP may be an inappropriate parameter to follow during fluid resuscitation.

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets

Multi-omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities. The learnt factors enable a variety of downstream analyses, including identification of sample subgroups, data imputation and the detection of outlier samples. We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profiled for somatic mutations, RNA expression, DNA methylation and ex vivo drug responses. MOFA identified major dimensions of disease heterogeneity, including immunoglobulin heavy-chain variable region status, trisomy of chromosome 12 and previously underappreciated drivers, such as response to oxidative stress. In a second application, we used MOFA to analyse single-cell multi-omics data, identifying coordinated transcriptional and epigenetic changes along cell differentiation.

[Management of Clostridium difficile infections at German intensive care units - results from a survey among intensivists]

BACKGROUND

Clostridium difficile associated colitis is a frequent cause of nosocomial diarrhea at the intensive care unit (ICU) and is associated with poor prognosis in critically ill patients. Few studies have evaluated the efficacy of treatment options or adherence to guideline recommendations of Clostridium difficile infections at the ICU.

METHODS

Therefore, on behalf of the Gastroenterology Intensive Care Medicine working group of the DGVS, we have conducted an online-based survey among leading intensivists in Germany.

RESULTS

Out of the 351 invited, 85 (24.2 %), primarily leading executive physicians at primary to tertiary care hospitals, completed the survey. They reported standardized diagnostic algorithms of 79.3 %, in line with current guideline recommendations (i. e., toxin testing in stool, possibly GDH screening, and endoscopy). First-line therapy of Clostridium difficile infections at the ICU was reported to be oral vancomycin in 48.3 % and oral metronidazole in 34.5 %. The success of first-line therapy was estimated at 67 % for clinical cure, 15 % persisting colitis, 5 % sepsis or megacolon, 10 % recurrence, and 3 % death. Hospitals of primary/secondary care more often used metronidazole compared to university hospitals. Standard treatments for recurrent infection were vancomycin orally (40 % alone, 29.1 % combined with metronidazole) or, more rarely, fidaxomicin (25.5 %). Fidaxomicin has been used at least once at the ICU in 79 % of the respondents. Eleven percent have used fecal microbiota transplant (FMT) in selected cases at the ICU.

CONCLUSION

Our survey indicated a high awareness of German intensivists for Clostridium difficile infections, but also marked differences in local therapeutic algorithms, especially in first-line treatment.

Accuracy and precision of ScvO2 measured with the CeVOX-device: A prospective study in patients with a wide variation of ScvO2-values

INTRODUCTION

Central-venous oxygen saturation (ScvO2) is a key parameter of hemodynamic monitoring and has been suggested as therapeutic goal for resuscitation. Several devices offer continuous monitoring features. The CeVOX-device (Pulsion Medical Systems) uses a fibre-optic probe inserted through a conventional central-venous catheter (CVC) to obtain continuous ScvO2.

OBJECTIVES

Since there is a lack of studies validating the CeVOX, we prospectively analyzed data from 24 patients with CeVOX-monitoring. To increase the yield of lower ScvO2-values, 12 patients were equipped with a femoral CVC.

METHODS

During the 8h study period ScvO2_CeVOX was documented immediately before withdrawal of blood to measure ScvO2 by blood gas analysis (ScvO2_BGA) 6min, 1h, 4h, 5h and 8h after the initial calibration. No further calibrations were performed.

RESULTS

In patients with jugular CVC (primary endpoint; 60 measurements), bias, lower and upper limits of agreement (LLOA; ULOA) and percentage error (PE) of the estimate of ScvO2 (ScvO2_CeVOX_jug) were acceptable with 0.45%, -13.0%, 13.9% and 16.6%, respectively. As supposed, ScvO2 was lower in the femoral compared to the jugular measurements (69.5±10.7 vs. 79.4±5.8%; p<0.001). While the bias (0.64%) was still acceptable, LLOA (-23.8%), ULOA (25.0%) and PE (34.5%) were substantially higher for femoral assessment of ScvO2 by the CeVOX (ScvO2_CeVOX_fem). Analysis of the entire data-pool with jugular as well as femoral CVCs allowed for a multivariate analysis which demonstrated that the position of the CVC per se was not independently associated with the bias ScvO2_CeVOX-ScvO2_BGA. The amount of the bias |ScvO2_CeVOX-ScvO2_BGA| was independently associated with the amount of the change of ScvO2_CeVOX compared to the initial calibration to ScvO2_BGA_baseline (|ScvO2_CeVOX-ScvO2_BGA_baseline|) as well as with low values of ScvO2_BGA_baseline. Furthermore, increasing time to the initial calibration was associated to the amount of the bias with borderline significance. A statistical model based on |ScvO2_CeVOX-ScvO2_BGA_baseline| and "time to last calibration" derived from an evaluation dataset (80 of 120 datasets, 16 of 24) provided a ROC-AUC of 0.903 to predict an amount of the bias |ScvO2_CeVOX-ScvO2_BGA| ≥5% in an independent validation group (40 datasets of 8 patients).

CONCLUSION

These findings suggest that the CeVOX device is capable to detect stability or instability of ScvO2_BGA. ScvO2_CeVOX accurately estimates ScvO2_BGA in case of stable values. However, intermittent measurement of ScvO2_BGA and re-calibration should be performed in case of substantial changes in ScvO2_CeVOX compared to baseline. Therefore, continuous measurement of ScvO2 with the CeVOX cannot replace ScvO2_BGA in instable patients. On the other hand, CeVOX might be useful for the monitoring of stable patients as a pre-test tool for more differentiated monitoring in case of changes in ScvO2_CeVOX.

Physical Work Capacity in Chronic Renal Disease

We studied the physical fitness of 71 patients with renal disease before dialysis, after starting dialysis, and after successful renal transplantation. Maximal muscle strength was determined in 58 patients and maximal cardiovascular capacity was assessed in 36 patients. Before dialysis there was a 31 percent reduction in muscle strength in men and 47 percent in women. The loss of muscle strength was most pronounced in the leg extensors. Cardiovascular capacity and muscle strength was positively correlated in the dialysis patients (p ≤ 0.05). The cardiovascular capacity was decreased 29% in predialysis patients, 45% in dialysis patients and 37% in transplanted patients compared to untrained healthy controls. The predialysis patients had a 19% greater cardiovascular capacity than the dialysis patients and a 9% greater cardiovascular capacity than the transplanted patients. While hemoglobin concentrations showed a positive correlation (p ≤ 0.05) with maximal cardiovascular capacity and creatinine concentration showed a negative correlation (p ≤ 0.05) with maximal cardiovascular capacity in the predialysis patients, hemoglobin concentrations and creatinine concentrations did not correlate with cardiovascular capacity in the dialysed and transplanted patients. In dialysis patients as well as in patients after kidney transplantation hemoglobin and creatinine concentrations, muscle strength, height, weight, and age are factors influencing the physical work capacity, but none of these variables alone seems to be a strong determination factor. Besides the complications of kidney disease which may itself reduce physical fitness, the lack of physical training is an important factor in determining the residual muscle strength and cardiovascular capacity for all patients with renal insufficiency.

Proteome-wide identification of ubiquitin interactions using UbIA-MS

Ubiquitin-binding proteins play an important role in eukaryotes by translating differently linked polyubiquitin chains into proper cellular responses. Current knowledge about ubiquitin-binding proteins and ubiquitin linkage-selective interactions is mostly based on case-by-case studies. We have recently reported a method called ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS), which enables comprehensive identification of ubiquitin interactors for all ubiquitin linkages from crude cell lysates. One major strength of UbIA-MS is the fact that ubiquitin interactors are enriched from crude cell lysates, in which proteins are present at endogenous levels, contain biologically relevant post-translational modifications (PTMs) and are assembled in native protein complexes. In addition, UbIA-MS uses chemically synthesized nonhydrolyzable diubiquitin, which mimics native diubiquitin and is inert to cleavage by endogenous deubiquitinases (DUBs). Here, we present a detailed protocol for UbIA-MS that proceeds in five stages: (i) chemical synthesis of ubiquitin precursors and click chemistry for the generation of biotinylated nonhydrolyzable diubiquitin baits, (ii) in vitro affinity purification of ubiquitin interactors, (iii) on-bead interactor digestion, (iv) liquid chromatography (LC)-MS/MS analysis and (v) data analysis to identify differentially enriched proteins. The computational analysis tools are freely available as an open-source R software package, including a graphical interface. Typically, UbIA-MS allows the identification of dozens to hundreds of ubiquitin interactors from any type of cell lysate, and can be used to study cell type or stimulus-dependent ubiquitin interactions. The nonhydrolyzable diubiquitin synthesis can be completed in 3 weeks, followed by ubiquitin interactor enrichment and identification, which can be completed within another 2 weeks.

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to isoform diversity in normal human physiology is unclear. To address this question, we investigated cell type-dependent differences in exon usage of over 18 000 protein-coding genes in 23 cell types from 798 samples of the Genotype-Tissue Expression Project. We found that about half of the expressed genes displayed tissue-dependent transcript isoforms. Alternative transcription start and termination sites, rather than alternative splicing, accounted for the majority of tissue-dependent exon usage. We confirmed the widespread tissue-dependent use of alternative transcription start sites in a second, independent dataset, Cap Analysis of Gene Expression data from the FANTOM consortium. Moreover, our results indicate that most tissue-dependent splicing involves untranslated exons and therefore may not increase proteome complexity. Thus, alternative transcription start and termination sites are the principal drivers of transcript isoform diversity across tissues, and may underlie the majority of cell type specific proteomes and functions.

Expression Atlas: gene and protein expression across multiple studies and organisms

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.

Drug-perturbation-based stratification of blood cancer

As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non-BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities

Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully understood but several cases of antisense-dependent gene expression regulation affecting the overlapping genes have been demonstrated. Using high-throughput yeast genetics and a limited set of four growth conditions we previously reported a regulatory function for ∼25% of asRNAs, most of which repress the expression of the sense gene. To further explore the roles of asRNAs we tested more conditions and identified 15 conditionally antisense-regulated genes, 6 of which exhibited antisense-dependent enhancement of gene expression. We focused on the sporulation-specific gene SPS100, which becomes upregulated upon entry into starvation or sporulation as a function of the antisense transcript SUT169. We demonstrate that the antisense effect is mediated by its 3' intergenic region (3'-IGR) and that this regulation can be transferred to other genes. Genetic analysis revealed that SUT169 functions by changing the relative expression of SPS100 mRNA isoforms from a short and unstable transcript to a long and stable species. These results suggest a novel mechanism of antisense-dependent gene regulation via mRNA isoform switching.

Two independent modes of chromatin organization revealed by cohesin removal

Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.

Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology

High-throughput biology presents unique opportunities and challenges for dermatological research. Drawing on a small handful of exemplary studies, we review some of the major lessons of these new technologies. We caution against several common errors and introduce helpful statistical concepts that may be unfamiliar to researchers without experience in bioinformatics. We recommend specific software tools that can aid dermatologists at varying levels of computational literacy, including platforms with command line and graphical user interfaces. The future of dermatology lies in integrative research, in which clinicians, laboratory scientists, and data analysts come together to plan, execute, and publish their work in open forums that promote critical discussion and reproducibility. In this article, we offer guidelines that we hope will steer researchers toward best practices for this new and dynamic era of data intensive dermatology.

miR-16 and miR-125b are involved in barrier function dysregulation through the modulation of claudin-2 and cingulin expression in the jejunum in IBS with diarrhoea

OBJECTIVE

Micro-RNAs (miRNAs) play a crucial role in controlling intestinal epithelial barrier function partly by modulating the expression of tight junction (TJ) proteins. We have previously shown differential messenger RNA (mRNA) expression correlated with ultrastructural abnormalities of the epithelial barrier in patients with diarrhoea-predominant IBS (IBS-D). However, the participation of miRNAs in these differential mRNA-associated findings remains to be established. Our aims were (1) to identify miRNAs differentially expressed in the small bowel mucosa of patients with IBS-D and (2) to explore putative target genes specifically involved in epithelial barrier function that are controlled by specific dysregulated IBS-D miRNAs.

DESIGN

Healthy controls and patients meeting Rome III IBS-D criteria were studied. Intestinal tissue samples were analysed to identify potential candidates by: (a) miRNA-mRNA profiling; (b) miRNA-mRNA pairing analysis to assess the co-expression profile of miRNA-mRNA pairs; (c) pathway analysis and upstream regulator identification; (d) miRNA and target mRNA validation. Candidate miRNA-mRNA pairs were functionally assessed in intestinal epithelial cells.

RESULTS

IBS-D samples showed distinct miRNA and mRNA profiles compared with healthy controls. TJ signalling was associated with the IBS-D transcriptional profile. Further validation of selected genes showed consistent upregulation in 75% of genes involved in epithelial barrier function. Bioinformatic analysis of putative miRNA binding sites identified hsa-miR-125b-5p and hsa-miR-16 as regulating expression of the TJ genes CGN (cingulin) and CLDN2 (claudin-2), respectively. Consistently, protein expression of CGN and CLDN2 was upregulated in IBS-D, while the respective targeting miRNAs were downregulated. In addition, bowel dysfunction, perceived stress and depression and number of mast cells correlated with the expression of hsa-miR-125b-5p and hsa-miR-16 and their respective target proteins.

CONCLUSIONS

Modulation of the intestinal epithelial barrier function in IBS-D involves both transcriptional and post-transcriptional mechanisms. These molecular mechanisms include miRNAs as master regulators in controlling the expression of TJ proteins and are associated with major clinical symptoms.

First description of spontaneous fungal peritonitis caused by Fusarium solani in a critically ill patient with liver cirrhosis

Fusarium spp., common soil moulds, are emerging fungal pathogens in immunocompromised subjects. We report the first case of Fusarium solani peritonitis in a patient with liver cirrhosis. Because of the high morbidity and mortality associated with fusariosis, an aggressive approach to treatment as well as identification of the species and drug susceptibilities is warranted.

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive neoplasm of mature T-cells with an urgent need for rationally designed therapies to address its notoriously chemo-refractory behavior. The median survival of T-PLL patients is <2 years and clinical trials are difficult to execute. Here we systematically explored the diversity of drug responses in T-PLL patient samples using an ex vivo drug sensitivity and resistance testing platform and correlated the findings with somatic mutations and gene expression profiles. Intriguingly, all T-PLL samples were sensitive to the cyclin-dependent kinase inhibitor SNS-032, which overcame stromal-cell-mediated protection and elicited robust p53-activation and apoptosis. Across all patients, the most effective classes of compounds were histone deacetylase, phosphoinositide-3 kinase/AKT/mammalian target of rapamycin, heat-shock protein 90 and BH3-family protein inhibitors as well as p53 activators, indicating previously unexplored, novel targeted approaches for treating T-PLL. Although Janus-activated kinase-signal transducer and activator of transcription factor (JAK-STAT) pathway mutations were common in T-PLL (71% of patients), JAK-STAT inhibitor responses were not directly linked to those or other T-PLL-specific lesions. Overall, we found that genetic markers do not readily translate into novel effective therapeutic vulnerabilities. In conclusion, novel classes of compounds with high efficacy in T-PLL were discovered with the comprehensive ex vivo drug screening platform warranting further studies of synergisms and clinical testing.

Evaluation of an ADVanced Organ Support (ADVOS) system in a two-hit porcine model of liver failure plus endotoxemia

Background

Novel extracorporeal procedures are constantly being developed and evaluated for use in patients with sepsis. Preclinical evaluation of such procedures usually requires testing in large animal models. In the present work, the safety and efficacy of a recently developed ADVanced Organ Support (ADVOS) system in a newly developed large animal two-hit model of liver failure combined with endotoxemia were tested.

Methods

After establishing the model in more than 50 animals, a randomized study was performed. An inflammatory cholestatic liver injury was initially provoked in pigs. Three days after surgery, endotoxin was gradually administered during 7½ h. Animals were randomized to receive standard medical treatment either with (ADVOS group, n = 5) or without ADVOS (control group, n = 5). The ADVOS treatment was started 2½ h after endotoxemia and continued for 7 h. Survival, cardiovascular, respiratory, renal, liver, coagulation, and cerebral parameters were analyzed.

Results

Three days after surgery, cholestatic injury resulted in hyperbilirubinemia [5.0 mg/dl (IQR 4.3–5.9 mg/dl)], hyperammonemia [292 μg/dl (IQR 291–296 μg/dl)], leukocytosis [20.2 10³/μl (IQR 17.7–21.8 10³/μl)], and hyperfibrinogenemia [713 mg/dl (IQR 654–803 mg/dl)]. After endotoxemia, the ADVOS procedure stabilized cardiovascular, respiratory, and renal parameters and eliminated surrogate markers as bilirubin [2.3 (IQR 2.3–3.0) vs. 5.5 (IQR 4.6–5.6) mg/dl, p = 0.001] and creatinine [1.4 (IQR 1.1–1.7) vs. 2.3 (IQR 2.1–3.1) mg/dl, p = 0.01]. Mortality: All animals in the ADVOS group survived, while all animals in the control group expired during the 10-h observation period (p = 0.002). No adverse events related to the procedure were observed.

Conclusions

The ADVOS procedure showed a promising safety and efficacy profile and improved survival in a sepsis-like animal model with dysfunction of multiple organs. An amelioration of major organ functions (heart and lung) combined with removal of markers for kidney and liver function was observed.

Electronic supplementary material

The online version of this article (doi:10.1186/s40635-017-0144-3) contains supplementary material, which is available to authorized users.

Femoral indicator injection for transpulmonary thermodilution using the EV1000/VolumeView(®): do the same criteria apply as for the PiCCO(®)?

OBJECTIVE

Comparison of global end-diastolic volume index (GEDVI) obtained by femoral and jugular transpulmonary thermodilution (TPTD) indicator injections using the EV1000/VolumnView(®) device (Edwards Lifesciences, Irvine, USA).

METHODS

In an 87-year-old woman with hypovolemic shock and equipped with both jugular and femoral vein access and monitored with the EV1000/VolumeView(®) device, we recorded 10 datasets, each comprising duplicate TPTD via femoral access and duplicate TPTD (20 ml cold saline) via jugular access.

RESULTS

Mean femoral GEDVI ((674.6±52.3) ml/m(2)) was significantly higher than jugular GEDVI ((552.3±69.7) ml/m(2)), with P=0.003. Bland-Altman analysis demonstrated a bias of (+122±61) ml/m(2), limits of agreement of -16 and +260 ml/m(2), and a percentage error of 22%. Use of the correction-formula recently suggested for the PiCCO(®) device significantly reduced bias and percentage error. Similarly, mean values of parameters derived from GEDVI such as pulmonary vascular permeability index (PVPI; 1.244±0.101 vs. 1.522±0.139; P<0.001) and global ejection fraction (GEF; (24.7±1.6)% vs. (28.1±1.8)%; P<0.001) were significantly different in the case of femoral compared to jugular indicator injection. Furthermore, the mean cardiac index derived from femoral indicator injection ((4.50±0.36) L/(min·m²)) was significantly higher (P=0.02) than that derived from jugular indicator injection ((4.12±0.44) L/(min·m²)), resulting in a bias of (+0.38±0.37) L/(min·m²) and a percentage error of 19.4%.

CONCLUSIONS

Femoral access for indicator injection results in markedly altered values provided by the EV1000/VolumeView(®), particularly for GEDVI, PVPI, and GEF.