Inhibition of the dipeptidyl peptidase DPP4 (CD26) reveals IL-33-dependent eosinophil-mediated control of tumor growth.

Post-translational modification of chemokines mediated by the dipeptidyl peptidase DPP4 (CD26) has been shown to negatively regulate lymphocyte trafficking, and its inhibition enhances T cell migration and tumor immunity by preserving functional chemokine CXCL10. By extending those initial findings to pre-clinical models of hepatocellular carcinoma and breast cancer, we discovered a distinct mechanism by which inhibition of DPP4 improves anti-tumor responses. Administration of the DPP4 inhibitor sitagliptin resulted in higher concentrations of the chemokine CCL11 and increased migration of eosinophils into solid tumors. Enhanced tumor control was preserved in mice lacking lymphocytes and was ablated after depletion of eosinophils or treatment with degranulation inhibitors. We further demonstrated that tumor-cell expression of the alarmin IL-33 was necessary and sufficient for eosinophil-mediated anti-tumor responses and that this mechanism contributed to the efficacy of checkpoint-inhibitor therapy. These findings provide insight into IL-33- and eosinophil-mediated tumor control, revealed when endogenous mechanisms of DPP4 immunoregulation are inhibited.

Performance of spleen stiffness measurement to rule out high-risk varices in patients with porto-sinusoidal vascular disorder.

BACKGROUND AND AIMS: Baveno VII consensus suggests that screening endoscopy can be spared in patients with compensated cirrhosis when spleen stiffness measurement (SSM) by vibration-controlled transient elastography (VCTE) is ≤40 kPa as they have a low probability of high-risk varices (HRV). Conversely, screening endoscopy is required in all patients with porto-sinusoidal vascular disorder (PSVD). This study aimed to evaluate the performance of SSM-VCTE to rule out HRV in patients with PSVD and signs of portal hypertension. APPROACH AND RESULTS: We retrospectively included patients with PSVD, ≥1 sign of portal hypertension, without a history of variceal bleeding, who underwent an SSM-VCTE within 2 years before or after an upper endoscopy in 21 VALDIG centers, divided into a derivation and a validation cohort. One hundred fifty-four patients were included in the derivation cohort; 43% had HRV. By multivariable logistic regression analysis, SSM-VCTE >40 kPa and serum bilirubin ≥1 mg/dL were associated with HRV. SSM-VCTE ≤40 kPa combined with bilirubin <1 mg/dL had a sensitivity of 96% to rule out HRV and could spare 38% of screening endoscopies, with 4% of HRV missed, and a 95% negative predictive value. In the validation cohort, including 155 patients, SSM combined with bilirubin could spare 21% of screening endoscopies, with 4% of HRV missed and a 94% negative predictive value. CONCLUSIONS: This study gathering a total of 309 patients with PSVD showed that SSM-VCTE ≤40 kPa combined with bilirubin <1 mg/dL identifies patients with PSVD and portal hypertension with a probability of HRV <5%, in whom screening endoscopy can be spared.

Alcohol Rehabilitation Within 3 Months After Alcohol Hepatitis and Survival - A National Analysis.

BACKGROUND & AIMS: There is limited understanding of the benefits of alcohol rehabilitation after alcohol hepatitis (AH). METHODS: We conducted a 2012 to 2021 national longitudinal study involving adult inpatients diagnosed with AH in France. We assessed the primary outcome of liver transplantation or death within 1 year after AH, including in its complicated form (CAH) defined as ≥2 hepatic or extrahepatic complications within 4 weeks after AH. The primary exposure was in-hospital alcohol rehabilitation within 3 months following AH. Patients who died (6.5%; n = 5282) or were censored (12.5%; n = 10,180) ≤4 weeks after AH were excluded. We measured adjusted hazard ratios (aHRs) and adjusted odds ratios (aORs) within the full cohort and propensity-matched samples. RESULTS: Among 65,737 patients (median age, 52 years; interquartile range [IQR], 44-60 years; 76% male), 12% died or underwent liver transplantation. In-hospital alcohol rehabilitation was noted for 25% of patients (15.2% among patients with CAH) and was the primary discharge diagnosis for 13.3%. The 1-year transplant-free survival rates were 94% (95% confidence interval [CI], 94%-95%) for rehabilitated patients, compared with 85% (95% CI, 85%-86%) for those without (aHR, 0.62; 95% CI, 0.57-0.69; P < .001). Among patients with CAH, transplant-free survival was 78% (95% CI, 76%-81%) with rehabilitation vs 70% (95% CI, 69%-71%) without (aHR, 0.82; 95% CI, 0.68-0.98; P = .025). In propensity-matched samples, rehabilitation was linked to an aOR of 0.54 (95% CI, 0.49-0.55; P < .001) overall, and 0.73 (95% CI, 0.60-0.89; P = .002) among matched patients with CAH. CONCLUSIONS: In-hospital alcohol rehabilitation within 3 months after AH and CAH improve transplant-free survival rate but remain underutilized.

Liver disease in germline mutations of telomere-related genes: Prevalence, clinical, radiological, pathological features, outcome, and risk factors.

BACKGROUND AND AIM: Germline mutations of telomere-related genes (TRG) induce multiorgan dysfunction, and liver-specific manifestations have not been clearly outlined. We aimed to describe TRG mutations-associated liver diseases. APPROACH AND RESULTS: Retrospective multicenter analysis of liver disease (transaminases > 30 IU/L and/or abnormal liver imaging) in patients with TRG mutations. Main measurements were characteristics, outcomes, and risk factors of liver disease in a TRG mutations cohort. The prevalence of liver disease was compared to a community-based control group (n = 1190) stratified for age and matched 1:3 for known risk factors of liver disease. Among 132 patients with TRG mutations, 95 (72%) had liver disease, with associated lung, blood, skin, rheumatological, and ophthalmological TRG diseases in 82%, 77%, 55%, 39%, and 30% of cases, respectively. Liver biopsy was performed in 52/95 patients, identifying porto-sinusoidal vascular disease in 48% and advanced fibrosis/cirrhosis in 15%. After a follow-up of 21 months (12-54), ascites, hepato-pulmonary syndrome, variceal bleeding, and HCC occurred in 14%, 13%, 13%, and 2% of cases, respectively. Five-year liver transplantation-free survival was 69%. A FIB-4 score ≥ 3·25 and ≥1 risk factor for cirrhosis were associated with poor liver transplantation-free survival. Liver disease was more frequent in patients with TRG mutations than in the paired control group [80/396, (20%)], OR 12.9 (CI 95%: 7.8-21.3, p < 0.001). CONCLUSIONS: TRG mutations significantly increase the risk of developing liver disease. Although symptoms may be mild, they may be associated with severe disease. Porto-sinusoidal vascular disease and cirrhosis were the most frequent lesions, suggesting that the mechanism of action is multifactorial.

The oncologic burden of hepatitis C virus infection: A clinical perspective.

Answer questions and earn CME/CNE Chronic hepatitis C virus (HCV) infection affects millions of people worldwide and is associated with cancer. Direct-acting antivirals (DAAs) have changed HCV treatment paradigms, but little is known about the management of HCV infection in patients with cancer. The substantial burden of HCV infection and the inconclusive evidence regarding its detection and management in patients with cancer prompted the authors to review the literature and formulate recommendations. Patients for whom HCV screening is recommended included all patients with hematologic malignancies, hematopoietic cell transplantation candidates, and patients with liver cancer. There is a lack of consensus-based recommendations for the identification of HCV-infected patients with other types of cancer, but physicians may at least consider screening patients who belong to groups at heightened risk of HCV infection, including those born during 1945 through 1965 and those at high risk for infection. Patients with evidence of HCV infection should be assessed by an expert to evaluate liver disease severity, comorbidities associated with HCV infection, and treatment opportunities. DAA therapy should be tailored on the basis of patient prognosis, type of cancer, cancer treatment plan, and hepatic and virologic parameters. HCV-infected patients with cancer who have cirrhosis (or even advanced fibrosis) and those at risk for liver disease progression, especially patients with HCV-associated comorbidities, should have ongoing follow-up, regardless of whether there is a sustained virologic response, to ensure timely detection and treatment of hepatocellular carcinoma. HCV infection and its treatment should not be considered contraindications to cancer treatment and should not delay the initiation of an urgent cancer therapy. CA Cancer J Clin 2017. © 2017 American Cancer Society. CA Cancer J Clin 2017;67:411-431. © 2017 American Cancer Society.

Evolution of minimally invasive liver surgery in France over the last decade.

BACKGROUND: Despite evidence of benefits on postoperative outcomes, minimally invasive liver surgery (MILS) had a very low diffusion up to 2014, and recent evolution is unknown. Our aim was to analyze the recent diffusion and adoption of MILS and compare the trends in indications, extent of resection, and institutional practice with open liver surgery (OLS). METHODS: We analyzed the French nationwide, exhaustive cohort of all patients undergoing a liver resection in France between January 1, 2013 and December 31, 2022. Average annual percentage changes (AAPC) in the incidence of MILS and OLS were compared using mixed-effects log-linear regression models. Time trends were analyzed in terms of extent of resection, indication, and institutional practice. RESULTS: MILS represented 25.2% of 74,671 liver resections and year incidence doubled from 16.5% in 2013 to 35.4% in 2022. The highest AAPC were observed among major liver resections [+ 22.2% (19.5; 24.9) per year], primary [+ 10.2% (8.5; 12.0) per year], and secondary malignant tumors [+ 9.9% (8.2; 11.6) per year]. The highest increase in MILS was observed in university hospitals [+ 14.7% (7.7; 22.2) per year] performing 48.8% of MILS and in very high-volume (> 150 procedures/year) hospitals [+ 12.1% (9.0; 15.3) per year] performing 19.7% of MILS. OLS AAPC decreased for all indications and institutions and accelerated over time from - 1.8% (- 3.9; - 0.3) per year in 2013-2018 to - 5.9% (- 7.9; - 3.9) per year in 2018-2022 (p = 0.013). CONCLUSIONS: This is the first reported trend reversal between MILS and OLS. MILS has considerably increased at a national scale, crossing the 20% tipping point of adoption rate as defined by the IDEAL framework.

Mental disorders, COVID-19-related life-saving measures and mortality in France: A nationwide cohort study.

BACKGROUND: Meta-analyses have shown that preexisting mental disorders may increase serious Coronavirus Disease 2019 (COVID-19) outcomes, especially mortality. However, most studies were conducted during the first months of the pandemic, were inconclusive for several categories of mental disorders, and not fully controlled for potential confounders. Our study objectives were to assess independent associations between various categories of mental disorders and COVID-19-related mortality in a nationwide sample of COVID-19 inpatients discharged over 18 months and the potential role of salvage therapy triage to explain these associations. METHODS AND FINDINGS: We analysed a nationwide retrospective cohort of all adult inpatients discharged with symptomatic COVID-19 between February 24, 2020 and August 28, 2021 in mainland France. The primary exposure was preexisting mental disorders assessed from all discharge information recorded over the last 9 years (dementia, depression, anxiety disorders, schizophrenia, alcohol use disorders, opioid use disorders, Down syndrome, other learning disabilities, and other disorder requiring psychiatric ward admission). The main outcomes were all-cause mortality and access to salvage therapy (intensive-care unit admission or life-saving respiratory support) assessed at 120 days after recorded COVID-19 diagnosis at hospital. Independent associations were analysed in multivariate logistic models. Of 465,750 inpatients with symptomatic COVID-19, 153,870 (33.0%) were recorded with a history of mental disorders. Almost all categories of mental disorders were independently associated with higher mortality risks (except opioid use disorders) and lower salvage therapy rates (except opioid use disorders and Down syndrome). After taking into account the mortality risk predicted at baseline from patient vulnerability (including older age and severe somatic comorbidities), excess mortality risks due to caseload surges in hospitals were +5.0% (95% confidence interval (CI), 4.7 to 5.2) in patients without mental disorders (for a predicted risk of 13.3% [95% CI, 13.2 to 13.4] at baseline) and significantly higher in patients with mental disorders (+9.3% [95% CI, 8.9 to 9.8] for a predicted risk of 21.2% [95% CI, 21.0 to 21.4] at baseline). In contrast, salvage therapy rates during caseload surges in hospitals were significantly higher than expected in patients without mental disorders (+4.2% [95% CI, 3.8 to 4.5]) and lower in patients with mental disorders (-4.1% [95% CI, -4.4; -3.7]) for predicted rates similar at baseline (18.8% [95% CI, 18.7-18.9] and 18.0% [95% CI, 17.9-18.2], respectively). The main limitations of our study point to the assessment of COVID-19-related mortality at 120 days and potential coding bias of medical information recorded in hospital claims data, although the main study findings were consistently reproduced in multiple sensitivity analyses. CONCLUSIONS: COVID-19 patients with mental disorders had lower odds of accessing salvage therapy, suggesting that life-saving measures at French hospitals were disproportionately denied to patients with mental disorders in this exceptional context.

RNAglib: a python package for RNA 2.5 D graphs.

SUMMARY: RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent progresses in machine learning techniques. RNAglib is a library that eases the use of this representation, by providing clean data, methods to load it in machine learning pipelines and graph-based deep learning models suited for this representation. RNAglib also offers other utilities to model RNA with 2.5 D graphs, such as drawing tools, comparison functions or baseline performances on RNA applications. AVAILABILITY AND IMPLEMENTATION: The method is distributed as a pip package, RNAglib. Data are available in a repository and can be accessed on rnaglib's web page. The source code, data and documentation are available at https://rnaglib.cs.mcgill.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Vernal: a tool for mining fuzzy network motifs in RNA.

MOTIVATION: RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space. RESULTS: Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs. AVAILABILITY AND IMPLEMENTATION: The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.

MOTIVATION: Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult task and requires extensive efforts to qualify a given interaction as an eligible target. To this end, besides the evident need to determine the role of PPIs in disease-associated pathways and their experimental characterization as therapeutics targets, prediction of their capacity to be bound by other protein partners or modulated by future drugs is of primary importance. RESULTS: We present InDeep, a tool for predicting functional binding sites within proteins that could either host protein epitopes or future drugs. Leveraging deep learning on a curated dataset of PPIs, this tool can proceed to enhanced functional binding site predictions either on experimental structures or along molecular dynamics trajectories. The benchmark of InDeep demonstrates that our tool outperforms state-of-the-art ligandable binding sites predictors when assessing PPI targets but also conventional targets. This offers new opportunities to assist drug design projects on PPIs by identifying pertinent binding pockets at or in the vicinity of PPI interfaces. AVAILABILITY AND IMPLEMENTATION: The tool is available on GitLab at https://gitlab.pasteur.fr/InDeep/InDeep. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Burden of liver disease progression in hospitalized patients with type 2 diabetes mellitus.

BACKGROUND & AIMS: There are uncertainties regarding the burden of liver disease in patients with type 2 diabetes (T2D). Thus, we aimed to quantify the burden of liver disease, identify risk factors, and estimate attributable risks in patients with T2D. METHODS: We measured adjusted hazard ratios of liver disease progression to hepatocellular carcinoma and/or decompensated cirrhosis in a 2010-2020 retrospective, bicentric, longitudinal, cohort of 52,066 hospitalized patients with T2D. RESULTS: Mean age was 64±14 years and 58% were men. Alcohol use disorders accounted for 57% of liver-related complications and were associated with all liver-related risk factors. Non-metabolic liver-related risk factors accounted for 37% of the liver burden. T2D control was not associated with liver disease progression. The incidence (95% CI) of liver-related complications and of competing mortality were 3.9 (3.5-4.3) and 27.8 (26.7-28.9) per 1,000 person-years at risk, respectively. The cumulative incidence of liver disease progression exceeded the cumulative incidence of competing mortality only in the presence of well-identified risk factors of liver disease progression, including alcohol use. The incidence of hepatocellular carcinoma was 0.3 (95% CI 0.1-0.5) per 1,000 person-years in patients with obesity and it increased with age. The adjusted hazard ratios of liver disease progression were 55.7 (40.5-76.6), 3.5 (2.3-5.2), 8.9 (6.9-11.5), and 1.5 (1.1-2.1), for alcohol-related liver disease, alcohol use disorders without alcohol-related liver disease, non-metabolic liver-related risk factors, and obesity, respectively. The attributable fractions of alcohol use disorders, non-metabolic liver-related risk factors, and obesity to the liver burden were 55%, 14%, and 7%, respectively. CONCLUSIONS: In this analysis of data from 2 hospital-based cohorts of patients with T2D, alcohol use disorders, rather than obesity, contributed to most of the liver burden. These results suggest that patients with T2D should be advised to drink minimal amounts of alcohol. LAY SUMMARY: There is uncertainty on the burden of liver-related complications in patients with type 2 diabetes. We studied the risks of liver cancer and complications of liver disease in over 50,000 patients with type 2 diabetes. We found that alcohol was the main factor associated with complications of liver disease. This finding has major implications on the alcohol advice given to patients with type 2 diabetes.

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories.

SUMMARY: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. AVAILABILITY AND IMPLEMENTATION: The method is available on GitHub and distributed as a pip package.

Augmented base pairing networks encode RNA-small molecule binding preferences.

RNA-small molecule binding is a key regulatory mechanism which can stabilize 3D structures and activate molecular functions. The discovery of RNA-targeting compounds is thus a current topic of interest for novel therapies. Our work is a first attempt at bringing the scalability and generalization abilities of machine learning methods to the problem of RNA drug discovery, as well as a step towards understanding the interactions which drive binding specificity. Our tool, RNAmigos, builds and encodes a network representation of RNA structures to predict likely ligands for novel binding sites. We subject ligand predictions to virtual screening and show that we are able to place the true ligand in the 71st-73rd percentile in two decoy libraries, showing a significant improvement over several baselines, and a state of the art method. Furthermore, we observe that augmenting structural networks with non-canonical base pairing data is the only representation able to uncover a significant signal, suggesting that such interactions are a necessary source of binding specificity. We also find that pre-training with an auxiliary graph representation learning task significantly boosts performance of ligand prediction. This finding can serve as a general principle for RNA structure-function prediction when data is scarce. RNAmigos shows that RNA binding data contains structural patterns with potential for drug discovery, and provides methodological insights for possible applications to other structure-function learning tasks. The source code, data and a Web server are freely available at http://rnamigos.cs.mcgill.ca.

Prognosis of French COVID-19 patients with chronic liver disease: A national retrospective cohort study for 2020.

BACKGROUND & AIMS: The impact of chronic liver disease on outcomes in patients with COVID-19 is uncertain. Hence, we aimed to explore this association. METHODS: We explored the outcomes of all adult inpatients with COVID-19 in France, in 2020. We computed adjusted odds ratios to measure the associations between chronic liver disease, alcohol use disorders, mechanical ventilation and day-30 in-hospital mortality. RESULTS: The sample comprised 259,110 patients (median [IQR] age 70 (54-83) years; 52% men), including 15,476 (6.0%) and 10,006 (3.9%) patients with chronic liver disease and alcohol use disorders, respectively. Death occurred in 38,203 (15%) patients, including 7,475 (28%) after mechanical ventilation, and 2,941 (19%) with chronic liver disease. The adjusted odds ratios for mechanical ventilation and day-30 mortality were 1.54 (95% CI 1.44-1.64, p <0.001) and 1.79 (1.71-1.87, p <0.001) for chronic liver disease; 0.55 (0.47-0.64, p <0.001) and 0.54 (0.48-0.61, p <0.001) for mild liver disease; 0.64 (0.53-0.76; p <0.001) and 0.71 (0.63-0.80, p <0.001) for compensated cirrhosis; 0.65 (0.52-0.81, p <0.001) and 2.21 (1.94-2.51, p <0.001) for decompensated cirrhosis; 0.34 (0.24-0.50; p <0.001) and 1.38 (1.17-1.62, p <0.001) for primary liver cancer; and 0.82 (0.76-0.89; p <0.001) and 1.11 (1.05-1.17; p <0.001) for alcohol use disorders. Chronic viral hepatitis; non-viral, non-alcoholic chronic hepatitis; organ, including liver, transplantation, and acquired immunodeficiency syndrome were not associated with COVID-19-related death. CONCLUSION: Chronic liver disease increased the risk of COVID-19-related death in France in 2020. Therapeutic effort limitation may have contributed to COVID-19-related death in French residents with a liver-related complication or an alcohol use disorder. LAY SUMMARY: We studied the outcomes, including mechanical ventilation and day-30 mortality, of all adults with COVID-19 who were discharged from acute and post-acute care in France in 2020 (N = 259,110). Patients with mild liver disease; compensated cirrhosis; organ, including liver, transplantation; or acquired immunodepression syndrome were not at increased risk of COVID-19-related mortality. Patients with alcohol use disorders, decompensated cirrhosis, or primary liver cancer were at increased risk of COVID-19-related mortality but were less likely to receive mechanical ventilation. Our results suggest that therapeutic effort limitation may have contributed to the excess mortality in French residents with a liver-related complication or an alcohol use disorder.

Can we differentiate HIV-associated obliterative portopathy from liver cirrhosis using MRI?

AIM: To describe the magnetic resonance imaging (MRI) features of HIV-associated obliterative portopathy (HIV-OP) and determine the most indicative appearance of this condition on MRI by using a retrospective case-control study. METHODS: MRI examinations of 24 patients with HIV-OP (16 men, 8 women; mean age = 48 ± 6.6 [SD] years; age range, 35-71 years) were analyzed by two blinded observers and compared with those obtained in 18 HIV-infected patients with hepatic cirrhosis (14 men, 4 women; mean age = 51 ± 3.4 [SD] years; age range, 35-60 years). Images were qualitatively and quantitatively analyzed with respect to imaging presentation. Comparisons were performed using uni- and multivariate analyses. RESULTS: Regular liver contours had the highest accuracy for the diagnosis of HIV-OP (83%, 35 of 42; 95% confidence interval [CI], 69-93%) and was the most discriminating independent variable for the diagnosis of HIV-OP (odds ratio, 51; 95%CI, 4.96-1272%) (p < 0.0001). At multivariate analysis, the width of segment 4 in millimeters (OR = 1.23 [95%CI, 1.05-1.44%]; p = 0.011) and the presence of regular liver contours (OR = 7.69 [95%CI, 1.48-39.92%]; p = 0.015) were the variables independently associated with the diagnosis of HIV-OP. CONCLUSIONS: Regular liver contours are the most discriminating independent variable for the diagnosis of HIV-OP but have limited accuracy. Familiarity with this finding may help differentiate HIV-OP from cirrhosis in HIV-infected patients. KEY POINTS: • Regular liver contour is the most discriminating independent variable for the diagnosis of HIV-OP (odds ratio = 51) with 83% accuracy. • At multivariate analysis, the width of segment 4 in millimeters and the presence of regular liver contours are the variables independently associated with the diagnosis of HIV-OP. • MRI helps diagnose HIV-OP in the presence of several categorical findings, which are more frequently observed in HIV-OP patients than in HIV patients with cirrhosis.

OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery.

Ligand-based drug design has recently benefited from the development of deep generative models. These models enable extensive explorations of the chemical space and provide a platform for molecular optimization. However, the vast majority of current methods does not leverage the structure of the binding target, which potentiates the binding of small molecules and plays a key role in the interaction. We propose an optimization pipeline that leverages complementary structure-based and ligand-based methods. Instead of performing docking on a fixed chemical library, we iteratively select promising compounds in the full chemical space using a ligand-centered generative model. Molecular docking is then used as an oracle to guide compound optimization. This allows for iterative generation of compounds that fit the target structure better and better, without prior knowledge about bioactives. For this purpose, we introduce a new graph to Selfies Variational Autoencoder (VAE) which benefits from an 18-fold faster decoding than the graph to graph state of the art, while achieving a similar performance. We then successfully optimize the generation of molecules toward high docking scores, enabling a 10-fold enrichment of high-scoring compounds found with a fixed computational cost.

Contributing factors and outcomes of burn-associated cholestasis.

BACKGROUND & AIMS: Cholestasis often occurs after burn injuries. However, the prevalence of cholestasis and its effect on outcomes in patients with severe burn injuries are unknown. The aim of this study was to describe the course and the burden of cholestasis in a cohort of severely burned adult patients. METHODS: We investigated the relationship between burn-associated cholestasis (BAC) and clinical outcomes in a retrospective cohort of patients admitted to our unit for severe burn injuries between 2012 and 2015. BAC was defined as an increased level of serum alkaline phosphatase (ALP) ≥1.5x the upper limit of normal (ULN) with an increased level of gamma-glutamyltransferase (GGT) ≥3x ULN, or as an increased level of total bilirubin ≥2x ULN. RESULTS: A total of 214 patients were included: 111 (52%) patients developed BAC after a median (IQR) stay of 9 (5-16) days. At 90 days, the mortality rate was 20%, including 34 and 9 patients with and without BAC (p <0.001), respectively, which corresponded to a 2.5-fold higher (95% CI 1.2-5.2, p = 0.012) risk of 90-day mortality for patients with BAC. After being adjusted for severity of illness, patients with BAC, hyperbilirubinemia and without elevated ALP and GGT levels had a hazard ratio of 4.51 (95% CI 1.87-10.87) for 90-day mortality. BAC was associated with the severity of the burn injury, shock and bacteraemia. BAC was present in 38 (51%) patients at discharge, and 7 (18%) patients had secondary sclerosing cholangitis. These patients maintained elevated levels of ALP and GGT that were 5.8x (1.7-15) the ULN and 11x the ULN (4.5-22), respectively, 20 months (3.5-35) after discharge. CONCLUSION: BAC is prevalent among patients with severe burn injuries and is associated with worse short-term outcomes, especially when total bilirubin levels were increased without elevated ALP and GGT levels. BAC survivors are at risk of developing sclerosing cholangitis. LAY SUMMARY: Cholestasis is common after burn injuries and is associated with burn severity, sepsis, organ failure and mortality. Patients with hyperbilirubinemia without elevated alkaline phosphatase and gamma-glutamyltransferase levels after the burn injury have a poor prognosis. Patients with burn-associated cholestasis may develop sclerosing cholangitis and secondary biliary cirrhosis.

The burden of hepatitis E among patients with haematological malignancies: A retrospective European cohort study.

BACKGROUND & AIMS: The burden of hepatitis E virus (HEV) infection among patients with haematological malignancy has only been scarcely reported. Therefore, we aimed to describe this burden in patients with haematological malignancies, including those receiving allogeneic haematopoietic stem cell transplantation. METHODS: We conducted a retrospective, multicentre cohort study across 11 European centres and collected clinical characteristics of 50 patients with haematological malignancy and RNA-positive, clinically overt hepatitis E between April 2014 and March 2017. The primary endpoint was HEV-associated mortality; the secondary endpoint was HEV-associated liver-related morbidity. RESULTS: The most frequent underlying haematological malignancies were aggressive non-Hodgkin lymphoma (NHL) (34%), indolent NHL (iNHL) (24%), and acute leukaemia (36%). Twenty-one (42%) patients had received allogeneic haematopoietic stem cell transplantation (alloHSCT). Death with ongoing hepatitis E occurred in 8 (16%) patients, including 1 patient with iNHL and 1 patient >100 days after alloHSCT in complete remission, and was associated with male sex (p = 0.040), cirrhosis (p = 0.006) and alloHSCT (p = 0.056). Blood-borne transmission of hepatitis E was demonstrated in 5 (10%) patients, and associated with liver-related mortality in 2 patients. Hepatitis E progressed to chronic hepatitis in 17 (34%) patients overall, and in 10 (47.6%) and 6 (50%) alloHSCT and iNHL patients, respectively. Hepatitis E was associated with acute or acute-on-chronic liver failure in 4 (8%) patients with 75% mortality. Ribavirin was administered to 24 (48%) patients, with an HEV clearance rate of 79.2%. Ribavirin treatment was associated with lower mortality (p = 0.037) and by trend with lower rates of chronicity (p = 0.407) when initiated <24 and <12 weeks after diagnosis of hepatitis E, respectively. Immunosuppressive treatment reductions were associated with mortality in 2 patients (28.6%). CONCLUSION: Hepatitis E is associated with mortality and liver-related morbidity in patients with haematological malignancy. Blood-borne transmission contributes to the burden. Ribavirin should be initiated early, whereas reduction of immunosuppressive treatment requires caution. LAY SUMMARY: Little is known about the burden of hepatitis E among patients with haematological malignancy. We conducted a retrospective European cohort study among 50 patients with haematological malignancy, including haematopoietic stem cell transplant recipients, with clinically significant HEV infection and found that hepatitis E is associated with hepatic and extrahepatic mortality, including among patients with indolent disease or among stem cell transplant recipients in complete remission. Hepatitis E virus infection evolved to chronic hepatitis in 5 (45.5%) patients exposed to a rituximab-containing regimen and 10 (47.6%) stem cell transplant recipients. Reducing immunosuppressive therapy because of hepatitis E was associated with mortality, while early ribavirin treatment was safe and effective.

Association between hydroxocobalamin administration and acute kidney injury after smoke inhalation: a multicenter retrospective study.

BACKGROUND: The use of hydroxocobalamin has long been advocated for treating suspected cyanide poisoning after smoke inhalation. Intravenous hydroxocobalamin has however been shown to cause oxalate nephropathy in a single-center study. The impact of hydroxocobalamin on the risk of acute kidney injury (AKI) and survival after smoke inhalation in a multicenter setting remains unexplored. METHODS: We conducted a multicenter retrospective study in 21 intensive care units (ICUs) in France. We included patients admitted to an ICU for smoke inhalation between January 2011 and December 2017. We excluded patients discharged at home alive within 24 h of admission. We assessed the risk of AKI (primary endpoint), severe AKI, major adverse kidney (MAKE) events, and survival (secondary endpoints) after administration of hydroxocobalamin using logistic regression models. RESULTS: Among 854 patients screened, 739 patients were included. Three hundred six and 386 (55.2%) patients received hydroxocobalamin. Mortality in ICU was 32.9% (n = 243). Two hundred eighty-eight (39%) patients developed AKI, including 186 (25.2%) who developed severe AKI during the first week. Patients who received hydroxocobalamin were more severe and had higher mortality (38.1% vs 27.2%, p = 0.0022). The adjusted odds ratio (95% confidence interval) of AKI after intravenous hydroxocobalamin was 1.597 (1.055, 2.419) and 1.772 (1.137, 2.762) for severe AKI; intravenous hydroxocobalamin was not associated with survival or MAKE with an adjusted odds ratio (95% confidence interval) of 1.114 (0.691, 1.797) and 0.784 (0.456, 1.349) respectively. CONCLUSION: Hydroxocobalamin was associated with an increased risk of AKI and severe AKI but was not associated with survival after smoke inhalation. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03558646.