Assessing parallel gene histories in viral genomes

Background: The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes. Results: The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. Conclusions: The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.IGB was funded by the disappeared Spanish Ministry for Science and Innovation (CGL2010-16713). Work in Valencia was supported by grant BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO) to SFE. BMC is the recipient of an IDIBELL PhD fellowship.Mengual-Chuliá, B.; Bedhomme, S.; Lafforgue, G.; Elena Fito, SF.; Bravo, IG. (2016). Assessing parallel gene histories in viral genomes. BMC Evolutionary Biology. 16:1-15. https://doi.org/10.1186/s12862-016-0605-4S11516Hess J, Goldman N. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited. PLoS ONE. 2011;6:e22783.Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. 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Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Mowat Wilson syndrome and Hirschsprung disease: a retrospective study on functional outcomes

International audienceAim of the study: Mowat Wilson syndrome (MWS) is a complex genetic disorder due to mutation or deletion of the ZEB2 gene (ZFHX1B), including multiple clinical features. Hirschsprung disease is associated with this syndrome with a prevalence between 43 and 57%. The aim of this study was to demonstrate the severe outcomes and the high complication rates in children with MWS, focusing on their complicated follow-up.Methods: A retrospective comparative study was conducted on patients referred to Robert-Debré Children's Hospital for MWS from 2003 to 2018. Multidisciplinary follow-up was carried out by surgeons, geneticists, gastroenterologists, and neurologists. Data regarding patient characteristics, surgical management, postoperative complications, and functional outcomes were collected.Results: Over this period of 15 years, 23 patients were diagnosed with MWS. Hirschsprung disease was associated with 10 of them (43%). Of these cases, two patients had recto-sigmoïd aganglionosis (20%), three had aganglionic segment extension to the left colic angle (30%), two to the right colic angle (20%), and three to the whole colon (30%). The median follow-up was 8.5 years (2 months-15 years). All patients had seizures and intellectual disability. Six children (60%) presented with cardiac defects. At the last follow-up, three patients still had a stoma diversion and 7 (70%) were fed orally. One patient died during the first months. Eight (80%) of these children required a second surgery due to complications. At the last follow-up, three patients reported episodes of abdominal bloating (42%), one recurrent treated constipation (14.3%), and one soiling (14.3%). Genetic analysis identified three patients with heterozygous deletions, three with codon mutations, and three with frameshift mutations.Conclusions: MWS associated with Hirschsprung disease has a high rate of immediate surgical complications but some patients may achieve bowel function comparable with non-syndromic HD patients. A multidisciplinary follow-up is required for these patients

Generation of three human induced pluripotent stem cell lines with IRX5 knockout and knockin genetic editions using CRISPR-Cas9 system

International audienceStudies on animal models have shown that Irx5 is an important regulator of cardiac development and that it regulates ventricular electrical repolarization gradient in the adult heart. Mutations in IRX5 have also been linked in humans to cardiac conduction defects. In order to fully characterize the role of IRX5 during cardiac development and in cardiomyocyte function, we generated three genetically-modified human induced pluripotent stem cell lines: two knockout lines (heterozygous and homozygous) and a knockin HA-tagged line (homozygous)

Inguinal hernia in premature boys: should we systematically explore the contralateral side?

International audienceOBJECTIVE: Bilateral surgery has been largely advocated in premature boys with unilateral inguinal hernia owing to the high incidence of contralateral patent processus vaginalis. Recently, the potential morbidity of herniotomy in low birth-weight babies and the progress in pediatric anesthesia questioned this attitude. This study aims to evaluate the incidence of contralateral metachronous hernia in a large series of premature boys and to compare the morbidity of preventive versus elective surgery.METHODS: This retrospective multicenter analysis of 964 premature boys presenting with unilateral inguinal hernia operated from 1998 to 2012 included 557 infants who benefited from a unilateral herniotomy and 407 from a bilateral herniotomy (median follow-up 12months).RESULTS: Contralateral metachronous hernia after unilateral surgery occurred in 11% (n=60) without significant difference according to the initial symptomatic side (9.5% on right vs 13% on left, p&gt;0.05). Postoperative morbidity on the contralateral side was higher after preventive surgery than elective surgery with metachronous hernia (2.45% versus 0.9%, p=0.05) especially for secondary cryptorchidism (1% vs 0%, p=0.03). Despite the risk of metachronous incarcerated hernia, elective surgery did not increase the rate of testicular hypotrophy on the opposite side (0.7%, vs 0.7%, p&gt;0.05).CONCLUSION: Systematic bilateral herniotomy is unnecessary in almost 90% of patients and has a significant morbidity. Secondary surgery for metachronous hernia does not increase the risk of testicular lesion and even reduces the risk of secondary cryptorchidism. These results, along with the risk of hypofertility reported after bilateral surgery, may justify treating only the symptomatic side in premature boys.</p

Characteristics and outcome of adults with severe autoimmune hemolytic anemia admitted to the intensive care unit: Results from a large French observational study

Adult'autoimmune hemolytic anemia (AIHA), which is often seen as a rare and "benign" autoimmune hematological disease, can be lifethreatening with an overall mortality rate from 8% to 20% depending on the series 1-3 and a short-term mortality rate that can be up to 30% in intensive care units (ICUs). 4 Factors associated with the need for ICU management of patients with severe AIHA remain partially unknown because only few data are available in the literature. 3-5 The aims of this retrospective observational multicenter study set up by the French reference center for adult immune cytopenias were to: (1) better describe the baseline characteristics and outcome of adults with severe AIHA admitted to an ICU, (2) investigate the factors associated with mortality in the ICU, and (3) identify factors at AIHA diagnosis associated with admission to an ICU. To be included in the study, patients had to (1) be ≥16 years old at the time of AIHA onset; (2) have a diagnosis of AIHA defined as hemoglobin level <12 g/dL, with ≥2 features of hemolysis among low haptoglobin level and/or elevated lactate dehydrogenase (LDH) level and/or elevated free bilirubin level, and a positive direct antiglobulin test (DAT) with no other cause of acquired or hereditary hemolytic anemia; and (3) at least one admission to an ICU specifically for AIHA management between January 2013 and December 2020. We excluded patients with nonautoimmune hemolytic anemia, DAT-negative AIHA and drug-induced immune hemolytic anemia and those admitted to the ICU for another reason than severity of AIHA. Baseline data in the ICU included the Charlson Comorbidity Index, the Knaus score, the Sequential Organ Failure Assessment (SOFA), and Simplified Acute Physiology Scor

Rituximab-resistant splenic memory B cells and newly engaged naive B cells fuel relapses in patients with immune thrombocytopenia

International audienceRituximab (RTX), an antibody targeting CD20, is widely used as a first-line therapeutic strategy in B cell–mediated autoimmune diseases. However, a large proportion of patients either do not respond to the treatment or relapse during B cell reconstitution. Here, we characterize the cellular basis responsible for disease relapse in secondary lymphoid organs in humans, taking advantage of the opportunity offered by therapeutic splenectomy in patients with relapsing immune thrombocytopenia. By analyzing the B and plasma cell immunoglobulin gene repertoire at bulk and antigen-specific single-cell level, we demonstrate that relapses are associated with two responses coexisting in germinal centers and involving preexisting mutated memory B cells that survived RTX treatment and naive B cells generated upon reconstitution of the B cell compartment. To identify distinctive characteristics of the memory B cells that escaped RTX-mediated depletion, we analyzed RTX refractory patients who did not respond to treatment at the time of B cell depletion. We identified, by single-cell RNA sequencing (scRNA-seq) analysis, a population of quiescent splenic memory B cells that present a unique, yet reversible, RTX-shaped phenotype characterized by down-modulation of B cell–specific factors and expression of prosurvival genes. Our results clearly demonstrate that these RTX-resistant autoreactive memory B cells reactivate as RTX is cleared and give rise to plasma cells and further germinal center reactions. Their continued surface expression of CD19 makes them efficient targets for current anti-CD19 therapies. This study thus identifies a pathogenic contributor to autoimmune diseases that can be targeted by available therapeutic agents