Metabolomics in Ecology and Bioactive Natural Products Discovery: Challenges and Prospects for a Comprehensive Study of the Specialised Metabolome

Metabolomics is playing an increasingly prominent role in chemical ecology and in the discovery of bioactive natural products (NPs). The identification of metabolites is a common/central objective in both research fields. NPs have significant biological properties and play roles in multiple chemical-ecological interactions. Classically, in pharmacognosy, their chemical structure is determined after a complex process of isolating and interpreting spectroscopic data. With the advent of powerful analytical techniques such as liquid chromatography-mass spectrometry (LC-MS) the annotation process of the specialised metabolome of plants and microorganisms has improved considerably. In this article, we summarise the possibilities opened by these advances and illustrate how we harnessed them in our own research to automate annotations of NPs and target the isolation of key compounds. In addition, we are also discussing the analytical and computational challenges associated with these emerging approaches and their perspective

Ontogenic Changes in Hematopoietic Hierarchy Determine Pediatric Specificity and Disease Phenotype in Fusion Oncogene-Driven Myeloid Leukemia.

Fusion oncogenes are prevalent in several pediatric cancers, yet little is known about the specific associations between age and phenotype. We observed that fusion oncogenes, such as ETO2-GLIS2, are associated with acute megakaryoblastic or other myeloid leukemia subtypes in an age-dependent manner. Analysis of a novel inducible transgenic mouse model showed that ETO2-GLIS2 expression in fetal hematopoietic stem cells induced rapid megakaryoblastic leukemia whereas expression in adult bone marrow hematopoietic stem cells resulted in a shift toward myeloid transformation with a strikingly delayed in vivo leukemogenic potential. Chromatin accessibility and single-cell transcriptome analyses indicate ontogeny-dependent intrinsic and ETO2-GLIS2-induced differences in the activities of key transcription factors, including ERG, SPI1, GATA1, and CEBPA. Importantly, switching off the fusion oncogene restored terminal differentiation of the leukemic blasts. Together, these data show that aggressiveness and phenotypes in pediatric acute myeloid leukemia result from an ontogeny-related differential susceptibility to transformation by fusion oncogenes. SIGNIFICANCE: This work demonstrates that the clinical phenotype of pediatric acute myeloid leukemia is determined by ontogeny-dependent susceptibility for transformation by oncogenic fusion genes. The phenotype is maintained by potentially reversible alteration of key transcription factors, indicating that targeting of the fusions may overcome the differentiation blockage and revert the leukemic state.See related commentary by Cruz Hernandez and Vyas, p. 1653.This article is highlighted in the In This Issue feature, p. 1631

Covichem: A biochemical severity risk score of COVID-19 upon hospital admission

Clinical and laboratory predictors of COVID-19 severity are now well described and combined to propose mortality or severity scores. However, they all necessitate saturable equipment such as scanners, or procedures difficult to implement such as blood gas measures. To provide an easy and fast COVID-19 severity risk score upon hospital admission, and keeping in mind the above limits, we sought for a scoring system needing limited invasive data such as a simple blood test and co-morbidity assessment by anamnesis. A retrospective study of 303 patients (203 from Bordeaux University hospital and an external independent cohort of 100 patients from Paris Pitié-Salpêtrière hospital) collected clinical and biochemical parameters at admission. Using stepwise model selection by Akaike Information Criterion (AIC), we built the severity score Covichem. Among 26 tested variables, 7: obesity, cardiovascular conditions, plasma sodium, albumin, ferritin, LDH and CK were the independent predictors of severity used in Covichem (accuracy 0.87, AUROC 0.91). Accuracy was 0.92 in the external validation cohort (89% sensitivity and 95% specificity). Covichem score could be useful as a rapid, costless and easy to implement severity assessment tool during acute COVID-19 pandemic waves

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

The Flavonoid Isoquercitrin Precludes Initiation of Zika Virus Infection in Human Cells

The medical importance of Zika virus (ZIKV) was fully highlighted during the recent epidemics in South Pacific islands and Americas due to ZIKV association with severe damage to fetal brain development and neurological complications in adult patients. A worldwide research effort has been undertaken to identify effective compounds to prevent or treat ZIKV infection. Fruits and vegetables may be sources of compounds with medicinal properties. Flavonoids are one class of plant compounds that emerge as promising antiviral molecules against ZIKV. In the present study, we demonstrated that flavonoid isoquercitrin exerts antiviral activity against African historical and Asian epidemic strains of ZIKV in human hepatoma, epithelial, and neuroblastoma cell lines. Time-of-drug addition assays showed that isoquercitrin acts on ZIKV entry by preventing the internalisation of virus particles into the host cell. Our data also suggest that the glycosylated moiety of isoquercitrin might play a role in the antiviral effect of the flavonoid against ZIKV. Our results highlight the importance of isoquercitrin as a promising natural antiviral compound to prevent ZIKV infection

L’extrait de Doratoxylon apetalum inhibe l’infection par l’arbovirus Zika en interférant avec l’internalisation cellulaire

Le virus Zika (ZIKV) est un arbovirus membre de la famille des Flaviviridae (Musso and Gubler, 2016). Il a été détecté pour la première fois dans la forêt Zika en Ouganda en 1947 chez un primate non-humain, plus précisément un macaque rhésus sentinelle lors d’un programme de surveillance de la fièvre jaune. La même étude a permis la détection de ZIKV chez un vecteur, le moustique Aedes africanus l’année suivante (Dick et al., 1952). Enfin, c’est en 1954 que la première infection humaine par le virus Zika est détectée, chez une fille de 10 ans au Nigéria (Macnamara, 1954)

Development of an Integrative Strategy to Leverage the Results of the Metabolomics Profiling and Anti-Trypanosomatid Screening of a Large Plant Extracts Collection

Nature is an inexhaustible source of new therapeutics, and humans have been using it to heal themselves for ages. Shaped by evolution, plants, bacteria, or fungi, among other living organisms, contain hundreds of potential bioactive metabolites, among which many are still to be discovered. Today, Ultra-High Performance Liquid Chromatography (UHPLC) coupled with High-Resolution tandem Mass Spectrometry (HRMS/MS) is the standard method to chemically profile these organisms and get an insight into their composition. Thanks to modern data processing workflows and annotation strategies, large amounts of spectral and structural data can be obtained and linked to biological screening results for each natural extract. In this thesis project, we aimed to develop innovative metabolomics workflows using UHPLC-HRMS/MS and biological screening results of large natural extracts collections to identify bioactive compounds in mixtures. The developed approach should help rationalize efforts to isolate valuable natural products (NP) only. As an application case, we used metabolomics and anti-trypanosomatid activity data - against Trypanosoma cruzi, T. brucei, and Leishmania donovani - obtained on a dataset of 1,600 plant extracts. We developed a novel MS/MS-based sample vectorization method, called MEMO, to highlight chemical similarities among extracts in large chemodiverse libraries without needing any retention time (RT) based feature-alignment step. Because such an alignment makes the iterative addition of new samples difficult, we developed a pythonbased framework to organize automatically, through molecular networking, and annotate, through state-of-the-art annotation tools, the LC-MS features’ fragmentation spectra of each sample independently. While such a sample-centric workflow allows for better iterative addition of samples by avoiding the necessity to recompute post-featurealignment annotations steps, it hinders the direct comparison of the considered samples using LC-MS features’ relative intensity among samples. To maintain a way to compare unaligned samples, the generated and standardized data produced at the sample scale were integrated into a single Experimental Natural Product Knowledge Graph (ENPKG). Such a format allows the integration of both chemical and bioactivity data and the connection of experimental data to other graph databases such as Wikidata and ChEMBL. Using the SPARQL language to query the data, we could demonstrate how such an organization represents an efficient strategy to link and interpret heterogeneous chemical and biological data to annotate bioactive compounds in extracts before their isolation.To confirm the generated bioactivity annotations, we isolated and characterized some metabolites of interest from different extracts using semi-preparative HPLC, NMR, and chiroptical methods. Because they do not require any RT-based feature alignment step and allow the easy addition of new samples over time, the MEMO method and the ENPKG workflow represent sustainable data exploitation and data management strategies in NP research. Integrating crosslinks to other DBs helps the ENPKG workflow avoid data loss into hermetic silos of information. Because of their versatility and integrative character, we believe that the developed tools should contribute to advancing the knowledge of Nature's fascinating chemistry.</p

Individual .ttl files for plate VGF147 samples

&lt;p&gt;Individual .ttl files for plate VGF147 samples processed using the ENPKG framework&lt;/p&gt

Individual .ttl files for plate VGF145 samples

Individual .ttl files for plate VGF145 samples processed using the ENPKG framewor

Individual .ttl files for plate VGF153 samples

Individual .ttl files for plate VGF153 samples processed using the ENPKG framewor