Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics

The consensus molecular subtypes (CMS) of colorectal cancer (CRC) is the most widely-used gene expression-based classification and has contributed to a better understanding of disease heterogeneity and prognosis. Nevertheless, CMS intratumoral heterogeneity restricts its clinical application, stressing the necessity of further characterizing the composition and architecture of CRC. Here, we used Spatial Transcriptomics (ST) in combination with single-cell RNA sequencing (scRNA-seq) to decipher the spatially resolved cellular and molecular composition of CRC. In addition to mapping the intratumoral heterogeneity of CMS and their microenvironment, we identified cell communication events in the tumor-stroma interface of CMS2 carcinomas. This includes tumor growth-inhibiting as well as -activating signals, such as the potential regulation of the ETV4 transcriptional activity by DCN or the PLAU-PLAUR ligand-receptor interaction. Our study illustrates the potential of ST to resolve CRC molecular heterogeneity and thereby help advance personalized therapy.

Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Motivation: The increasing availability of metabolomic data and their analysis are improving the understanding of cellular mechanisms and how biological systems respond to different perturbations. Currently, there is a need for novel computational methods that facilitate the analysis and integration of increasing volume of available data.

Results: In this paper, we present Totoro a new constraint-based approach that integrates quantitative non-targeted metabolomic data of two different metabolic states into genome-wide metabolic models and predicts reactions that were most likely active during the transient state. We applied Totoro to real data of three different growth experiments (pulses of glucose, pyruvate, succinate) from Escherichia coli and we were able to predict known active pathways and gather new insights on the different metabolisms related to each substrate. We used both the E. coli core and the iJO1366 models to demonstrate that our approach is applicable to both smaller and larger networks.

Availability:Totoro is an open source method (available at https://gitlab.inria.fr/erable/totoro) suitable for any organism with an available metabolic model. It is implemented in C++ and depends on IBM CPLEX which is freely available for academic purposes.

Conseils de bonnes pratiques pour les praticiens spécialisés en laryngologie et en phoniatrie en contexte d’épidémie COVID-19

Les gestes mettant le personnel soignant en contact étroit avec les voies aériennes sont particulièrement à risque de contamination par le virus SARS-Cov-2, en particulier en cas de crachats, toux, ou présence d’une trachéotomie. Dans la phase pandémique actuelle, tous les patients sont à considérer comme potentiellement infectés donc l’attitude du soignant est à adapter au statut COVID-19 du patient mais aussi et surtout au geste effectué. Ainsi, s’il s’agit d’un geste invasif comme une fibroscopie ou une pose de sonde naso-gastrique notamment, les précautions sont identiques pour tous les patients quel que soit leur statut COVID. Les rééducations vocales sont à considérer comme non urgentes dans ce contexte. Les recommandations présentées ici en date du 9 avril 2020 sont donc surtout destinées à la prise en charge des troubles de la déglutition (ceci pouvant parfois être dangereux pour le patient) ou d’une dysphonie récente inquiétante. Dès qu’elles sont possibles techniquement et réglementairement, les télé-consultations seront à privilégier. Seules les urgences non différables seront réalisées en présentiel et ce après décision collégiale (ou en fonction des informations venues des autorités de santé) et en prenant les précautions adéquates détaillées ici.

Guidelines of clinical practice for the management of swallowing disorders and recent dysphonia in the context of the COVID-19 pandemic

Procedures putting healthcare workers in close contact with the airway are particularly at risk of contamination by the SARS-Cov-2 virus, especially when exposed to sputum, coughing, or a tracheostomy. In the current pandemic phase, all patients should be considered as potentially infected. Thus, the level of precaution recommended for the caregivers depends more on the type of procedure than on the patient's proved or suspected COVID-19 status. Procedures that are particularly at high risk of contamination are clinical and flexible endoscopic pharyngo-laryngological evaluation, and probably also video fluoroscopic swallowing exams. Voice rehabilitation should not be considered urgent at this time. Therefore, recommendations presented here mainly concern the management of swallowing disorders, which can sometimes be dangerous for the patient, and recent dysphonia. In cases where they are considered possible and useful, teleconsultations should be preferred to face-to-face assessments or rehabilitation sessions. The latter must be maintained only in few selected situations, after team discussions or in accordance with the guidelines provided by health authorities.

OptPipe - a pipeline for optimizing metabolic engineering targets

BACKGROUND

We propose OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets, based on a consensus approach. The method generates consensus hypotheses for metabolic engineering applications by combining several optimization solutions obtained from distinct algorithms. The solutions are ranked according to several objectives, such as biomass and target production, by using the rank product tests corrected for multiple comparisons.

RESULTS

OptPipe was applied in a genome-scale model of Corynebacterium glutamicum for maximizing malonyl-CoA, which is a valuable precursor for many phenolic compounds. In vivo experimental validation confirmed increased malonyl-CoA level in case of ΔsdhCAB deletion, as predicted in silico.

CONCLUSIONS

A method was developed to combine the optimization solutions provided by common knockout prediction procedures and rank the suggested mutants according to the expected growth rate, production and a new adaptability measure. The implementation of the pipeline along with the complete documentation is freely available at https://github.com/AndrasHartmann/OptPipe .

A Combinatorial Algorithm for Microbial Consortia Synthetic Design

Synthetic biology has boomed since the early 2000s when it started being shown that it was possible to efficiently synthetize compounds of interest in a much more rapid and effective way by using other organisms than those naturally producing them. However, to thus engineer a single organism, often a microbe, to optimise one or a collection of metabolic tasks may lead to difficulties when attempting to obtain a production system that is efficient, or to avoid toxic effects for the recruited microorganism. The idea of using instead a microbial consortium has thus started being developed in the last decade. This was motivated by the fact that such consortia may perform more complicated functions than could single populations and be more robust to environmental fluctuations. Success is however not always guaranteed. In particular, establishing which consortium is best for the production of a given compound or set thereof remains a great challenge. This is the problem we address in this paper. We thus introduce an initial model and a method that enable to propose a consortium to synthetically produce compounds that are either exogenous to it, or are endogenous but where interaction among the species in the consortium could improve the production line.