Planification dans les jeux-vidéos : À quoi servent les coûts des actions ?

Co-localisées avec la Plate-Forme Intelligence Artificielle (PFIA 2019)International audienceThis paper suggests a reflection on the costs of the actions used by the planner G.O.A.P. (Goal-Oriented Action Planning) which is used in some video games like F.E.A.R. to have real-time control of the non-playable character. We have analysed the planning activity of F.E.A.R. to study the utility of the costs in the planner. We show and explain why they have little impact in practice.Nous discutons de l’intérêt des coûts des actions dans le planificateur G.O.A.P. (Goal-Oriented Action Planning), qui est utilisé pour le contrôle en temps-réel des personnages non-joueurs dans certains jeux-vidéos. Nous avons instrumenté l’activité de planification du jeu vidéo F.E.A.R. afin d’étudier l’usage des coûts des actions par le planificateur. Nous montrons et nous expliquons pourquoi leur impact est faible en pratique

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Abstract It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies

Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival

Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification

Relation, interactions and functions of alternative proteins

Si en transcriptomique le dogme accepté par la communauté veut qu’un ARNm code pour une protéine unique, la protéomique vient de montrer l’inverse. Force de constater que les ARNm peuvent traduire plusieurs protéines. Celles ne suivant pas le cadre de référence sont appelées protéines alternatives (AltProts) et forme le protéome caché ou fantôme. Ces AltProts nécessitent la mise en place de stratégies adaptées pour leur mise en évidence. Leurs caractéristiques physicochimiques spécifiques, telles que leur petite taille permet d’adapter les méthodes classiques de protéomique à leur étude. Dans cet objectif la mise en évidence des AltProts par différentes méthodes d’extraction, notamment adaptées des méthodes de peptidomique, a permis de mettre en évidence les conditions d’enrichissement avant une analyse bottom-up. Ces AltProts sont une nouvelle classe de protéines pour laquelle très peu d’informations fonctionnelle sont connues. Les prédictions de fonction avancées lors des premières constructions de base de données, annonçaient des fonctions dans la régulation des ARN, de la synthèse de protéines et de la régulation d’expression des gènes par association avec des facteurs de transcriptions. Ces prédictions étaient basées sur les homologies de séquences entre les AltProts et les protéines de références (RefProts). Cependant très peu d’études montrent le rôle de ces protéines de manière expérimentale. Afin de mettre en évidence les fonctions de ces AltProts, nous avons choisi de retrouver leurs partenaires d’interaction. À l’heure actuelle, plusieurs méthodes existent permettant d’étudier l’interactome des protéines, toutefois la majorité est dirigée vers une cible, nécessitant parfois des constructions biochimiques ou l’utilisation d’anticorps dirigés, rendant ces méthodes difficiles à mettre en place pour les AltProts. Seule la méthode de Crosslink couplée à la spectrométrie de masse (XL-MS) permet d’observer des interactions cellulaires de manière non ciblée. Cette méthode de pontage chimique, bien que connaissant ses propres limitations, est applicable à la recherche des partenaires d’interaction des AltProts. Cet outil, associé aux logiciels de traitement des réseaux d’interaction, enrichi par les interactions connues entre RefProts dans la littérature, permet de replacer les AltProts dans ces réseaux. Ces réseaux, peuvent ensuite être traités afin de mettre en évidence les voies de signalisation impliquant les RefProts et ainsi déduire les différentes voies de signalisation associées aux AltProts observées crosslinkées aux RefProts.In transcriptomics the dogma accepted by the community is that a single mRNA codes for a single protein, proteomics has just shown the opposite. It must be said that mRNAs can translate several proteins. These not following the reference framework are called alternative proteins (AltProts) and form the hidden or ghost proteome. These AltProts require the implementation of appropriate strategies to highlight them. Their specific physicochemical characteristics, such as their small size, make it possible to adapt classical proteomic methods to their study. With this objective in mind, the identification of AltProts by different extraction methods, particularly adapted to peptidomic methods, made it possible to highlight the enrichment conditions before a bottom-up analysis. These AltProts are a new class of proteins for which very little functional information is known. Advanced function predictions in the early database constructions announced functions in RNA regulation, protein synthesis and gene expression regulation by association with transcriptional factors. These predictions were based on sequence homologies between AltProts and reference proteins (RefProts). However, very few studies show the role of these proteins in an experimental way. In order to highlight the functions of these AltProts, we have chosen to find their interaction partners. At present, several methods exist to study the protein interactome, however the majority are directed towards a target, sometimes requiring biochemical constructs or the use of directed antibodies, making these methods difficult to implement for AltProts. Only the Crosslink method coupled with mass spectrometry (XL-MS) allows to observe cellular interactions in a non-targeted way. This chemical bridging method, although aware of its own limitations, is applicable to the search for AltProts interaction partners. This tool, combined with the software for processing interaction networks, enriched by the known interactions between RefProts in the literature, makes it possible to replace AltProts in these networks. These networks can then be processed to highlight the signaling pathways involving RefProts and thus deduce the different signaling pathways associated with the observed AltProts crosslinked to the RefProts

SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data

Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this “ghost proteome” was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts, we were interested in finding out their interaction with the viral protein coming from the SARS-CoV-2 virus, responsible for the 2020 COVID-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by affinity purification in co-immunoprecipitation (co-IP) in the perspective of drug repurposing. The initial work revealed the interaction between 332 human cellular reference proteins (RefProts) with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study), plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the ghost proteome for discovering new therapeutic targets, and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies

Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation

International audienceGhost proteins are issued from alternative Open Reading Frames (ORFs) and are missing a genome annotation. Indeed, historical filters applied for the detection of putative translated ORFs led to a wrong classification of transcripts considered as non-coding although translated proteins can be detected by proteomics. This Ghost (also called Alternative) proteome was neglected, and one major issue is to identify the implication of the Ghost proteins in the biological processes. In this context, we aimed to identify the protein-protein interactions (PPIs) of the Ghost proteins. For that, we re-explored a cross-link MS study performed on nuclei of HeLa cells using cross-linking mass spectrometry (XL-MS) associated with the HaltOrf database. Among 1679 cross-link interactions identified, 292 are involving Ghost Proteins. Forty-Four of these Ghost proteins are found to interact with 7 Reference proteins related to ribonucleoproteins, ribosome subunits and zinc finger proteins network. We, thus, have focused our attention on the heterotrimer between the RE/poly(U)-binding/degradation factor 1 (AUF1), the Ribosomal protein 10 (RPL10) and AltATAD2. Using I-Tasser software we performed docking models from which we could suggest the attachment of AUF1 on the external part of RPL10 and the interaction of AltATAD2 on the RPL10 region interacting with 5S ribosomal RNA as a mechanism of regulation of the ribosome. Taken together, these results reveal the importance of Ghost Proteins within known protein interaction networks

Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins

International audienceLarge scale proteomic strategies rely on database interrogation. Thus, only referenced proteins can be identified. Recently, Alternative Proteins (AltProts) translated from nonannotated Alternative Open reading frame (AltORFs) were discovered using customized databases. Because of their small size which confers them peptide-like physicochemical properties, they are more difficult to detect using standard proteomics strategies. In this study, we tested different preparation workflows for improving the identification of AltProts in NCH82 human glioma cell line. The highest number of identified AltProts was achieved with RIPA buffer or boiling water extraction followed by acetic acid precipitation

NanoLC-MS coupling of liquid microjunction microextraction for on-tissue proteomic analysis

International audienceMass spectrometry (MS)-based microproteomics on localized regions of tissue sections was achieved by direct coupling of liquid microjunction microextraction with a nanoscale liquid chromatography-tandem MS, resulting in the identification of >500 protein groups from a region as small as 250μm in diameter representing only a few hundred of cells. The method was applied on the examination of benign and tumor regions initially defined by imaging mass spectrometry (IMS) analysis of a consecutive high grade serous ovarian tumor tissue section. Results identified the higher abundance of eukaryotic translation initiation factors eIF4A, its isoform eIF4A2, and eIF5A and its isoform eIF5A2, and lower abundance of actin-binding proteins OBSCN, TAGLN and CNN3 on tumor regions, concomitant with previous findings. This demonstrates the use of the method for downstream characterization of distinct regions identified by IMS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann

Reference and Ghost Proteins Identification in Rat C6 Glioma Extracellular Vesicles

International audienceExtracellular vesicles (EVs) mediate intercellular communication and regulate a broad range of biological processes. Novel therapeutic strategies have emerged based on the use of EVs as biological nanoparticles. To separate isolated EVs from protein aggregates and the external part of EVs membrane proteins, we performed a Trypsin/Lys C digestion treatment of EVs pellets, followed by Amicon filtration. After these steps, all the fractions have been subjected to proteomic analyses. Comparison between 6 h Trypsin/Lys C treatment or non-treated EVs revealed a quantitative variation of the surface proteins. Some surface proteins have been demasked after 6 h enzymatic digestion like CD81, CD82, Ust, Vcan, Lamp 1, Rab43, Annexin A2, Synthenin, and VSP37b. Moreover, six ghost proteins have also been identified and one corresponds to a long noncoding RNA. We thus demonstrate the presence of ghost proteins in EVs produced by glioma cells that can contribute to tumorigenesis

Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome

Summary: Eukaryotic mRNA has long been considered monocistronic, but nowadays, alternative proteins (AltProts) challenge this tenet. The alternative or ghost proteome has largely been neglected and the involvement of AltProts in biological processes. Here, we used subcellular fractionation to increase the information about AltProts and facilitate the detection of protein-protein interactions by the identification of crosslinked peptides. In total, 112 unique AltProts were identified, and we were able to identify 220 crosslinks without peptide enrichment. Among these, 16 crosslinks between AltProts and Referenced Proteins (RefProts) were identified. We further focused on specific examples such as the interaction between IP_2292176 (AltFAM227B) and HLA-B, in which this protein could be a potential new immunopeptide, and the interactions between HIST1H4F and several AltProts which can play a role in mRNA transcription. Thanks to the study of the interactome and the localization of AltProts, we can reveal more of the importance of the ghost proteome