Publications of Marc Joiret
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See detailRibosome exit tunnel electrostatics
Joiret, Marc ULiege; Kerff, Frédéric ULiege; Rapino, Francesca ULiege et al

in Physical Review E (2022), 105(1), 014409-1--014409-43

The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have ... [more ▼]

The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show that a strong electrostatic screening is due to water molecules (not mobile ions) attracted to the ribosomal nucleic acid phosphate moieties buried in the immediate vicinity of the tunnel wall. We also show how the tunnel wall components and local ribosomal protein protrusions impact on the electrostatic potential profile and impede charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of −40% to +85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derive, at single-residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall, shape, and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, x-ray crystallography, physical chemistry, biomechanics, and synthetic and multiomics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control, and the role of the ribosome's mechanochemistry in the cotranslational protein folding. [less ▲]

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See detailRibosome exit tunnel electrostatics
Joiret, Marc ULiege; Rapino, Francesca ULiege; Close, Pierre ULiege et al

Poster (2021, September 09)

The impact of the ribosome exit tunnel electrostatics on the protein elongation rate or on the forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers ... [more ▼]

The impact of the ribosome exit tunnel electrostatics on the protein elongation rate or on the forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here, we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show that a strong electrostatic screening is due to water molecules (not mobile ions) attracted to the ribosomal nucleic acid phosphate moieties buried in the immediate vicinity of the tunnel wall. We also show how the tunnel wall components and local ribosomal protein protrusions impact on the electrostatic potential profile and impede charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of minus 40% to plus 85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derived, at single residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall, the shape and the size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, X-ray crystallography, physical chemistry, biomechanics, synthetic and multi-omics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control and into the role of the ribosome's mechanochemistry in the co-translational protein folding. [less ▲]

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See detailTumor exposed-lymphatic endothelial cells promote primary tumor growth via IL6.
Van de Velde, Maureen; Ebroin, Marie ULiege; Durré, Tania ULiege et al

in Cancer Letters (2021), 497

Solid tumors are composed of tumor cells and stromal cells including lymphatic endothelial cells (LEC), which are mainly viewed as cells forming lymphatic vessels involved in the transport of metastatic ... [more ▼]

Solid tumors are composed of tumor cells and stromal cells including lymphatic endothelial cells (LEC), which are mainly viewed as cells forming lymphatic vessels involved in the transport of metastatic and immune cells. We here reveal a new mechanism by which tumor exposed-LEC (teLEC) exert mitogenic effects on tumor cells. Our conclusions are supported by morphological and molecular changes induced in teLEC that in turn enhance cancer cell invasion in 3D cultures and tumor cell proliferation in vivo. The characterization of teLEC secretome by RNA-Sequencing and cytokine array revealed that interleukine-6 (IL6) is one of the most modulated molecules in teLEC, whose production was negligible in unexposed LEC. Notably, neutralizing anti-human IL6 antibody abrogated teLEC-mediated mitogenic effects in vivo, when LEC were mixed with tumor cells in the ear sponge assay. We here assign a novel function to teLEC that is beyond their role of lymphatic vessel formation. This work highlights a new paradigm, in which teLEC exert "fibroblast-like properties", contribute in a paracrine manner to the control of tumor cell properties and are worth considering as key stromal determinant in future studies. [less ▲]

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See detailEstetrol combined to progestogen for menopause or contraception indication is neutral on breast cancer
Gallez, Anne ULiege; Blacher, Silvia ULiege; Maquoi, Erik ULiege et al

in Cancers (2021)

Hormonal treatments, especially those used to treat menopause symptoms are known to increase breast cancer risk. It is thus necessary to identify new formulations with a better benefit/risk pro-file. The ... [more ▼]

Hormonal treatments, especially those used to treat menopause symptoms are known to increase breast cancer risk. It is thus necessary to identify new formulations with a better benefit/risk pro-file. The aim of this translational study was to evaluate the breast cancer risk associated to a combination of a natural estrogen, named estetrol, with progestogens such as natural progesterone and drospirenone. Since the assessment of breast cancer risk in patients during drug development is not possible given the requirement of long-term studies in large populations, this study provides new evidences that a therapeutic dose of estetrol for menopause treatment or contraception, combined with progesterone or drospirenone, may provide a better benefit/risk profile towards breast cancer risk compared to hormonal treatments currently available for patients. [less ▲]

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See detailWobble tRNA modification and hydrophilic amino acid patterns dictate protein fate.
Rapino, Francesca ULiege; ZHOU, ZHAOLI; RONCERO SANCHEZ, Ana Maria et al

in Nature Communications (2021), 12(1), 2170

Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate features linking regulation of codon ... [more ▼]

Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate features linking regulation of codon-dependent translation elongation to protein expression and homeostasis. Using knockdown models of enzymes that catalyze the mcm(5)s(2) wobble uridine tRNA modification (U(34)-enzymes), we show that gene codon content is necessary but not sufficient to predict protein fate. While translation defects upon perturbation of U(34)-enzymes are strictly dependent on codon content, the consequences on protein output are determined by other features. Specific hydrophilic motifs cause protein aggregation and degradation upon codon-dependent translation elongation defects. Accordingly, the combination of codon content and the presence of hydrophilic motifs define the proteome whose maintenance relies on U(34)-tRNA modification. Together, these results uncover the mechanism linking wobble tRNA modification to mRNA translation and aggregation to maintain proteome homeostasis. [less ▲]

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See detailProtein synthesis at the speed of codons
Joiret, Marc ULiege; Geris, Liesbet ULiege; Close, Pierre ULiege

Speech/Talk (2020)

Introduction to open boundaries transport model on a 1D lattice and presentation of the totally asymmetric simple exclusion process and its application to protein synthesis modeling.

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See detailmRNA translation rate modeling with an extended TASEP incorporating tRNAs modifications
Joiret, Marc ULiege; Rapino, Francesca ULiege; Close, Pierre ULiege et al

Poster (2019, September 05)

Translational regulation through synonymous codon usage has been recently shown to play an important role in health and disease. Modified tRNAs are important actors involved in regulating protein ... [more ▼]

Translational regulation through synonymous codon usage has been recently shown to play an important role in health and disease. Modified tRNAs are important actors involved in regulating protein expression levels by optimizing the decoding of differentially used codons, nevertheless their contribution in protein synthesis dynamics remain unclear. Totally Asymmetric Simple Exclusion Process (TASEP) models have been used to quantify the transcripts translation rate by ribosomes. Our work aims at extending TASEP modeling to accommodate for tRNA modifications effects. We generated a computational stochastic model quantifying protein synthesis rates. The algorithm uses ribosome residence time per codon from transcripts codons sequences, relative transcripts abundance and tables of (modified or not) tRNA relative abundance. Important features in the model include the elongation rate variation caused by charged amino-acids in the ribosomal exit tunnel, proline ring opening delay at the peptide transfer center and optionally transcript secondary structure slow down effects. The model allows to compare relative protein expression levels as well as RiboSeq profiles in different scenarios with a controllable pool of ribosomes. We intend to use our model to help understand how codon usage and tRNA modifications dynamically interact and impact on protein synthesis. [less ▲]

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See detailConfounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies
Joiret, Marc ULiege; Mahachie John, Jestinah ULiege; Gusareva, Elena et al

in BioData Mining (2019), 12(11), 1-23

Background: In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag the actual causal variants. In Genome-Wide ... [more ▼]

Background: In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag the actual causal variants. In Genome-Wide Association Interaction Studies (GWAIS), similar principles hold for pairs of causal variants. However, Linkage Disequilibrium (LD) may also interfere with the detection of genuine epistasis signals in that there may be complete confounding between Gametic Phase Disequilibrium (GPD) and interaction. GPD may involve unlinked genetic markers, even residing on different chromosomes. Often GPD is eliminated in GWAIS, via feature selection schemes or so-called pruning algorithms, to obtain unconfounded epistasis results. However, little is known about the optimal degree of GPD/LD-pruning that gives a balance between false positive control and sufficient power of epistasis detection statistics. Here, we focus on Model-Based Multifactor Dimensionality Reduction as one large-scale epistasis detection tool. Its performance has been thoroughly investigated in terms of false positive control and power, under a variety of scenarios involving different trait types and study designs, as well as error-free and noisy data, but never with respect to multicollinear SNPs. Results: Using real-life human LD patterns from a homogeneous subpopulation of British ancestry, we investigated the impact of LD-pruning on the statistical sensitivity of MB-MDR. We considered three different non-fully penetrant epistasis models with varying effect sizes. There is a clear advantage in pre-analysis pruning using sliding windows at r2 of 0.75 or lower, but using a threshold of 0.20 has a detrimental effect on the power to detect a functional interactive SNP pair (power <25%). Signal sensitivity, directly using LD-block information to determine whether an epistasis signal is present or not, benefits from LD-pruning as well (average power across scenarios: 87%), but is largely hampered by functional loci residing at the boundaries of an LD-block. Conclusions: Our results confirm that LD patterns and the position of causal variants in LD blocks do have an impact on epistasis detection, and that pruning strategies and LD-blocks definitions combined need careful attention, if we wish to maximize the power of large-scale epistasis screenings. [less ▲]

Detailed reference viewed: 49 (14 ULiège)