Biology subjects

Liaubet, L.

Publications and source records attributed to Liaubet, L..

6 recordsLinked to original sources

bioRxiv2026

CDC25B couples ribosome biogenesis to cell cycle kinetics to promote spinal cord neurogenesis

During neurogenesis, neural progenitors undergo a tightly regulated transition from proliferation to differentiation, which requires precise coordination between cell cycle progression and molecular reprogramming. Although the role of CDC25B is well established in promoting G2/M transition through CDK1 activation, we previously showed that it is both necessary and sufficient to trigger neural progenitor differentiation, via CDK-dependent and CDK-independent mechanisms. However, the molecular networks underlying this neurogenic activity remain poorly understood. Here, using a gain-of-function approach in the chicken spinal cord combined with bulk RNA sequencing, we show that CDC25B overexpression upregulates transcripts encoding ribosomal proteins and enhances ribosome biogenesis (RiBi) in neural progenitors. Consistent with these findings, during normal development, RiBi increases in neurogenic progenitor domains expressing CDC25B. Notably, the increase in RiBi is not associated with an increase in translation in neural progenitors. Instead, it is followed by an increase in mTORC1 activity in neuronal precursors and subsequently by a rise in the global translation rate in differentiating neurons. Moreover, increasing mTORC1 activity is sufficient to trigger a premature transition of neuronal precursors to the next step of differentiation. Altogether, our data support a model in which CDC25B coordinates cell cycle progression with RiBi in neurogenic progenitors, thereby initiating a program that culminates in translation in differentiating neurons.

developmental biology↗

bioRxiv2026

Investigating the dynamics of heat acclimation in pig through transcriptome analysis of blood samples

This study aimed to investigate the dynamics of gene expression in pigs during heat stress (HS), focusing on both short-term (STHA) and long-term (LTHA) heat acclimation phases. A total of 12 castrated males were exposed to thermoneutral temperatures (24{degrees}C) for 14 days (TN) and then to a constant temperature of 30{degrees}C for 21 days. Rectal temperature measurements indicated a biphasic thermoregulatory response, with an initial peak followed by acclimation. Using whole blood transcriptome analysis at seven time points between day 5 before the initiation of HS challenge and day 13 post HS. A total of 525 genes were differentially expressed during the STHA (day 0-day 2) phase. A switch in the expression of most genes was observed around 20 hours after HS. Functional pathway enrichment analysis identified through shape-based clustering revealed the activation of the immune system, especially mediated through toll-like receptor signaling pathways. The LTHA phase (day 2-day 13) revealed 985 differentially expressed genes, with pathways associated with various metabolisms, including mitochondrial fatty acid beta-oxidation, and electron transport, ATP synthesis, and heat production by uncoupling proteins. Interestingly, oxidative phosphorylation was predicted to be activated during the LTHA, particularly in Complex V, whereas other complexes showed mixed regulation. Comparative pathway analysis indicated distinct metabolic adaptations between STHA and LTHA, with up-regulation of glucose and lipid metabolism in late STHA and down-regulation of lipid metabolism during LTHA. This study contributes to a better understanding of the time course of adaptation mechanisms in pigs to HS, underlying a coordinated regulation during STHA involving several stress-specific mechanisms (via the HSP) and metabolic variation to help pigs achieve homeothermy.

systems biology↗

bioRxiv2025

An extensive and unbiased genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting

Genomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields including evolution, molecular genetics and epigenetics and determinism of complex traits. Although next generation sequencing technologies enable nowadays to detect imprinted genes in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and mice. Here, we propose to map genes showing a parental expression bias in hypothalamus, muscle and placenta in piglets around birth using an extensive and unbiased strategy that relied on reciprocal crosses, genetics reconstruction of parental phases after imputation and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 440 unique genes with a weak to exclusive parental expression bias including 114 unique genes with an imbalance ratio above 25:75. About thirty imprinted genes are common to human and/or mice and an equivalent number is shared between tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental (PITRM1, Pitrilysin Metallopeptidase 1) and fetal growth (FAM20B, Glycosaminoglycan Xylosylkinase and POU6F2, POU Class 6 Homeobox 2) functions. In addition, deeper analyses of specific loci likely highlighted lineage-specific imprinted genes such as a Zinc Finger Protein 300-like gene as well as specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2), a gene showing conflicting data in the literature. Altogether, our results bring pig as the most comprehensively and exhaustively documented species for genomic imprinting after human and mice organisms. A weak conservation of this mechanism across species and tissues suggested a distinction between a small number of core imprinted genes and others parent-of-origin expressed genes that seemed subjected to evolutionary forces for acquiring their imprinting status either in a lineage-specific or tissue-specific manner.

genomics↗

bioRxiv2020

Joint automatic metabolite identification and quantification of a set of 1H NMR spectra

Metabolomics is a promising approach to characterize phenotypes or to identify biomarkers. It is also easily accessible through NMR, which can provide a comprehensive understanding of the metabolome of any living organisms. However, the analysis of 1H NMR spectrum remains difficult, mainly due to the different problems encountered to perform automatic identification and quantification of metabolites in a reproducible way. In addition, methods that perform automatic identification and quantification of metabolites often do it for one given complex mixture spectrum. Hence, when a set of complex mixture spectra coming from the same experiment has to be processed, the approach is simply repeated independently for every spectrum, despite their resemblance. Here, we present a new method that is the first to identify and quantify metabolites by integrating information coming from several complex spectra of the same experiment. The performances of this new method are then evaluated on both simulated and real datasets. The results show an improvement in the metabolite identification and in the accuracy of metabolite quantifications, especially when the concentration is low. This joint procedure is available in version 2.0 of ASICS package.

bioinformatics↗

bioRxiv2020

The maturity in fetal pigs using a multi-fluid metabolomic approach

In mammalian species, the first days after birth are an important period for survival and the rates of mortality before weaning are high. In pigs, the perinatal deaths average 20% of the litter, with important economic and societal consequences. Among the factors influencing piglet survival at birth, the maturity is likely to be one of the most important. Maturity can be defined as the outcome of complex mechanisms of intra-uterine development and maturation occurring during the last month of gestation. Here, we provide new insights on maturity by studying the end of gestation at two different stages (three weeks before term and close to term) in two breeds of pigs that strongly differ in terms of neonatal survival. Since metabolomics is a promising approach for phenotype characterization or biomarker discovery, we provide a complete understanding of the metabolome of the fetuses in late gestation in three fluids (plasma, urine, and amniotic fluid). We found that biological processes related to amino acid and carbohy-drate metabolisms are critical for piglet maturity. We also confirmed some previously described metabolites associated with delayed growth (e.g., proline and myo-inositol). Altogether, our study proposes new routes for a better characterization of piglet maturity at birth.

developmental biology↗

bioRxiv2018

ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra

In metabolomics, the detection of new biomarkers from NMR spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses.\n\nWe present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independant datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketting. It also found new relevant metabolites involved in metabolic pathways related to risk factors associated with the conditions.\n\nThis workflow is available through the R package ASICS, available on the Bioconductor platform.

systems biology↗