Biology subjects

Lacroix, M.

Publications and source records attributed to Lacroix, M..

12 recordsLinked to original sources

bioRxiv2026

THE MULTIFUNCTIONAL PROTEIN E4F1 REGULATES MELANOCYTIC FUNCTIONS IN MICE THROUGH PROTEIN TRANSLATION AND MITF EXPRESSION

The multifunctional protein E4 transcription factor 1 (E4F1) is an essential regulator of skin homeostasis, playing a critical role in epidermal stem cell maintenance and keratinocyte differentiation. However, the functions of E4F1 in other skin cell type remain poorly investigated. Here, we describe its role in melanogenesis, the physiological process for synthesis of melanin pigments. Using genetically engineered mouse models that enabled conditional inactivation of E4f1 specifically in melanocytes, we demonstrated that E4f1 loss induces severe pigmentation defects without affecting melanocyte survival nor differentiation. At the molecular level, E4f1 depletion reduces the expression of its direct transcriptional target genes involved in protein translation, including Elp3 and Eef1g, leading to translation alterations and consequently the induction of the Integrated Stress Response (ISR). This response resulted in microphthalmia-associated transcription factor (MITF) downregulation, inducing a decrease in the expression of enzymes involved in melanin synthesis. Consistent with these findings, Elp3 or Eef1g depletion recapitulated the decrease in MITF levels in vitro, and pharmacological inhibition of ISR partially rescued melanin content in vivo, confirming a key role of the E4F1-protein translation-ISR cascade in melanogenesis. Together, our data identify E4F1-associated translation functions as a key regulator of the melanocytic lineage.

physiology↗

bioRxiv2026

Androgen Receptor mediates beige adipocyte homeostasis and plasticity

Male adipose tissue undergoes profound post-pubertal remodeling characterized by the progressive transition of beige adipocytes toward a white adipocyte phenotype. Although androgen signaling has been implicated in adipose tissue biology, its role in beige adipocyte remodeling and metabolic plasticity remains poorly understood. Here we show that androgen receptor (AR) signaling is dynamically activated in inguinal white adipose tissue during the post-pubertal beige-to-white transition in male mice. Inducible deletion of AR in beige adipocytes impaired this remodeling process, resulting in the persistence of multilocular beige-like adipocytes despite reduced thermogenic competence and marked mitochondrial abnormalities. Transcriptomic and cistromic analyses identified AR as a direct regulator of adipocyte metabolic and differentiation programs, whereas immune-related transcriptional signatures in AR-deficient adipose tissue primarily reflected macrophage infiltration and inflammatory remodeling. Loss of AR promoted mitochondrial dysfunction, mitophagy, and altered glucose handling, while cell-autonomous AR silencing in beige adipocytes recapitulated key defects in mitochondrial organization and adipocyte identity. Longitudinal and metabolic challenge studies further demonstrated that AR signaling is required for age-associated adipose remodeling and adaptive beige adipocyte plasticity during high-fat diet feeding and cold exposure. Together, these findings identify AR as a central regulator of beige adipocyte remodeling, mitochondrial homeostasis, and adaptive metabolic function in male adipose tissue.

physiology↗

bioRxiv2026

Chemical augmentation of the validated HepaRGTM CYP enzyme induction test method Part 1: The Goliath two laboratory study

Cytochrome P450 (CYP) enzymes play a key role in the metabolism of both xenobiotics and endogenous compounds, and the activity of some CYP isoforms are susceptible to induction and/or inhibition by certain chemicals. As CYP induction and inhibition can significantly alter the in vivo fate of xenobiotics i.e., levels of parent chemicals and/or metabolites, and thus toxicity, CYP induction/inhibition data is needed for regulatory chemical toxicity hazard assessment. Utilizing available human in vivo pharmaceutical data, a successful validation was previously conducted on the in vitro HepaRG CYP induction test method for measurement of induction of three key human CYP enzymes CYP1A1/1A2, 2B6 and 3A4. However, further validation data was required to demonstrate applicability of the test method to also accurately detect CYP induction mediated by industrial and pesticidal chemicals. Here we report on the supplementary validation of the HepaRG CYP enzyme induction test method carried out in two laboratories under the auspices of the EU Horizon2020-funded project "GOLIATH", to expand the chemical applicability domain beyond pharmaceutical chemicals. Successful transfer was demonstrated and reproducibility assessed for the original 10 selected proficiency pharmaceuticals, plus three reference inducers together with six additional non-pharmaceutical augmentation chemicals. The method and chemical selection were found to be reliable and relevant for the routine assessment of human CYP induction. For the augmentation chemicals being proposed as additional proficiency chemicals, the test method achieved a reasonable but not optimum reproducibility. Recommendations are proposed to improve the test methods specificity, reflecting the inherent uncertainty around borderline CYP inducing chemicals. Plain language summaryCytochrome P450 (CYP) enzymes help break down drugs and other chemicals in the body. Their activity can be increased (induced) or decreased (inhibited), which can change how toxic a chemical is and when it is excreted. Because of this, CYP data is important for chemical safety assessments. A laboratory-based method using HepaRG cells was previously validated to measure induction of key CYP enzymes (CYP1A1/1A2, CYP2B6 and CYP3A4) using pharmaceutical chemicals. This study aimed to show that it also works well for industrial and pesticidal chemicals. In the EU funded GOLIATH project, two laboratories tested 10 pharmaceutical and 6 non-pharmaceutical chemicals. The method showed good reliability overall and strong reproducibility for pharmaceuticals. For non-pharmaceutical chemicals, results were acceptable but less consistent. The study concludes that the method is useful for routine testing, but improvements are needed to increase accuracy and better handle chemicals that show weak or borderline CYP induction effects.

pharmacology and toxicology↗

bioRxiv2026

Distinct thresholds condition sense PTGS initiation and amplification.

It has long been known that Pro35S-driven sense transgenes have a high propensity to undergo post-transcriptional gene silencing (S-PTGS). However, what exactly conditions S-PTGS initiation and amplification to make it systemic remains unknown. Through genetic screens, we show that antagonistic chromatin-related mutations enhancing and reducing transgene expression, result in enhanced and reduced S-PTGS amplification capacities, respectively, without affecting the initiation rate. Analysis of a large set of independent transgenic plants confirm a direct relationship between transgene expression and its capacity to amplify S-PTGS. Combining an inducible or a tissue-specifically expressed GUS transgene with a Pro35S:GUS transgene locus prone to amplify S-PTGS but unable to spontaneously initiate it induces systemic S-PTGS, indicating that transient and/or local passing of a discrete threshold is sufficient to initiate S-PTGS. Together, these results call for the existence of distinct thresholds related to transiently produced aberrant RNA and permanently produced target mRNA levels, which condition S-PTGS initiation and amplification, respectively. We show that this model also applies to endogenous genes for which RNA Quality Control (RQC) acts as a first layer of protection against S-PTGS, and DCL2s obscuration by DCL4 as a second layer, allowing RQC to dysfunction locally without translating into the drama of systemic S-PTGS.

plant biology↗

bioRxiv2025

Pyruvate promotes ciliogenesis bypassing IFT88 dependency and attenuates DSS-induced colitis

Primary cilia (PC) are important signaling rheostats, yet their biology in colon remains understudied. We previously reported that the presence of PC on colonic fibroblasts in mice (CF) modulates their susceptibility to colitis. Here, we demonstrate that extracellular pyruvate levels influence both ciliary length and ciliogenesis in CF. Pyruvate supplementation to CF enhanced tubulin and histone acetylation, with the latter promoting MAPK signaling and tubulin detyrosination within PC. MAPK-inhibition reduced tubulin detyrosination and shortened ciliary length, while inhibition of -tubulin acetylation specifically affected ciliogenesis. Col6a1cre-Ift88flx/flx mice, lacking ciliary Ift88 gene in Col6a1-expressing CF, displayed reduced ciliogenesis and increased susceptibility to DSS-induced colitis. Surprisingly, in primary CF cultures from these mice, pyruvate supplementation restored PC formation. Moreover, pyruvate administration via drinking water rescued PC formation in Col6a1cre-Ift88flx/flx mice and attenuated DSS-induced colitis. These findings identify pyruvate as a regulator of PC biology in CF and as a therapeutically relevant factor in colitis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/694572v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@170091dorg.highwire.dtl.DTLVardef@66870corg.highwire.dtl.DTLVardef@12c5124org.highwire.dtl.DTLVardef@834660_HPS_FORMAT_FIGEXP M_FIG Pyruvate promotes ciliogenesis bypassing IFT88 dependency and attenuates DSS-induced colitis C_FIG

pathology↗

bioRxiv2024

Acute dietary methionine restriction highlights sensitivity of neocortex development to metabolic variations

Methionine -an essential amino acid that has to be provided by nutrition- and its metabolite S-Adenosyl methionine (SAM) are indispensable for cell proliferation, stem cell maintenance and epigenetic regulation 1-5, three processes that are central to embryonic development 6. Previous studies using chronic dietary restriction of methyl donors prior to and during gestation indicated that methionine restriction (MR) is detrimental to the development or growth of the neocortex 7,8, however, the consequences of acute MR have not been extensively studied. Here, we designed a dietary MR regime coinciding with the neurogenic phases of neocortex development in the mouse. Our results indicate that dietary MR for 5 days leads to a severe reduction in neocortex growth and neuronal production. In comparison, growth of the liver and heart was unaffected, highlighting an organ-specific response to MR which was also observed at the cellular and molecular levels. Progenitor cohort labeling revealed a time-dependent sensitivity to MR and cell cycle analyses indicated that after 5 days of MR, progenitors are stalled in the S/G2 phases. Unexpectedly, neocortex growth reduction induced after 5 days of MR is completely rescued at birth when switching the dam back to control diet for the remaining of gestation, uncovering a mechanism of catch-up growth. Using multiplexed imaging we probed metabolic and epigenetic markers following MR and during catch-up growth and show that pyruvate metabolism is rewired in progenitors. Altogether, our data uncover a transient state of quiescence in G2/S which is metabolically distinct from G0 quiescence and associated with efficient catch-up growth. More globally, our study highlights both the extreme sensitivity of the developing neocortex to acute dietary changes and its remarkable plasticity.

developmental biology↗

bioRxiv2024

Deciphering Oxygen Distribution and Hypoxia Profiles in the Tumor Microenvironment: A Data-Driven Mechanistic Modeling Approach

The distribution of hypoxia within tissues plays a critical role in tumor diagnosis and prognosis. Recognizing the significance of tumor oxygenation and hypoxia gradients, we introduce mathematical frameworks grounded in mechanistic modeling approaches for their quantitative assessment within a tumor microenvironment. Our approach provides a non-invasive method to measure and predict hypoxia using known blood vasculature. Formulating a reaction-diffusion model for oxygen distribution, we apply it to derive the corresponding hypoxia profile. The modeling and simulations successfully replicate the observed inter- and intra-tumor heterogeneity in experimentally obtained hypoxia profiles across various tumor tissues (breast, ovarian, and pancreatic) in our dataset. Employing a data-driven approach, we propose a method to deduce partial differential equation (PDE) models with spatially dependent parameters, enabling us to comprehend the variability of hypoxia profiles within a tissue. The versatility of our framework lies not only in capturing diverse and dynamic behaviors of tumor oxygenation but also in categorizing states of vascularization. These categories are distinguished based on the dynamics of oxygen molecules, as identified by the model parameters.

cancer biology↗

bioRxiv2022

E4F1 COORDINATES PYRUVATE METABOLISM AND THE ACTIVITY OF THE ELONGATOR COMPLEX TO ENSURE PROTEIN TRANSLATION FIDELITY DURING NEURONAL DEVELOPMENT

Pyruvate metabolism defects lead to severe neuropathies such as the Leigh syndrome (LS) but the molecular mechanisms underlying neuronal cell death remain poorly understood. Here, we unravel a connection between pyruvate metabolism and the regulation of the epitranscriptome that is relevant to LS pathogenesis. We identified the transcription factor E4F1 as a key coordinator of AcetylCoenzyme A (AcCoA) production by the pyruvate dehydrogenase complex (PDC) and its utilization as an essential co-factor by the Elongator complex to acetylate tRNAs at the wobble position uridine 34 (U34). E4F1-mediated direct transcriptional regulation of Dlat and Elp3, two genes encoding key subunits of the PDC and of the Elongator complex, respectively, ensured proper translation fidelity and cell survival in the central nervous system (CNS) during mouse embryonic development. Furthermore, analysis of PDH-deficient cells highlighted a crosstalk linking the PDC to ELP3 expression that is perturbed in LS patients.

developmental biology↗

bioRxiv2022

Adaptive radioresistance of Enterohemorrhagic Escherichia coli O157:H7 results in genomic loss of shiga toxin-encoding prophages

Enterohemorragic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen producing shiga toxins (Stx1 and Stx2), can cause hemorrhagic diarrhea, and life-threatening infections. O157:H7 strain EDL933 carries prophages CP-933V and BP-933W that encode shiga toxin genes (stx1 and stx2 respectively). The aim of this work was to investigate the mechanisms of adaptive resistance of EHEC strain EDL933 to a typically "lethal" dose of {gamma}-irradiation (1.5 kGy). Adaptive selection through six passages of exposure to 1.5 kGy resulted in the loss of CP-933V and BP-933W prophages from the genome and mutations within three genes: wrbA, rpoA, and Wt_02639 (molY). Three selected EHEC clones that became irradiation-adapted to the 1.5 kGy dose (C1, C2 and C3) demonstrated increased resistance to oxidative stress, sensitivity to acid pH, and decreased cytotoxicity to Vero cells. To confirm that loss of prophages plays a role in increased radioresistance, C1 and C2 clones were exposed to bacteriophage containing lysates. Although, phage BP-933W could lysogenize C1, C2, and E.coli K-12 strain MG1655, it was not found to have integrated into the bacterial chromosome in C1-{Phi} and C2-{Phi} lysogens. Interestingly, for the E. coli K-12 lysogen (K12-{Phi}), BP-933W DNA had integrated at the wrbA gene (K12-{Phi}). Both C1-{Phi} and C2-{Phi} lysogens regained sensitivity to oxidative stress, were more effectively killed by a 1.5 kGy {gamma}-irradiation dose and had regained cytotoxicity and acid resistance phenotypes. Further, the K12-{Phi} lysogen became cytotoxic, more sensitive to {gamma}-irradiation and oxidative stress and slightly more acid resistant. ImportanceGamma ({gamma})-irradiation of food products can provide an effective means of eliminating bacterial pathogens such as enterohemorrhagic Escherichia coli (EHEC) O157:H7, a significant foodborne pathogen that can cause severe disease due to the production of Shiga toxins. To decipher the mechanisms of adaptive resistance of the O157:H7 strain EDL933, we evolved clones of this bacterium resistant to a lethal dose of {gamma}-irradiation by repeatedly exposing bacterial cells to irradiation following a growth restoration over six successive passages. Our findings provide evidence that adaptive selection involved modifications in the bacterial genome including deletion of the CP-933V and BP-933W prophages. These mutations in EHAC O157:H7 resulted in loss of stx1, stx2, loss of cytotoxicity to epithelial cells and decreased resistance to acidity, critical virulence determinants of EHEC, concomitant with increased resistance to lethal irradiation and oxidative stress. These findings demonstrate that the potential adaptation of EHEC to high doses of radiation would involve elimination of the Stx encoding phages and likely lead to a substantial attenuation of virulence.

microbiology↗

bioRxiv2022

Computational Model of Heterogeneity in Melanoma: Designing Therapies and Predicting Outcomes

Cutaneous melanoma is a highly invasive tumor and, despite the development of recent therapies, most patients with advanced metastatic melanoma have a poor clinical outcome. The most frequent mutations in melanoma affect the BRAF oncogene, a protein kinase of the MAPK signaling pathway. Therapies targeting both BRAF and MEK are effective for only 50% of patients and, almost systematically, generate drug resistance. Genetic and non-genetic mechanisms associated with the strong heterogeneity and plasticity of melanoma cells have been suggested to favor drug resistance but are still poorly understood. Recently, we have introduced a novel mathematical formalism allowing the representation of the relation between tumor heterogeneity and drug resistance and proposed several models for the development of resistance of melanoma treated with BRAF/MEK inhibitors. In this paper, we further investigate this relationship by using a new computational model that copes with multiple cell states identified by single cell mRNA sequencing data in melanoma treated with BRAF/MEK inhibitors. We use this model to predict the outcome of different therapeutic strategies. The reference therapy, referred to as "continuous" consists in applying one drug (or several drugs) without disruption. In "combination therapy", several drugs are used sequentially. In "adaptive therapy" drug application is interrupted when the tumor size is below a lower threshold and resumed when the size goes over an upper threshold. We show that, counter-intuitively, the optimal protocol in combination therapy of BRAF/MEK inhibitors with a hypothetical drug targeting cell states that develop later during the tumor response to kinase inhibitors, is to treat first with this hypothetical drug. Also, even though there is little difference in the timing of emergence of the resistance between continuous and adaptive therapies, the spatial distribution of the different melanoma subpopulations is more zonated in the case of adaptive therapy.

systems biology↗

bioRxiv2021

Crisscross multilayering of cell sheets

Simple hydrostatic skeletons such as the Hydras consist of two stacked layers of cells perpendicularly oriented. Although this crisscross architecture can be recapitulated in vitro, little is known on the formation of such multilayers starting from a monolayer. In the present article, we show that bilayering of myoblasts results from the organization and activity of the cells originally in the monolayer which can be described as a contractile active nematic. As expected, most of the +1/2 topological defects that are associated with this nematic order self-propel. However, a subpopulation of these defects remains immobile. Perpendicular bilayering occurs exclusively at these motionless defects. Indeed, cells located at the head of these defects converge toward the (immobile) core and accumulate there until they start migrating on top of the tail of the first layer while the tail cells migrate in the opposite direction under the head cells. Since the cells keep their initial orientations, the two stacked layers end up perpendicularly oriented. This concerted process leading to a bilayer is dependent on the apical secretion of Extra Cellular Matrix (ECM) by the cells. Indeed, we evidence the presence of ECM between the cell layers and at the apical surface of the topmost layer. ECM molecules are oriented in the direction of the cells that produce them, which may guide the migration of the subsequent cell layers on their apical side. Significance StatementHydrostatic skeletons such as that of the Hydra consist of two stacked layers of cells perpendicularly oriented whose coordinated contraction allows for complex movements. Such crisscross organization is also observed with myoblasts in culture. Confluent monolayers organize in well-aligned domains between which topological defects position themselves. Although these singularities are generally self-propelled, a fraction of them remains motionless. Perpendicular bilayering occurs exclusively at these particular pinned defects. Cells first accumulate at the head of the defects until they split in two perpendicular layers migrating in an antiparallel way on top of each other. Such a concerted process is highly dependent on the precise organization of the cell-secreted Extra Cellular Matrix (ECM).

biophysics↗

bioRxiv2019

SingleCellSignalR: Inference of intercellular networks from single-cell transcriptomics

Single-cell transcriptomics offers unprecedented opportunities to infer the ligand-receptor interactions underlying cellular networks. We introduce a new, curated ligand-receptor database and a novel regularized score to perform such inferences. For the first time, we try to assess the confidence in predicted ligand-receptor interactions and show that our regularized score outperforms other scoring schemes while controlling false positives. SingleCellSignalR is implemented as an open-access R package accessible to entry-level users and available from https://github.com/SCA-IRCM. Analysis results come in a variety of tabular and graphical formats. For instance, we provide a unique network view integrating all the intercellular interactions, and a function relating receptors to expressed intracellular pathways. A detailed comparison with related tools is conducted. Among various examples, we demonstrate SingleCellSignalR on mouse epidermis data and discover an oriented communication structure from external to basal layers.

bioinformatics↗