Biology subjects

Alexandre, C.

Publications and source records attributed to Alexandre, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Xrp1 integrates cellular stress through different control modes in Drosophila

Cells and tissues have the ability to respond to different stresses and maintain their homeostasis. The b-Zip transcription factor Xrp1 was found to play a pivotal role in this context in Drosophila. Xrp1 is required for the response to irradiation, in genetic conditions of ribosomal protein (Rp) deficiency leading to cell competition, and more generally in mediating the Integrated Stress Response (ISR). However, how these diverse stresses converge to and activate Xrp1 is still unclear. Our results demonstrate the existence of three separate mechanisms of Xrp1 induction. In response to Rp stress, a short isoform of Xrp1 is produced and requires the function of the ribosomal protein RpS12. In response to irradiation, a specific mRNA isoform is transcriptionally induced, which encodes the Xrp1-short protein isoform, in a p53-dependent manner. In response to the ISR, the long isoform of Xrp1 is translated by the derepression of a uORF present on the Xrp1 5'UTR, a mechanism that requires eIF2 phosphorylation, RpS12, and a transcriptional induction by ATF4. Therefore, our work provides a comprehensive understanding of the role of Xrp1 in different situations of cellular stress, illustrating the complex level of integration of the mechanisms controlling this central gene.

developmental biology↗

bioRxiv2026

An in vivo chemical genetic approach for targeted glycoproteome analysis in Drosophila melanogaster

Glycans impact every aspect of physiology. Despite the rapid increase in relevance and translational potential, there remains a lack of tools for studying glycosylation in vivo. Here, we present FlyMOE, a chemical-genetic platform for targeted glycoprotein profiling in Drosophila melanogaster. Transgenic flies are equipped with biosynthetic capabilities to install bioorthogonally-tagged monosaccharides into the cellular glycoproteome. The genetic tractability of Drosophila allows for versatile application based on developmental stages, genetic drivers and glycosyltransferase enzymes. We employ FlyMOE to create an overview of the glycoproteome of Drosophila tissues and embryos based on mass spectrometry glycoproteomics, and investigate the substrates of individual members of the PGANT glycosyltransferase family in vivo. FlyMOE will allow the detailed investigation of the glycoproteome in Drosophila and similarly genetically modifiable in vivo model systems.

bioengineering↗

bioRxiv2026

UbiB proteins mediate an ATP-dependent decarboxylation step in bacterial ubiquinone biosynthesis

Polyisoprenoid quinones such as ubiquinone (UQ) play an essential role in cellular physiology, acting as membrane-bound electron and proton carriers in respiratory chains and other biological processes across all domains of life. In Escherichia coli, the canonical UQ biosynthesis pathway is well characterized. It involves twelve proteins (UbiA-UbiK and UbiX), most of which catalyzing one of the eight modifications of the aromatic ring derived from 4-hydroxybenzoic acid (4-HB), while others (UbiB, UbiJ, UbiK) act as accessory factors ensuring efficient UQ production. Following prenylation by UbiA and subsequent decarboxylation by the UbiX/UbiD system, the final six reactions are catalyzed within a soluble Ubi-complex. UbiB, an atypical protein kinase-like enzyme, was proposed to extract decarboxylated intermediates from the membrane and mediate their delivery to the Ubi-complex. In this study, we demonstrate the existence of an alternative decarboxylation system in E. coli, as UQ biosynthesis can proceed in the absence of the UbiX/UbiD system. Our results show that this alternative decarboxylation activity depends on UbiB and requires its ATPase activity. Bioinformatic analyses further revealed that approximately 27% of Pseudomonadota species lack UbiX/UbiD homologs, and we found that UbiB proteins from two such species enhance the alternative decarboxylation activity when expressed in E. coli. In addition, we identified conserved residues in UbiB that are specifically required for decarboxylation but dispensable for the delivery of UQ intermediates to the Ubi-complex. Taken together, our findings support a model in which UbiB acts as an ATP-dependent decarboxylase, thereby broadening the functional scope of this poorly characterized protein. ImportancePolyisoprenoid quinones, including ubiquinone (UQ, also known as coenzyme Q), are essential electron and proton carriers in respiratory chains across all domains of life. After prenylation and decarboxylation, the final six steps of UQ biosynthesis are carried out by a soluble Ubi-complex. The only decarboxylation system currently identified in the UQ pathway, the UbiX/UbiD system, is absent from numerous bacterial genomes, and no isofunctional enzymes have been described to date. UbiB, an atypical protein kinase-like enzyme, has been proposed to mediate the extraction of UQ precursors from the membrane, thereby rendering them accessible to the soluble Ubi-complex. Here, we show that UbiB proteins fulfill an additional function in bacteria. Specifically, they contribute to the decarboxylation of UQ precursors through a mechanism that remains unknown but depends on ATP hydrolysis. Given that UbiB is conserved in all UQ-producing bacteria, it may represent a widespread decarboxylation system within this essential metabolic pathway.

biochemistry↗

bioRxiv2026

Membrane lipid composition and endocytosis modulate Wingless release from secreting cells

Wnts are secreted signalling molecules that regulate development and adult homeostasis. Most Wnts carry a lipid moiety that must be shielded from the aqueous environment. In the secretory pathway, this is achieved by a hydrophobic tunnel in Wntless, a multipass transmembrane protein. However, the Wnt lipid moiety must be released from Wntless before Wnts can engage with Frizzled receptors on receiving cells. Here we address the cell biological basis of Wnt-Wntless dissociation, using as a model the secretion of Drosophila Wingless in wing primordia. Super-resolution microscopy shows that Wingless first reaches the apical surface before being re-internalized to reach, without Wntless, specialized Rab7/Rab4-positive endosomes. From there Wingless traffics to the basolateral membrane where it can engage with glypicans to form a basolateral gradient. Acute inhibition of endocytosis, either with a temperature-sensitive dynamin mutant or a novel optogenetic means of inhibiting clathrin, leads to apical Wingless release in abnormal punctae devoid of Wntless, suggesting that Wingless-Wntless dissociation commences at the apical surface, perhaps because of a distinct lipid composition there. Indeed, similar looking punctae are produced upon genetic abrogation of the ceramide synthase Schlank, specifically in Wingless-producing cells. These punctae resemble insoluble aggregates that form in vitro upon detergent removal. Accordingly, punctae formation can be prevented by shielding the Wingless lipid, in vivo with excess Dally-like protein (Dlp) or in vitro with liposomes. Our results show that membrane lipid composition modulates the orderly transfer of Wingless lipid from Wntless to the inner endosomal surface thus preventing aggregation and ensuring seamless secretion in the basolateral space.

cell biology↗

bioRxiv2025

The blood-brain barrier regulates brain tumour growth specifically via the SLC36 amino acid transporter Pathetic in Drosophila

Tumours adapt their metabolism to sustain increased proliferation, rendering them particularly vulnerable to fluctuations in nutrient availability. However, the role of the tumour microenvironment in modulating sensitivity to nutrient restriction (NR) remains poorly understood. Using a Drosophila brain dedifferentiation neural stem cell (NSC) tumour model induced by Prospero (Pros) inhibition, we show that tumour sensitivity to NR is governed by the perineural glial (PG) cells of the blood-brain barrier (BBB), a major component of the glial niche surrounding the tumour. We identify the SLC36 amino acid transporter Pathetic (Path) as a crucial regulator of nutrient sensitivity. Under NR, while wildtype buffers against low nutrient levels by upregulating Path, tumour glia downregulate Path. Furthermore, Path is specifically required by the tumour (but not wildtype) PG; its downregulation causes reduced proliferation of PG cells and, in turn, restricts NSC tumour growth. Path influences PG proliferation via the mTor-S6K pathway, and its expression is controlled by Ilp6 levels and the Insulin/PI3K pathway. Overexpression of Path is sufficient to counteract the inhibitory effects of NR on tumour growth. These findings suggest that Path levels at the BBB play a key role in determining tumour sensitivity to NR.

cancer biology↗

bioRxiv2025

Insect wings arose with a genetic circuit that extends the useful range of a BMP morphogen

Morphogens are produced by a subset of cells to trigger a signalling gradient that provides positional information to surrounding tissues. At increasing distances from the source, the dwindling number of morphogen molecules is expected to constrain the useful range of morphogen gradients. We have identified a genetic circuit that counteracts this limitation in developing wings of Drosophila by boosting BMP signalling at the distal end of the gradient without amplifying the signal near the source. This circuit involves Brinker, a transcription factor that represses BMP target genes while itself being repressed by BMP signalling. We suggest that temporal averaging inherent to the production of the inverse Brk gradient contributes to the enhancement of the positional information far from the Dpp source. Despite being a core component of BMP signalling in flies, Brinker is exclusively found in insects, likely in all insect species. Genomic analysis across a wide range of insects and gene expression analysis in limb primordia of the apterygote Thermobia domestica suggests that Brinker is an insect-specific innovation that was subsequently wired into the BMP signalling network in pterygotes, perhaps to enable wing development.

developmental biology↗

bioRxiv2024

Identification of a specialized lipid barrier for Drosophila metamorphosis

In many terrestrial insects, the onset of metamorphosis marks a transition from humid to dry environments. Yet how metamorphosing insect pupae protect themselves against the threat of dehydration remains unclear. Here, we identify the chemical composition and biosynthetic origins of a lipid desiccation barrier specific to the pupal and sexually-immature adult stages of Drosophila melanogaster. This barrier comprises unisex hyper-long hydrocarbons, 29-37 carbons in length, which are synthesized by larval oenocytes and stored in the larval fat body before being deployed on the pupal and young adult cuticles. We show that the fatty acid elongase EloHL is required for the biosynthesis of hyper-long hydrocarbons that are essential for the barrier to water loss during metamorphosis. Across the Drosophila genus, many species express unisex profiles of hyper-long hydrocarbons and, as young adults, transition to sex-specific shorter hydrocarbons with known pheromonal functions. The desert species D. mojavensis, however, retains hyper-long hydrocarbons during adulthood likely as an adaptation to an arid environment. Our study reveals how the cuticular lipid barrier is tuned to meet changing environmental pressures during insect development and evolution.

developmental biology↗

bioRxiv2024

Growth-induced physiological hypoxia correlates with growth deceleration during normal development

Growth deceleration is a universal feature of growth during development: most organs and tissues slow down their growth rate much before growth termination. Using transcriptomics analysis, we show that during their two-day period of growth deceleration, wing imaginal discs of Drosophila undergo a progressive metabolic shift away from oxidative phosphorylation and towards glycolysis. We then develop an ultra-sensitive reporter HIF-1 activity, which reveals that imaginal discs become increasingly hypoxic during development in normoxic conditions, suggesting that limiting oxygen supply could underlie growth deceleration. Growth is energetically expensive and thus expected to contribute, indirectly, to oxygen consumption. Indeed, excess TOR signalling, a key stimulator of growth, triggers hypoxia locally and systemically, highlighting the need to rein in growth when oxygen becomes limiting. This is achieved by a negative feedback loop whereby the classic TOR-inhibitory function of HIF-1 is deployed in response to developmental hypoxia. The absence of Sima/HIF-1 leads to cellular stress, which is alleviated by reduced TOR signalling. Conversely, a small increase in oxygen supply reduces the stress induced by excess TOR activity. We conclude that mild hypoxia is a normal feature of organ development and that Sima/HIF-1 prevents growth-induced oxygen demand from exceeding supply.

developmental biology↗

bioRxiv2024

An Amygdalar Oscillator Coordinates Cellular and Behavioral Rhythms

Circadian rhythms are generated by the master pacemaker suprachiasmatic nucleus (SCN), in concert with local clocks throughout the body. While many brain regions exhibit cycling clock gene expression, the identity of a discrete extra-SCN brain oscillator that produces rhythmic behavior has remained elusive. Here, we show that an extra-SCN oscillator in the lateral amygdala (LA) is defined by expression of the clock-output molecule mWAKE/ANKFN1. mWAKE is enriched in the anterior/dorsal LA (adLA), and strikingly, selective disruption of clock function or excitatory signaling in adLAmWAKE neurons abolishes Period2 (Per2) rhythms throughout the LA. mWAKE levels rise at night and promote rhythmic excitability of adLAmWAKE neurons by upregulating Ca2+-activated K+ channel activity specifically at night. adLAmWAKE neurons coordinate rhythmic sensory perception and anxiety in a clock-dependent and WAKE-dependent manner. Together, these data reveal the cellular identity of an extra-SCN brain oscillator and suggest a multi-level hierarchical system organizing molecular and behavioral rhythms.

neuroscience↗

bioRxiv2023

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair

Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.

genetics↗

bioRxiv2023

Drosophila AHR limits tumor growth and stem cell proliferation in the intestine

The aryl hydrocarbon receptor (AHR) plays important roles in intestinal homeostasis, limiting tumour growth and promoting differentiation in the intestinal epithelium. Spineless, the Drosophila homolog of AHR, has only been studied in the context of development but not in the adult intestine. Here, we show that spineless is upregulated in the adult intestinal epithelium after infection with Pseudomonas entomophila (P.e.). Spineless knockdown increased stem cell proliferation following infection-induced injury. Spineless overexpression limited intestinal stem cell proliferation and reduced survival after infection. In two tumour models, using either Notch RNAi or constitutively active Yorkie, Spineless suppressed tumour growth and doubled the lifespan of tumour-bearing flies. At the transcriptional level it reversed the gene expression changes induced in Yorkie tumours, counteracting cell proliferation and altered metabolism. These findings demonstrate a new role for Spineless in the adult Drosophila midgut and highlight the evolutionarily conserved functions of AHR/Spineless in the control of proliferation and differentiation of the intestinal epithelium.

cancer biology↗

bioRxiv2023

Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

Ex-vivo drug sensitivity screening allows the prediction of cancer treatment effectiveness in a personalized fashion. However, it only provides a readout on mixtures of cells, potentially occulting important information on clinically relevant cell subtypes. To address this shortcoming, we developed a machinelearning framework to decompose drug sensitivity recorded at the bulk level into cell subtype-specific drug sensitivity. We first determined that our method could decipher the cellular composition of bulk samples with top-ranking accuracy across five cancer types compared to state-of-the-art bulk deconvolution methods. We emphasize its effectiveness in the realm of Acute Myeloid Leukemia, where it appears to offer the most precise estimation of leukemic stem cell fractions across three test datasets and three patient cohorts. We then optimized an algorithm capable of estimating cell subtype- and single-cell-specific drug sensitivity, which we evaluated by performing in-vitro drug studies and in-depth simulations. We then applied our deconvolution strategy to the beatAML cohort dataset, currently the most extensive database of ex-vivo drug screening data. We developed a drug sensitivity profile tailored to specific cell subtypes, focusing on four therapeutic compounds predicted to target leukemic stem cells: the previously known midostaurin and A-674563, as well as SNS-032 and foretinib, which have not been previously linked to leukemic stem cells. Our work provides an attractive new computational tool for drug development and precision medicine.

bioinformatics↗

bioRxiv2023

Signalling-dependent refinement of cell fate choice during tissue remodelling

How biological form emerges from cell fate decisions and tissue remodelling is a fundamental question in development biology. However, an understanding of how these processes operate side-by-side to set precise and robust patterns is largely missing. Here, we investigate this interplay during the process of vein refinement in the Drosophila pupal wing. By following reporters of signalling activity dynamically, together with tissue flows, we show that longitudinal vein refinement arises from a combination of local tissue deformation and cell fate adjustments controlled by a signalling network involving Notch, Dpp, and EGFR. Perturbing large-scale convergence and extension tissue flows does not affect vein refinement, showing that pre-patterned vein domains are able to intrinsically refine to the correct width. A minimal biophysical description taking into account key signalling interactions recapitulates the intrinsic tissue ability to establish a thin, regular vein independently of large-scale tissue flows. Supporting this prediction, artificial proveins optogenetically generated orthogonal to the axis of wing elongation refine against large-scale flows. Overall, we find that signalling-mediated updating of cell fate is a key contributor to reproducible patterning.

developmental biology↗

bioRxiv2023

The ecdysone receptor promotes or suppresses proliferation according toligand level

Steroid hormones control various cellular activities in a context-dependent manner. For example, ecdysone, which acts through a type II nuclear receptor, has seemingly opposite effects in Drosophila wing precursors, promoting proliferation during larval stages, and triggering proliferation arrest at pupariation. We find that wing precursors proliferate normally in the complete absence of the ecdysone receptor (EcR), whether ecdysone is present or not, suggesting that ecdysone overrides a default antiproliferative activity of the receptor. By contrast, termination of proliferation by high concentration of 20E at the end of larval life involves conventional gene regulation by the ligand-receptor complex. The switch from one mode of regulation to the other is determined by ligand level, as measured with a calibrated EcR transcriptional reporter and ex vivo proliferation assays. Accordingly, RNA Seq analysis uncovers distinct transcriptional responses to different doses of ecdysone. Some genes are only activated at high doses (high threshold targets) and likely to comprise genes that stop proliferation at pupariation, when ecdysone titres are high. We find that other target genes respond to all physiological concentrations of ecdysone. Some of these genes are known to promote proliferation and could therefore contribute to the pro-proliferation activity of low-level ecdysone. Finally, we show mathematically and with synthetic reporters that relatively simple combinations of regulatory elements can recapitulate the behaviour of both types of target genes.

developmental biology↗

bioRxiv2020

The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

In plants, chromatin accessibility - the primary mark of regulatory DNA - is relatively static across tissues and conditions. This scarcity of accessible sites that are dynamic or tissue-specific may be due in part to tissue heterogeneity in previous bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to A. thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. However, even this vast increase relative to bulk studies in the number of dynamic sites does not resolve the poor correlation at individual loci between accessibility and expression. Instead, we find that the entirety of a cells regulatory landscape and its transcriptome each capture cell type identity independently. We leverage this shared information on cell identity to integrate accessibility and transcriptome data in order to characterize developmental progression, endoreduplication and cell division in the root. We further use the combined data to characterize cell type-specific motif enrichments of large transcription factor families and to link the expression of individual family members to changing accessibility at specific loci, taking the first steps toward resolving the direct and indirect effects that shape gene expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.

genomics↗

bioRxiv2020

Frizzled-dependent Planar Cell Polarity without Wnt Ligands

Planar cell polarity (PCP) organizes the orientation of cellular protrusions and migratory activity within the tissue plane. PCP establishment involves the subcellular polarization of core PCP components. It has been suggested Wnt gradients could provide a global cue that coordinates local PCP with tissue axes. Here we dissect the role of Wnt ligands in the orientation of hairs of Drosophila wings, an established system for study of PCP. We found that PCP was normal in quintuple mutant wings that rely solely on membrane-tethered Wingless for Wnt signaling, suggesting that a Wnt gradient is not required. We then used a nanobody-based approach to trap Wntless in the endoplasmic reticulum, and hence prevent all Wnt secretion, specifically during the period of PCP establishment. PCP was still established. We conclude that, even though Wnt ligands could contribute to PCP, they are not essential, and another global cue must exist for tissue-wide polarization.

developmental biology↗

bioRxiv2019

Lessons in genome engineering: opportunities, tools and pitfalls

CRISPR/Cas technology allows the creation of double strand breaks and hence loss of function mutations at any location in the genome. This technology is now routine for many organisms and cell lines. Here we describe how CRISPR/Cas can be combined with other DNA manipulation techniques (e.g. homology-based repair, site-specific integration and Cre or FLP-mediated recombination) to create sophisticated tools to measure and manipulate gene activity. In one class of applications, a single site-specific insertion generates a transcriptional reporter, a loss-of function allele, and a tagged allele. In a second class of modifications, essential sequences are deleted and replaced with an integrase site, which serves as a platform for the creation of custom reporters, transcriptional drivers, conditional alleles and regulatory mutations. We describe how these tools and protocols can be implemented easily and efficiently. Importantly, we also highlight unanticipated failures, which serve as cautionary tales, and suggest mitigating measures. Our tools are designed for use in Drosophila but the lessons we draw are likely to be widely relevant.\n\nAUTHOR SUMMARYThe genome contains all the information that an organism needs to develop and function throughout its life. One of the goal of genetics is to decipher the role of all the genes (typically several thousands for an animal) present in the genome. One approach is to delete each gene and assay the consequences. Deletion of individual genes is now readily achieved with a technique called CRISPR/Cas9. However, simple genetic deletion provides limited information. Here we describe strains and DNA vectors that streamline the generation of more sophisticated genetic tools. We describe general means of creating alleles (genetic variants) that enable gene activity to be measured and experimentally modulated in space and time. Although the tools we describe are universally applicable, each gene requires special consideration. Based on our experience of successes and failures, we suggest measures to maximise the chances that engineered alleles serve their intended purpose. Although our methods are designed for use in Drosophila, they could be adapted to any organism that is amenable to CRISPR/Cas9 genome modification.

genetics↗

bioRxiv2019

Membrane-type 1 matrix metalloproteinase (MMP-14) modulates tissue homeostasis by a non-proteolytic mechanism

Membrane-type 1 matrix metalloproteinase (MT1-MMP, MMP-14), a transmembrane proteinase with a short cytoplasmic tail, is a major effector of extracellular matrix (ECM) remodeling. Genetic silencing of MT1-MMP in mouse (Mmp14-/-) and man causes dwarfism, osteopenia, arthritis and lipodystrophy, abnormalities ascribed to defective collagen turnover. We have previously shown non-proteolytic functions of MT1-MMP mediated by its cytoplasmic tail, where the unique tyrosine (Y573) controls intracellular signaling. The Y573D mutation blocks TIMP2/MT1-MMP-induced Erk1/2 and Akt signaling without affecting proteolytic activity. Here we report that a mouse with the MT1-MMP Y573D mutation (Mmp14Y573D/Y573D) shows abnormalities similar to, but also different from those of Mmp14-/- mice. Skeletal stem cells (SSC) of Mmp14Y573D/Y573D mice show defective differentiation consistent with the mouse phenotype, which is rescued by wild-type SSC transplant. These results provide the first in vivo demonstration that MT1-MMP modulates bone, cartilage and fat homeostasis by controlling SSC differentiation through a mechanism independent of proteolysis.

cell biology↗