Biology subjects

Olmedo, M.

Publications and source records attributed to Olmedo, M..

15 recordsLinked to original sources

bioRxiv2026

In vivo functional classification of PTEN variants reveals context-dependent oncogenicity and interindividual variability

Gene variants, secondary mutations, and stochastic individual variability complicate cancer diagnosis, prognosis, and treatments. Here, we systematically assess the functional impact of PTEN cancer-related missense mutations in mammalian cell lines, yeast, and Caenorhabditis elegans. While cell-based assays revealed alterations in lipid phosphatase activity, CRISPR-based engineering of orthologous mutations in C. elegans enabled classification of variants based on organismal phenotypes and transcriptional profiles, providing a rapid framework to predict oncogenic potential. We further show that secondary mutations, such as gain-of-function of cdc-25.1/CDC25A, can enhance the phenotypic impact of specific daf-18/PTEN variants, revealing context-dependent oncogenicity. Finally, single-worm transcriptomic analyses uncovered substantial interindividual variability among isogenic animals with identical cdc-25.1 and daf-18 mutations, linking transcriptional states to divergent phenotypic outcomes. Together, our results establish C. elegans as a powerful in vivo platform to integrate genetic, functional, and transcriptional information for the interpretation of cancer-associated variants.

cancer biology↗

bioRxiv2026

A high-throughput assay quantifies thermal scaling of Drosophila development with minute-scale precision

Precise regulation of developmental timing is essential for coordinated growth and robust development, yet staging remains technically challenging in many model systems. In Drosophila melanogaster, developmental timing has traditionally been assessed using low-throughput or coarse staging methods, limiting insight into how individual larval stages respond to environmental and genetic perturbations. Here, we present a high-throughput, real-time luminometry assay that enables continuous, automated measurement of postembryonic development in individual Drosophila larvae. By monitoring feeding-dependent luciferase activity, this method reliably detects transitions between larval instars and molts of individual larvae with minute-scale temporal resolution. Using this platform, we provide a quantitative, minute-precision, stage-resolved description of larval development across large cohorts, revealing distinct patterns of variability and weak temporal coupling between stages. We next examine how temperature shapes developmental timing across a broad thermal range. Increasing temperature uniformly accelerates larval development while preserving the proportional contribution of each stage, indicating that the temporal architecture of development is maintained as overall pace changes. Developmental rate follows predictable thermodynamic scaling within a defined temperature window, enabling precise estimation of thermal parameters at both whole-organism and stage-specific levels. Finally, we demonstrate that the assay is compatible with genetic perturbations. This work establishes a scalable, high-precision framework for measuring postembryonic development in Drosophila melanogaster. By revealing the modular and coordinated nature of larval growth, it enables systematic dissection of genetic, metabolic, and environmental control of developmental timing and provides a platform to explore fundamental principles of development and robustness across species.

developmental biology↗

bioRxiv2025

Mitochondrial redox homeostasis links organellar stress surveillance to germline and somatic integrity in Caenorhabditis elegans

Mitochondrial redox homeostasis is essential for cellular metabolism and organismal development. To investigate the consequences of disrupting redox homeostasis in this organelle in a metazoan organism, we generated a double mutant lacking mitochondrial glutathione reductase (gsr-1a) and thioredoxin reductase (trxr-2) genes in Caenorhabditis elegans. While gsr-1a or trxr-2 single mutants are phenotypically normal, double gsr-1a trxr-2 mutants displayed small body size, gonadal migration defects, reduced brood size, and prolonged egg-laying period, without developmental delay or lethality. Transcriptomic analysis revealed strong induction of ATFS-1-dependent stress and detoxification genes. Consistent with this, gsr-1a trxr-2 worms exhibited constitutive ATFS-1 nuclear localization and robust Phsp-6::gfp expression. Triple gsr-1a trxr-2; atfs-1 mutants were nonviable, demonstrating that unfolded protein response (UPRmt) activation is essential under mitochondrial redox stress. Despite the induction of a stress response at the transcriptional level, gsr-1a trxr-2 double mutants were not more resistant to oxidative or pathogen stressors. Moreover, these mutants maintained normal respiration, ATP and ROS production while displaying altered mitochondrial morphology in a tissue-specific manner, independent of mitophagy genes but dependent on mitochondrial fission or fusion machinery. Functionally, gsr-1a trxr-2 mutants showed impaired motility, reduced calcium uptake upon carbachol stimulation, enhanced hypodermal wound repair, and decreased fertilization efficiency associated with lower muscle exopher production. Overall, our data show that simultaneous loss of mitochondrial GSR-1a and TRXR-2 compromises growth, fertility and muscle performance and triggers a constitutive ATFS-1-dependent UPRmt that sustains viability revealing mitochondrial redox control as a core determinant of organismal proteostasis. HighlightsO_LIgsr-1a or trxr-2 single mutants have no overt phenotypes. C_LIO_LIgsr-1a trxr-2 double mutants are viable but show small size, gonad migration defects and reduced progeny. C_LIO_LILoss of both reductases in mitochondria triggers a constitutive ATFS-1-dependent UPRmt. C_LIO_LIATFS-1 is essential for gsr-1a trxr-2 worms survival. C_LIO_LIgsr-1a trxr-2 animals remodel mitochondrial morphology in a tissue-specific manner. C_LIO_LIgsr-1a trxr-2 double mutants exhibit impaired muscle and sperm function but enhanced wound healing. C_LI Graphical abstract (to be incorporated)

genetics↗

bioRxiv2025

HLH-30/TFEB is necessary for chromatin reorganization and maintenance of cell quiescence during starvation in C. elegans

Cellular quiescence is a metabolically active, non-proliferative state critical for tissue maintenance and regenerative capacity, with broad implications for aging and age-related diseases. In Caenorhabditis elegans, L1 developmental arrest upon hatching in the absence of food provides a robust in vivo model to study quiescence. Here, we investigate the roles of the transcription factors HLH-30/TFEB and DAF-16/FOXO during L1 arrest. We show that HLH-30 and DAF-16 collaborate to ensure survival under starvation, with reciprocal regulation of their subcellular localization and transcriptional activity. HLH-30 exerts broad transcriptional control during L1 arrest, modulating genes involved in chromosome organization and cell cycle progression. Profiling of chromatin spatial distribution reveals that HLH-30 is required for fasting-induced 3D chromatin reorganization. Loss of HLH-30 disrupts seam cell cycle arrest and leads to overactivation of the pioneer transcription factor BLMP-1, leading to premature initiation of developmental programs under starvation. Our findings uncover previously unrecognized functions of HLH-30 in genome architecture and quiescence regulation, highlighting conserved mechanisms of transcriptional control during nutrient deprivation with implications for aging and disease.

developmental biology↗

bioRxiv2025

The interplay between Caenorhabditis elegans larval development and Orsay virus infection

Caenorhabditis elegans development can be altered by its interactions with pathogens, such as bacteria1,2 or fungi3. However, the impact of viral infections on the nematodes development remains largely unexplored, and conversely, whether molting periods affect viral replication is unknown. Studying infections with Orsay virus (OrV), the only known natural C. elegans virus4, we investigated the role of molting on virus replication dynamics and the impact of OrV infection on C. elegans larval development. We found that OrV replicates during C. elegans molting periods. Indeed, nematodes inoculated near molt initiation exhibited higher OrV viral loads and the virus infected more intestinal cells. Moreover, nematodes inoculated right after hatching accelerated the start of the first molt and lengthened the second larval stage, effectively resynchronizing normal developmental timing. Overall, our work enhances understanding of OrV dynamics in C. elegans and elucidates the interplay between viral infection and nematode development. HIGHLIGHTSO_LIrsay virus replication peaks during molting periods, with larvae acquiring virus later in the first larval stage producing higher viral loads and more widespread intestinal infection than larvae acquiring it right after hatching. C_LIO_LIinfection alters the expression of key developmental regulators, particularly those with oscillatory profiles synchronized with molting cycles (such as let-7, lin-42 and nhr-23). C_LIO_LInematodes display temporal plasticity in development: accelerating the first molt while extending the second larval stage, ultimately resynchronizing their developmental timeline. C_LIO_LIis a bidirectional interaction between Orsay virus infection and C. elegans development: molting appears to transiently weaken antiviral defenses, while host development adapts to infection through temporal plasticity. C_LI

microbiology↗

bioRxiv2024

Circadian clock disruption engages the DREAM complex in suppressing cellular health.

Circadian clock disruption and lack of sleep impair organismal health, but remedies remain elusive. Here, we used multi-omics, molecular and functional assays in C. elegans, human retinal cells and mouse brain to identify the DREAM complex as a conserved mediator of sleep and clock benefits at the cellular level. We show that DREAM abundance is under circadian control with high levels seen during wakefulness. DREAM elevation confers increased chromatin compaction and shields DNA from damage while altering fundamental cellular processes such as translation, stress responses and OXPHOS. Conversely, DREAM levels are lowered during sleep enabling cellular maintenance and repair. When sleep or clock are altered, DREAM levels remain high, and repair activities remain suppressed triggering cellular and organismal deterioration that can be reversed by genetic and pharmacological inhibition of DREAM in vivo and in vitro. We thus reveal the potential of DREAM inhibitors to replicate the benefits of sleep in sleep-deprived and clock-impaired organisms.

physiology↗

bioRxiv2024

Desynchronization between timers provokes transient arrest during C. elegans development

In multicellular organisms, development entails the progression of diverse cellular processes that need to be temporally coordinated. During C. elegans postembryonic development, the events of molting and cell divisions progress in parallel during four larval stages and are modulated by external cues such as temperature and nutrient availability. While seam cell divisions occur predominantly before ecdysis of the cuticle, the order of the events can change, suggesting that they are controlled by independent mechanisms. Here, we have analyzed the impact of reduced insulin signaling in molting and in stage-specific cell divisions. We find that reduced insulin signaling in the daf-2(e1370) allele delays both of these events but has a larger impact on the timing of cell divisions, thus increasing the desynchrony between the events. The relative delay in seam cell divisions leads to a delay in the initiation of the subsequent stage of the molting program, providing a mechanism for resynchronization of developmental processes to the beginning of the larval stages.

developmental biology↗

bioRxiv2023

Methanolic extracts of the edible halophyte Crithmum maritimum enhance oxidative stress resistance in Caenorhabditis elegans through hormetic mechanisms

Halophytes are promising sources of bioactive phenolic compounds for the food and pharmaceutical industries. However, their phenolic composition is influenced by environmental conditions, and the in vivo antioxidant activity of their phytochemicals is largely unknown. We evaluated the antioxidant capacity of phenolic-rich methanolic extracts from the edible halophyte Crithmum maritimum, grown in wild and greenhouse conditions. Additionally, their in vivo antioxidant capacity was analyzed for the first time using the model Caenorhabditis elegans. Wild plant extracts showed higher phenolic content and diversity, and in vitro antioxidant activity. Both extracts enhanced oxidative stress resistance and increased nematode survival rates, albeit to varying extents, and increased reactive oxygen species production in nematodes, without affecting their lifespan, suggesting a hormetic mechanism. Although no neuroprotective effects were observed in models of neurodegenerative diseases, these findings highlight the potential of C. maritimum as a valuable source of phenolics with antioxidant properties for the food industry.

pharmacology and toxicology↗

bioRxiv2023

Control of C. elegans growth arrest by stochastic, yet synchronized DAF-16/FOXO nuclear translocation pulses

FOXO transcription factors are highly conserved effectors of insulin and insulin-like growth factor signaling, that are crucial for mounting responses to a broad range of stresses. Key signaling step is the stress-induced translocation of FOXO proteins to the nucleus, where they induce expression of stress response genes. Insulin signaling and FOXO proteins often control responses that impact the entire organism, such as growth or starvation-induced developmental arrest, but how body-wide coordination is achieved is poorly understood. Here, we leverage the small size of the nematode C. elegans, to quantify translocation dynamics of DAF-16, the sole C. elegans FOXO transcription factor, with single-cell resolution, yet in a body-wide manner. Surprisingly, when we exposed individual animals to constant levels of stress that cause larval developmental arrest, DAF-16/FOXO translocated between the nucleus and cytoplasm in stochastic pulses. Even though the occurrence of translocation pulses was random, they nevertheless exhibited striking synchronization between cells throughout the body. DAF-16/FOXO pulse dynamics were strongly linked to body-wide growth, with isolated translocation pulses causing transient reduction of growth and full growth arrest observed only when pulses were of sufficiently high frequency or duration. Finally, we observed translocation pulses of FOXO3A in mammalian cells under nutrient stress. The link between DAF-16/FOXO pulses and growth provides a rationale for their synchrony, as uniform proportions are only maintained when growth and, hence, pulse dynamics are tightly coordinated between all cells. Long-range synchronization of FOXO translocation dynamics might therefore be integral also to growth control in more complex animals.

cell biology↗

bioRxiv2021

Differential regulation of developmental stages supports a linear model for C. elegans postembryonic development

The repetitive nature of C. elegans postembryonic development is considered an oscillatory process, a concept that has gained traction from regulation by a circadian clock gene homolog. Nevertheless, each larval stage has a defined duration and entails specific events. We have measured the duration of each stage of development for over 2,500 larvae, under varied environmental conditions known to alter overall developmental rate. Our results show that distinct developmental stages respond differently to environmental perturbations, including changes in temperature, in food quantity and quality, and amount of insulin signaling. Furthermore, our high-resolution measurement of the effect of temperature on the stage-specific duration of development has unveiled novel features of temperature dependence in C. elegans postembryonic development. Altogether, our results support a model of linear progression of C. elegans development, with the duration of each stage determined by a unique program.

developmental biology↗

bioRxiv2020

Neuronal perception of the social environment intergenerationally controls germline development and generation time in C. elegans

An old and controversial question in biology is whether information perceived by the nervous system of an animal can cross the Weismann barrier to alter the phenotypes and fitness of their progeny. Here we show that such intergenerational transmission of sensory information occurs in the model organism, C. elegans, with a major effect on fitness. Specifically, that perception of social pheromones by chemosensory neurons controls the post-embryonic timing of development of one tissue - the germline - relative to others in an animals progeny. Neuronal perception of the social environment thus intergenerationally controls the generation time of this animal.

genetics↗

bioRxiv2020

Social chemical communication determines recovery from L1 arrest via DAF-16 activation

In a population, chemical communication determines the response of animals to changing environmental conditions, what leads to an enhanced resistance against stressors. In response to starvation, the nematode Caenorhabditis elegans arrest post-embryonic development as L1 larva right after hatching. As arrested L1 larvae, C. elegans become more resistant to diverse stresses, allowing them to survive for several weeks expecting to encounter more favorable conditions. However, prolonged periods in L1 arrest lead to the accumulation of detrimental signs of aging, which ultimately provoke animal death. When arrested L1s feed, they undergo a recovery process to erase these harmful signs before resuming the developmental program. L1 arrested larvae secrete unidentified soluble compounds that improve survival to starvation. This protection is proportional to larval population density. Thus, animals arrested at high densities display an enhanced resistance to starvation. Here we show that this chemical communication also influences recovery after prolonged periods in L1 arrest. Animals at high density recovered faster than animals at low density. We found that the density effect on survival depends on the final effector of the insulin signaling pathway, the transcription factor DAF-16. Moreover, DAF-16 activation was higher at high density, consistent with a lower expression of the insulin-like peptide DAF-28 in the neurons. The improved recovery of animals after arrest at high density depended on soluble compounds present in the media of arrested L1s. In a try to find the nature of these compounds, we investigated the disaccharide trehalose as putative signaling molecule, since its production is enhanced during L1 arrest and it is able to activate DAF-16. We detected the presence of secreted trehalose in the medium of arrested L1 larvae at a low concentration. The addition of this concentration of trehalose to animals arrested at low density was enough to rescue DAF-28 production and DAF-16 activation to the levels of animals arrested at high density. However, despite activating DAF-16, trehalose was not capable of reversing survival and recovery phenotypes, suggesting the participation of additional signaling molecules. We finally identified GUR-3 as a possible trehalose receptor in C. elegans. With all, here we describe a molecular mechanism underlying social communication that allows C. elegans to maintain arrested L1 larvae ready to quickly recover as soon as they encounter nutrient sources.

developmental biology↗

bioRxiv2018

Prolonged quiescence delays somatic stem cell-like division in Caenorhabditis elegans and is controlled by insulin signalling

Cells can enter quiescence in adverse conditions and resume proliferation when the environment becomes favourable. Prolonged quiescence comes with a cost, reducing proliferation potential and survival. Interestingly, cellular quiescence also occurs in normal development, with many cells spending most of their lifetime at this state. Elucidating the mechanisms involved in surviving long-term quiescence and in maintenance of cellular proliferation potential will contribute to a better understanding of the process of tissue regeneration. Developmental arrest of C. elegans at the L1 stage is an emerging model for the study of cellular quiescence and reactivation. During arrest, L1 larvae undergo a process that shares phenotypic hallmarks with the ageing of the adult. Interestingly, insulin signalling, a prominent pathway in the regulation of ageing, also balances cell proliferation and activation of stress resistance pathways during quiescence, becoming a candidate regulator of proliferation potential. Here we report that prolonged L1 quiescence delays reactivation of blast cell divisions in C. elegans, leading to a delay in the initiation of postembryonic development. This delay is accompanied by increased inter-individual variability. We propose that the delay in cell division results from the decline that animals suffer during L1 arrest. To that end, we show that insulin signalling modulates the rate of L1 ageing, affecting proliferative potential after quiescence. These findings support that the insulin signalling pathway has a comparable role in L1 arrest to that in ageing adults. Furthermore, we show that variable yolk provisioning to the embryos as a consequence of maternal age is one of the sources of inter-individual variability in recovery after quiescence of genetically identical animals. Taken together, these results support the relevance of L1 arrest as a model to study in vivo proliferation after quiescence and to understand the mechanisms for maintenance of proliferation potential.

developmental biology↗

bioRxiv2018

Adenylosuccinate Lyase activity in the Purine recycling pathway is essential for developmental timing, germline maintenance and muscle integrity in C. elegans.

Purine homeostasis is ensured through a metabolic network widely conserved from prokaryotes to humans. Purines can either be synthesized de novo, reused, or produced by interconversion of extant metabolites using the so-called recycling pathway. Although thoroughly characterized in microorganisms, such as yeast or bacteria, little is known about the regulation of this biosynthesis network in metazoans. In humans, several diseases are linked to purine biosynthesis deficiencies through yet poorly understood etiologies. Particularly, the deficiency in Adenylosuccinate Lyase (ADSL), one enzyme involved both in the purine de novo and recycling pathways, causes severe muscular and neuronal symptoms. In order to address the mechanisms underlying this deficiency, we established Caenorhabditis elegans as a metazoan model organism to study purine metabolism, while focusing on ADSL. We show that the purine biosynthesis network is functionally conserved in C. elegans. Moreover, ADSL is required for developmental timing and germline stem cell maintenance, and muscle integrity. Our results allow to ascribe developmental and tissue specific phenotypes to separable steps of the purine metabolic network in an animal model. Particularly, the muscle, germline and developmental defects are linked specifically to the ADSL role in the purine recycling pathway.

genetics↗

bioRxiv2017

Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans

BackgroundThe advancement in automated image based microscopy platforms coupled with high throughput liquid workflows has facilitated the design of large scale screens utilizing multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high throughput approaches.\n\nResultsIn C. elegans, non-conditional lethal mutations can be maintained in heterozygosis using chromosome balancers, commonly labelled with GFP in the pharynx. Moreover gene-expression is typically monitored by the use of fluorescent reporters marked with the same fluorophore. Therefore, the separation of the different populations of animals at early larval stages represents a challenge. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at early larval stages. Because sorting is not completely error-free, we develop an automated high-throughput image-analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image-analysis in a functional genomic RNAi screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while, homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both, known and new PHB genetic interactors affecting the UPRmt and growth.\n\nConclusionsA systematic way to analyse genetic interactions of essential genes in multicellular organisms is lacking. The method presented here allows the study of balanced lethal mutations in a high-throughput manner and can be easily adapted depending on the users requirements. Therefore, it will serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks.

genetics↗