Biology subjects

Cruz, P.

Publications and source records attributed to Cruz, P..

8 recordsLinked to original sources

bioRxiv2025

Bcl-xL interaction with VDAC1 reduces mitochondrial Ca2+ uptake, allowing the establishment of Therapy-Induced Senescence.

Cellular senescence, a state of irreversible growth arrest, is characterized by various phenotypic changes, including altered mitochondrial function. While the role of mitochondria in senescence is well-established, the mechanisms underlying their involvement remain unclear. Here, we investigate the early stages of therapy-induced senescence (TIS) and identify a novel anti-apoptotic mechanism mediated by Bcl-xL and VDAC1, two key regulators of mitochondrial calcium (Ca{superscript 2}) homeostasis. We find that Bcl-xL expression increases in early TIS cells and localizes to the mitochondria, where it interacts with the voltage-dependent anion channel 1 (VDAC1). This interaction dampens mitochondrial Ca{superscript 2} uptake, thereby preventing Ca{superscript 2} overload and apoptosis. Disrupting this interaction using the BH3 mimetic ABT-263 or Bcl-xL-targeting siRNA increases mitochondrial Ca{superscript 2} uptake, leading to apoptosis and blocking the formation of senescent cells. These findings uncover a previously unrecognized role of the Bcl-xL-VDAC1 axis in regulating mitochondrial Ca{superscript 2} dynamics during the onset of senescence. Our work provides mechanistic insight into how senescent cells evade apoptosis,highlighting potential therapeutic targets for selectively eliminating them in cancer and age-related diseases.

cell biology↗

bioRxiv2025

FAIRTraits: an environmentally, methodologically and semantically enriched database of plant traits from Mediterranean populations of 240 species

Trait-based approaches have proven, and continue to offer strong potential to tackle key issues in ecology, including: (i) understanding the functioning of organisms and how it relates to the environment, (ii) identifying the rules governing the assembly of communities and the coexistence of species, (iii) understanding how the functioning of organisms scales up to that of ecosystems and controls some of the services they deliver to humans. We present FAIRTraits, a data set of plant traits assembled from a set of studies designed to address these issues in the pedo-climatic context of the Northern Mediterranean Basin, considered both a biodiversity and a climatic hotspot. The FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles were followed to ensure maximum visibility and reusability of these data. FAIRTraits compiles and standardizes trait data collected over the 1997-2023 period on six sites by the same research group, ensuring that a consistent methodology was followed. These data were obtained on individuals from 1,955 populations of 240 species belonging to 155 genera and 48 families (172 herbaceous and 39 woody species). It contains 189,452 records for 183 quantitative traits from the different plant organs (leaves, stems, roots, and reproductive parts), which have been grouped into 10 categories: allocation ratio, architecture, chemistry, dynamics, mechanics, microbial associations, morphology, phenology, physiology and plant size. Trait values are given at the level of individual measurements. Species-level values of height and phenology taken from a Mediterranean flora are also given. Species are characterized by plant family, life cycle, Raunkiaer lifeform, photosynthetic pathway and by an original successional stage indicator value. As trait values strongly depend on environmental conditions, we also provide information on the climatic conditions and soil properties of the sites, as well as on disturbance regimes of the plots in which sampled individuals were collected. The following steps were taken to ensure the FAIRness of the data set. Findable: metadata are described using the Ecological Metadata Language, and are deposited both on the InDoRES (CNRS/MNHN) metadata catalogue and on the GBIF data portal (see below); Accessible: FAIRTraits is available on the InDoRES repository, with a subset available on the GBIF data portal (see below); Interoperable: recognized taxonomical and terminological resources to qualify taxa and attributes have been used whenever possible, and fully described sampling protocols and measurement methods are given both for traits and environmental data. A subset of the data could be mapped onto the Darwin Core biodiversity standard, making it possible to display part of the data set on the GBIF portal, more traditionally used for taxonomic occurrence data. Reusable: (meta)data are thoroughly described using domain-relevant community standards, and the full data set is released under the CC-BY 4.0 license. We believe that these multiple efforts, spanning from the very content of the data set to its careful formatting, will make of FAIRTraits a highly valuable resource for trait-based research, both in terms of data analysis and reusability.

ecology↗

bioRxiv2024

A KCNC1 Variant Linked to Rett Syndrome Disrupts ER to Golgi Trafficking of Kv3.1 Channel

Intrinsic neuronal excitability, defined by the balance between input and output signals, is crucial to neural function, and its disruption underlies various neurological diseases. Kv3.1 channels, encoded by KCNC1, are essential for high-frequency action potential firing. Variants in these channels are associated with several subtypes of epilepsy. We report a patient with developmental regression and epilepsy, meeting Rett syndrome criteria, who carries a KCNC1 variant encoding the S474C substitution in Kv3.1 (Kv3.1S474C). Electrophysiological and biochemical assays reveal that Kv3.1S474C reduces channel presence in the plasma membrane and is retained in the endoplasmic reticulum (ER). In murine primary cultures expressing Kv3.1S474C, we observed reduced neuronal firing frequency and exclusion of the channel from the axon initial segment (AIS). Consistently, we found a decreased firing frequency using a conductance-based computational neuronal model. In summary, this study identifies a novel link between a KCNC1 variant and Rett syndrome, highlighting the importance of S474 residue in Kv3.1 channel trafficking and function in neurons. SummaryThis study identifies and characterizes a novel KCNC1 variant associated with classical Rett syndrome. This variant disrupts endoplasmic reticulum (ER) to Golgi trafficking of the Kv3.1 channels, highlighting the variants potential role in altered neuronal excitability and neurodevelopmental disorders.

cell biology↗

bioRxiv2024

Metabolic PCTA-Based Shift Reagents for the Selective Detection of Extracellular Lactate Using CEST MRI

Lactate is a key metabolic driver in oncology and immunology. Even in the presence of physiological oxygen levels, most cancer cells upregulate anaerobic glycolysis, resulting in abnormal lactate production and accumulation in the tumor microenvironment. The development of more effective, sensitive, and safe probes for detecting extracellular lactate holds the potential to impact cancer metabolic profiling and staging significantly. Macrocyclic-based PARACEST agents have been reported to act as shift reagents (SRs) and detect extracellular lactate via CEST MRI. Here, we introduce a new family of SRs based on the PCTA ligand, an inherently stable and kinetically inert group of molecules with the potential for (pre)clinical translation. We observed that Yb-PCTA and Eu-PCTA can significantly shift lactate -OH signals in CEST spectra. In vitro, CEST MRI experiments proved that imaging extracellular lactate with these complexes is feasible and maintains high specificity even in the presence of competing small metabolites in blood and the tumor microenvironment. In vivo, preclinical imaging demonstrated that Yb-PCTA can be safely administered intravenously in mice to detect extracellular lactate non-invasively. This work represents a significant step towards precision and molecular imaging, demonstrating that the PCTA-ligand is a promising scaffold for developing molecular imaging sensors. These chemical sensors have broad medical applications, particularly in oncology and physiology.

biochemistry↗

bioRxiv2024

Human ESCRT-I and ALIX function as scaffolding helical filaments in vivo

The Endosomal Sorting Complex Required for Transport (ESCRT) is an evolutionarily conserved machinery that performs reverse-topology membrane scission in cells universally required from cytokinesis to budding of enveloped viruses. Upstream acting ESCRT-I and ALIX control these events and link recruitment of viral and cellular partners to late-acting ESCRT-III CHMP4 through incompletely understood mechanisms. Using structure-function analyses combined with super-resolution imaging, we show that ESCRT-I and ALIX function as distinct helical filaments in vivo. Together, they are essential for optimal structural scaffolding of HIV-1 nascent virions, the retention of viral and human genomes through defined functional interfaces, and recruitment of CHMP4 that itself assembles into corkscrew-like filaments intertwined with ESCRT-I or ALIX helices. Disruption of filament assembly or their conformationally clustered RNA binding interfaces in human cells impaired membrane abscission, resulted in major structural instability and leaked nucleic acid from nascent virions and nuclear envelopes. Thus, ESCRT-I and ALIX function as helical filaments in vivo and serve as both nucleic acid-dependent structural scaffolds as well as ESCRT-III assembly templates. Significance statementWhen cellular membranes are dissolved or breached, ESCRT is rapidly deployed to repair membranes to restore the integrity of intracellular compartments. Membrane sealing is ensured by ESCRT-III filaments assembled on the inner face of membrane; a mechanism termed inverse topology membrane scission. This mechanism, initiated by ESCRT-I and ALIX, is universally necessary for cytokinesis, wound repair, budding of enveloped viruses, and more. We show ESCRT-I and ALIX individually oligomerize into helical filaments that cluster newly discovered nucleic acid-binding interfaces and scaffold-in genomes within nascent virions and nuclear envelopes. These oligomers additionally appear to serve as ideal templates for ESCRT-III polymerization, as helical filaments of CHMP4B were found intertwined ESCRT-I or ALIX filaments in vivo. Similarly, corkscrew-like filaments of ALIX are also interwoven with ESCRT-I, supporting a model of inverse topology membrane scission that is synergistically reinforced by inward double filament scaffolding.

cell biology↗

bioRxiv2022

CaPTrends: A global database of Carnivoran Population Trends

MotivationPopulation trend information is an Essential Biodiversity Variable for monitoring change in biodiversity over time. Here, we present a global dataset of 1122 population trends describing changes in abundance over time in large mammals from the Order Carnivora - some of the worlds most charismatic and functionally important fauna. Main types of variables includedKey data fields for each record: species, coordinates, trend timeframe, methods of data collection and analysis, and population timeseries or summarised trend value. Population trend values are reported using quantitative metrics in 75% of records that collectively represent more than 6500 population estimates. The remaining records qualitatively describe population change (e.g. increase). Spatial location and grainRecords represent locations across the globe (latitude: -51.0 to 80.0; longitude: -166.0 to 166.0) with more trends found within the northern temperate zone. Time period and grainRecords span from 1726 to 2017, with 92% of trends starting after 1950. Major taxa and level of measurementWe conducted a semi-systematic search for population trend data in 87 species from four families in the order Carnivora: Canidae, Felidae, Hyaenidae and Ursidae. We compiled data for 50 of the 87 species. Software format.csv

ecology↗

bioRxiv2020

Isomerization of antimalarial drug WR99210 explains its inactivity in a commercial stock

ABSTRACTWR99210, a former antimalarial drug candidate now widely used for the selection of Plasmodium transfectants, selectively targets the parasite dihydrofolate reductase thymidine synthase bifunctional enzyme (DHFR-TS) but not human DHFR, which is not fused with TS. Accordingly, WR99210 and plasmids expressing human dhfr have become valued tools for the genetic modification of parasites in the laboratory. Concerns over the ineffectiveness of WR99210 from some sources encouraged us to investigate the biological and chemical differences of supplies from two different companies (compounds 1 and 2). Compound 1 proved effective at low nanomolar concentrations against Plasmodium falciparum parasites, whereas compound 2 was ineffective even at micromolar concentrations. Intact and fragmented mass spectra indicated identical molecular formulae of the unprotonated (free base) structures of 1 and 2; however, the compounds displayed differences by thin layer chromatography, reverse phase high performance liquid chromatography, and ultraviolet-visible spectroscopy, indicating important isomeric differences. Structural evaluations by 1H, 13C, and 15N nuclear magnetic resonance spectroscopy confirmed 1 as WR99210 and 2 as an isomeric dihydrotriazine. Induced fit, computational docking models showed that 1 binds tightly and specifically in the P. falciparum DHFR active site whereas 2 fits poorly to the active site in loose and varied orientations. Stocks and concentrates of WR99210 should be monitored for the presence of isomer 2, particularly when they are not supplied as the hydrochloride salt or are exposed to basic conditions that can promote isomerization. Absorption spectroscopy may serve for assays of the unrearranged and rearranged triazines.Competing Interest StatementOne author, Gavin Heffernan, is an employee of Jacobus Pharmaceutical Company, Inc. The rest of the authors have no competing interest.View Full Text

biochemistry↗

bioRxiv2018

Alzheimer’s disease Phospholipase C-gamma-2 (PLCG2) protective variant is a functional hypermorph

Recent Genome Wide Association Studies (GWAS) have identified novel rare coding variants in immune genes associated with late onset AD (LOAD). Amongst these, a polymorphism in Phospholipase C-gamma 2 (PLCG2) P522R, has been reported to be protective against LOAD. PLC enzymes are key elements in signal transmission networks and are potentially druggable targets. PLCG2 is highly expressed in the hematopoietic system. Hypermorphic mutations in PLCG2 in humans have been reported to cause autoinflammation and immune disorders, suggesting a key role for this enzyme in the regulation of immune cell function.\n\nWe confirmed that PLCG2 expression is restricted primarily to microglia in both the healthy and AD brain. Functional analysis of the P522R variant in heterologous systems demonstrated a small hypermorphic effect of the mutation on enzyme function. PLC{gamma}2 is therefore a potential target for modulating microglia function in AD, and a small molecule drug that weakly activates PLC{gamma}2 may be one potential therapeutic approach.\n\nSUMMARYThe PLCG2 P522R variant is protective against Alzheimers disease (AD). We show that PLCG2 is expressed in CNS-resident myeloid cells, and the P522R polymorphism weakly activates enzyme function. These data suggest that activation of PLCG2 and not inhibition could be therapeutically beneficial in AD.

neuroscience↗