Biology subjects

Dumeaux, V.

Publications and source records attributed to Dumeaux, V..

At least 19 recordsLinked to original sources

bioRxiv2026

An agentic AI environment to support biomedical research in collaborative academic environments

Agentic artificial intelligence (AAI) is increasingly used by biomedical scientists, where it has substantially lowered the difficulty of integrating computational, statistical and data-science approaches into day-to-day research activities, assisting with project design, analysis and manuscript preparation. Significant barriers remain, however, which are unlikely to be removed solely by releasing more capable AI models. Meaningful use still demands a technical fluency that many biomedical researchers lack: a PI and their lab members must learn how to use the AAI system, establish standard operating procedures (SOPs) for managing, sharing and curating data, and enforce rules that address data privacy and security. Existing commercial AAI systems, which were designed primarily for software engineering purposes, need to be significantly re-purposed for biomedical-related data science. We present Murmurent, shared software that sits beneath the agentic AI and provides the skills, procedures and protections to address the concerns above, removing the need for a lab to develop them independently. This includes (1) infrastructure to support projects and so-called choreographies} involving multiple group members; (2) a set of specialized agents each dedicated to typical biomedical data science tasks including software and statistical development, data visualization, literature search, equity, diversity, inclusion, and decolonization (EDID) review, and others; (3) a tiered memory which can retain important research decisions, intermediate, derived outputs and sensitive data, and which can exploit this information to automatically build better contexts in AAI sessions; (4) traceability records which are used by the AAI session to better plan and execute data analyses and software builds by, for example, helping to avoid repeating decisions that lead to dead-ends; (5) enforcement of SOPs for data maintenance and data governance across all lab members; and (6) multi-user capacity to allow groups to interact and collaborate. We use the system to identify putative inhibitors of Peptidyl-prolyl cis-trans Isomerase NIMA-interacting 1 (Pin1), a protein with a shallow catalytic site making it difficult to target. We describe the construction of several approaches to identify Pin1 inhibitors and the results they yield. Murmurent is open source.

bioinformatics↗

bioRxiv2026

Differential requirement for the Ire1 luminal domain in Candida albicans drug susceptibility and pathogenicity

The opportunistic human pathogen Candida albicans depends on the unfolded protein response (UPR) for cell wall integrity, antifungal tolerance, filamentous growth, and virulence. The UPR is driven by the conserved transmembrane sensor Ire1, which is activated either by misfolded proteins through its luminal domain or by lipid bilayer stress (LBS) through its transmembrane domain. In budding yeast, these two activation modes deploy divergent transcriptional programs. Whether the requirement for these two input domains is separable in C. albicans, where the cell membrane and cell wall are themselves the targets of major antifungal drug classes, remains unknown. Here, we engineered a C. albicans strain expressing Ire1 lacking an intact luminal domain (ire1{Delta}LD), which no longer detects proteotoxic stress. The ire1{Delta}LD strain grew in the presence of the azole antifungals fluconazole and miconazole but was highly sensitive to heat shock, cell wall stress, and the echinocandin caspofungin. It was also unable to sustain filamentous growth and showed reduced virulence in a Caenorhabditis elegans infection model. RNA sequencing revealed only modest changes to the steady-state transcriptome of ire1{Delta}LD cells. Together, these findings define a differential requirement for the input domains of C. albicans Ire1, uncoupling growth under azole-induced membrane stress from the cell wall, thermal, and virulence-associated outputs that depend on proteotoxic sensing, a distinction that could inform antifungal strategies targeting the UPR.

cell biology↗

bioRxiv2025

Distinct Ire1-driven transcriptional responses control morphogenesis in Candida albicans

The pathogenic yeast Candida albicans relies on morphogenesis--the transition from spherical yeast to filamentous hyphal forms--for infection. While morphogenesis requires Ire1, a transmembrane protein that canonically initiates the Unfolded Protein Response (UPR) through HAC1 mRNA splicing, the specific mechanisms linking Ire1 to filamentation remain unclear. Using transcriptome analysis, we found that the Ire1-dependent transcriptional response driving morphogenesis is fundamentally distinct from the canonical UPR response to proteotoxic stress, with minimal overlap between programs. Remarkably, morphogenesis occurs without detectable HAC1 splicing, and HAC1 deletion only partially impairs filamentation, unlike complete loss with IRE1 deletion. These findings establish that Ire1 regulates hyphal development through previously uncharacterized HAC1-independent pathways. Our data reveal decreased transcription of secretory proteins in an Ire1-dependent manner, providing compelling evidence that C. albicans possesses regulated Ire1-dependent decay (RIDD) activity--a post-transcriptional mechanism not previously characterized in this pathogen. Additionally, we identify cell wall integrity as a key HAC1-independent mechanism, with Ire1--but not Hac1--essential for cell wall stress tolerance and upregulation of cell wall biosynthesis genes during filamentation. Given Ire1s essential role in pathogenesis and extensive development of Ire1-targeting compounds for mammalian systems, our findings position Ire1 as a highly promising druggable target for novel antifungal therapeutics and development of fungal-specific inhibitors.

cell biology↗

bioRxiv2025

Astrocytic Chromatin Remodeler ATRX Gates Hippocampal Memory Consolidation through Metabolic and Synaptic Regulation

Astrocytes are increasingly recognized as active regulators of synaptic transmission and memory, yet the epigenetic mechanisms underlying their contribution to cognitive processes remain poorly defined. Here, we investigated the role of the chromatin remodeler ATRX in astrocytes by generating mice with inducible, astrocyte-specific Atrx deletion (aiKO) using tamoxifen administration at postnatal days 10-12, resulting in ATRX loss in approximately half of hippocampal and cortical astrocytes. Transcriptomic profiling of hippocampal tissue at one and three months revealed a progressive increase in differentially expressed genes, with early enrichment for cytoskeletal and immune pathways and later dysregulation of energy metabolism, ion transport, and synaptic gene sets. Electrophysiological recordings from CA1 pyramidal neurons in aiKO slices demonstrated increased neuronal excitability, reduced membrane capacitance, and decreased frequency of spontaneous excitatory postsynaptic currents, indicating non-cell-autonomous neuronal dysfunction. Morphological analysis identified a transient reduction in dendritic branching at one month and a selective loss of thin dendritic spines by three months, without changes in total dendrite length or overall spine density. Behaviorally, aiKO mice displayed normal locomotion, anxiety, and short-term memory, but exhibited deficits in 24-hour novel object recognition and long-term spatial memory in the Morris water maze. These findings demonstrate that ATRX-mediated chromatin remodeling in astrocytes is essential for maintaining hippocampal transcriptional homeostasis, neuronal function, and long-term memory. Our results highlight a critical role for astrocytic epigenetic regulation in cognitive processes and suggest that astrocyte dysfunction may contribute to the pathogenesis of ATR-X syndrome and related intellectual disability disorders, underscoring the importance of targeting multiple cell types for therapeutic intervention. HighlightsO_LIAstrocytic ATRX loss causes non-cell-autonomous neuronal hyperexcitability C_LIO_LIInducing ATRX deficiency in astrocytes causes selective long-term memory deficits C_LIO_LIDynamic transcriptomic changes reveal metabolic and synaptic pathway dysregulation C_LI

neuroscience↗

bioRxiv2025

Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material

Formalin-fixed paraffin embedded (FFPE) samples are challenging to profile using existing high-throughput sequencing technologies, including RNA-seq. This difficulty primarily arises from the degradation of nucleic acids, a problem that becomes particularly acute with samples stored for extended periods. FFPE-derived RNA-seq (fRNA-seq) data have a high rate of transcript dropout, a property shared with single cell RNA-seq. Transcript counts also have high variance and are prone to extreme values. We introduce the PaRaffin Embedded Formalin-FixEd Cleaning Tool (PREFFECT), a probabilistic framework for the analysis of fRNA-seq data. PREFFECT uses generative models to fit distributions to observed expression counts while adjusting for technical and biological variables. The framework can exploit multiple expression profiles generated from matched tissues for a single sample (e.g., a tumor and morphologically normal tissue) in order to stabilize profiles and impute missing counts. PREFFECT can also leverage sample-sample adjacency networks that assist graph attention mechanisms to identify the most informative correlations in the data. We demonstrate how PREFFECT uses this information to more accurately compute downstream analyses such as sample clustering in several datasets.

bioinformatics↗

bioRxiv2025

Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

Understanding the functional diversity of the gut microbiome is essential for decoding its roles in health and disease. Using a deep-learning framework, we identified three functional archetypes defining healthy adult gut microbiomes, each characterized by specific metabolic potentials: sugar metabolism with branched-chain amino acid and cell wall synthesis (Archetype 1), fatty acid and TCA cycle metabolism (Archetype 2), and amino acid and nitrogen metabolism (Archetype 3). Archetype proximity is linked to stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility. Functional diversity emerged as a confounder in disease-associated microbial signatures. In inflammatory bowel disease, we observed archetype-specific shifts, including increased carbohydrate metabolism in Archetype 1-dominant samples and inflammatory pathways in Archetype 3-dominant samples, suggesting distinct opportunities for microbiome-targeted interventions. This framework addresses key challenges in microbiome research, including inter-individual variability and confounding, while providing robust insights into disease-associated functional shifts and microbial ecosystem dynamics. HighlightsO_LIAdult gut microbiomes are defined by three functional archetypes C_LIO_LIArchetypes reveal distinct metabolic potentials and inform on microbiome stability C_LIO_LIArchetype-specific functional profiles confound disease associations and reveal therapeutic targets C_LIO_LIA deep-learning framework enables robust characterization of microbial functional ecosystems C_LI

microbiology↗

bioRxiv2022

Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination

Neurodevelopmental disorders are often characterized by abnormal production of myelin, an extension of the oligodendrocyte plasma membrane wrapped around axons to facilitate nerve conduction. However, the molecular mechanisms that control myelination during brain development are incompletely resolved. Here, we provide evidence that loss of ATRX, encoded by the gene mutated in the ATR-X intellectual disability syndrome, leads to myelin deficits in the mouse CNS. While postnatal systemic thyroxine administration can improve myelination, the rescue is incomplete, pointing to additional roles of ATRX in this process. We show that targeted inactivation of ATRX in postnatal oligodendrocyte progenitor cells (OPCs), but not in neurons, also leads to myelination deficits, demonstrating cell-intrinsic effects of ATRX deficiency. A subset of ATRX-null OPCs express lower levels of oligodendrocyte specification and differentiation markers, including the basic helix-loop-helix Olig2 transcription factor. Mechanistically, we provide evidence that ATRX occupies genomic sites in OPCs marked by H3K27Ac, CHD7 and CHD8 and demonstrate that reduced Olig2 expression is associated with decreased H3K27Ac. Finally, our data suggest that ATRX-null OPCs acquire a more plastic state and can exhibit astrocyte-like features in vitro and in vivo, supporting a model in which ATRX regulates the onset of myelination by promoting OPC identity and suppressing astrogliogenesis. These previously unrecognized functions of ATRX might explain white matter pathogenesis in ATR-X syndrome patients.

neuroscience↗

bioRxiv2022

Paternal obesity alters the sperm epigenome and is associated with changes in the placental transcriptome and cellular composition

Paternal obesity has been implicated in adult-onset metabolic disease in offspring. However, the molecular mechanisms driving these paternal effects and the developmental processes involved remain poorly understood. One underexplored possibility is the role of paternally driven gene expression in placenta function. To address this, we investigated paternal high-fat diet-induced obesity in relation to sperm epigenetic signatures, the placenta transcriptome and cellular composition. C57BL6/J males were fed either a control or high-fat diet for 10 weeks beginning at 6 weeks of age. Males were timed-mated with control-fed C57BL6/J females to generate pregnancies, followed by collection of sperm, and placentas at embryonic day (E)14.5. Chromatin immunoprecipitation targeting histone H3 lysine 4 tri-methylation (H3K4me3) followed by sequencing (ChIP-seq) was performed on sperm to define obesity-associated changes in enrichment. Paternal obesity corresponded with altered sperm H3K4me3 enrichment at imprinted genes, and at promoters of genes involved in metabolism and development. Notably, sperm altered H3K4me3 was localized at placental enhancers and genes implicated in placental development and function. Bulk RNA-sequencing on placentas detected paternal obesity-induced sex-specific changes in gene expression associated with hypoxic processes such as angiogenesis, nutrient transport and imprinted genes. Paternal obesity was also linked to placenta development; specifically, a deconvolution analysis revealed altered trophoblast cell lineage specification. These findings implicate paternal obesity-effects on placenta development and function as one mechanism underlying offspring metabolic disease. Summary sentencePaternal obesity impacts the sperm epigenome at genes implicated in placenta development and is associated with an altered placenta transcriptome and trophoblast cell lineage specification.

developmental biology↗

bioRxiv2022

Exposure of Greenlandic Inuit and South African VhaVenda men to the persistent DDT metabolite is associated with an altered sperm epigenome at regions implicated in paternal epigenetic transmission and developmental disease - a cross-sectional study

BackgroundThe persistent organochlorine dichlorodiphenyltrichloroethane (DDT) is banned world-wide due to its negative health effects and persistence in the environment. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the arctic where its endocrine disrupting metabolite, p,p-dichlorodiphenyldichloroethylene (p,p-DDE) accumulates in marine mammals and fish. DDT and p,p-DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come. Generational effects of toxicant exposures have been described in animal models and implicated germline epigenetic factors. Similar generational effects have been shown in epidemiological studies. Although advances in understanding the molecular mechanisms mediating this epigenetic inheritance have been made, there remain major knowledge gaps in how this occurs in humans. In animal and human models, DNA methylation (DNAme) has been implicated in paternal epigenetic effects. In animal models, histone H3K4 trimethylation (H3K4me3) has been shown to be responsive to the paternal environment and linked with epigenetic transmission to the embryo. Our objectives were to define the associations between p,p-DDE serum levels and alterations in the sperm methylome and H3K4me3 enrichment using next generation sequencing. We aimed to compare regions of epigenomic sensitivity between geographically diverse populations with different routes and levels of exposures, and to identify interactions between altered DNAme and H3K4me3 regions. The potential for p,p-DDE to impact the health of the next generation was explored by examining the functions of the genomic regions impacted, their roles during embryo development, and in health and disease. MethodsIn the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men from 12 villages that either used indoor residual spraying with DDT for malaria control or not. We selected 49 paired blood and semen samples, from men that ranged from 18 to 32 years of age (mean 25 years). Sample inclusion was based on normal sperm counts (> 15 million/ml), normal sperm DNA fragmentation index, and testing a range of p,p-DDE exposure levels (mean 10,462.228 {+/-} 1,792.298 ng/ml). From a total of 193 samples, 47 Greenlandic Inuit blood and semen paired samples were selected from the biobank of the INUENDO cohort. The subjects ranged from 20 to 44 years of age (mean 31 years), were born in Greenland, and all had proven fertility. Sample selection was based on obtaining a range of p,p-DDE exposure levels (mean 870.734 {+/-} 134.030 ng/ml). Here we determined the molecular responses at the level of the sperm epigenome to serum p,p-DDE levels using MethylC-Capture-seq (MCC-seq) and chromatin-immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. We used in silico analyses to discover regions of differential methylation associated with p,p-DDE levels that were predicted to be transmitted and persist in the embryo. ResultsAlterations in DNAme and H3K4me3 enrichment followed dose response-like trends, and we identified overlapping genomic regions with DNAme sensitivities in both populations. Altered DNAme and H3K4me3 in sperm occurred at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with altered sperm DNAme and H3K4me3 were predicted to persist in the pre-implantation embryo and were associated with embryonic gene expression. LimitationsThe samples were collected from remote areas of the world thus sample size is relatively small. The populations differed in the routes of exposure, timing of collection, mean age (mean of 25 versus 31 years of age in South African and Greenlandic populations respectively) and in the timing of p,p-DDE measurement. Moreover, the Greenlandic Inuit men were proven fertile whereas the fertility status of the South African men was unknown. Confounding factors such as other environmental exposures and selection bias cannot be ruled out. ConclusionsThese findings suggest that in men, DDT and p,p-DDE exposure impacts the sperm epigenome in a dose-responsive manner and may negatively impact the health of future generations through epigenetic mechanisms.

genomics↗

bioRxiv2022

Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to anti-fungal compounds

Candida albicans is an opportunistic human pathogen which represents a significant threat to human health and is associated with substantial socio-economic burden. Current antifungal treatments fail at least in part because C. albicans can initiate a strong drug tolerance response, allowing cells to grow at concentrations above their minimal inhibitory concentration. Our goal is to better characterize this cytoprotective tolerance program at the molecular single cell level. We present here a nano-liter droplet-based fungal single cell transcriptomics platform capable of profiling thousands of individual C. albicans SC5314 cells in an efficient manner. Profiles of untreated cells partition into three transcriptional clusters with each highlighting a cell cycle checkpoint coupled with specific metabolic and stress responses, as perhaps expected. After just two days post-treatment with fluconazole, surviving cells bifurcate into two distinct subpopulations: the so-called response involving upregulation of protein translation, rRNA processing and mitochondrial cellular respiration, and the {beta} response involving processes and stress responses that assist damaged cells. By extending our time series to six days and profiling with other antifungals and bioactive compounds, we provide evidence that surviving cells transition from the to {beta} responses mediated by the Ribosome Assembly Stress Response (RASTR).

microbiology↗

bioRxiv2021

Genetic-epigenetic interactions in paternal transgenerational inheritance of metabolic disorders

ObjectiveParental environmental exposures can strongly influence descendant risks for adult disease. How paternal obesity changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. The objective of this study was to assess: (1) whether obesity induced by a high-fat diet alters sperm histone methylation; (2) whether paternal obesity can induce metabolic disturbances across generations; (3) whether there could be cumulative damage to the sperm epigenome leading to enhanced metabolic dysfunction in descendants; and (4) whether obesity-sensitive regions associate with embryonic epigenetic and transcriptomic profiles. Using a genetic mouse model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. This transgenic mouse overexpresses the histone demethylase enzyme KDM1A in the developing germline and has an altered sperm epigenome at the level of histone H3K4 methylation. We hypothesized that challenging transgenic sires with a high-fat diet would further erode the sperm epigenome and lead to enhanced metabolic disturbances in the next generations. MethodsTo assess whether paternal obesity can have inter- or transgenerational impacts, and if so, to identify potential mechanisms of this non-genetic inheritance, we used wildtype C57BL/6NCrl and transgenic males with a pre-existing altered sperm epigenome. To induce obesity, sires were fed either a control or high-fat diet (10% or 60% kcal fat, respectively) for 10-12 weeks, then bred to wildtype C57BL/6NCrl female fed a regular diet. F1 and F2 descendants were characterized for metabolic phenotypes by examining the effects of paternal obesity by sex, on body weight, fat mass distribution, the liver transcriptome, intraperitoneal glucose and insulin tolerance tests. To determine whether obesity altered the F0 sperm chromatin, native chromatin immunoprecipitation-sequencing targeting H3K4me3 was performed. To gain insight into mechanisms of paternal transmission, we compared our sperm H3K4me3 profiles with embryonic and placental chromatin states, histone modification and gene expression profiles. ResultsObesity-induced alterations in H3K4me3 occurred at genes implicated in metabolic, inflammatory, and developmental processes. These processes were associated with offspring metabolic dysfunction and corresponded to genes enriched for H3K4me3 in embryos, and overlapped embryonic and placenta gene expression profiles. Transgenerational susceptibility to metabolic disease was only observed when obese F0 had a pre-existing modified sperm epigenome. This coincided with increased H3K4me3 alterations in sperm and more severe phenotypes affecting their offspring. ConclusionsOur data suggest sperm H3K4me3 might serve as a metabolic sensor that connects paternal diet with offspring phenotypes via the placenta. This non-DNA based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease. This study highlights the need to further study the connection between the sperm epigenome, placental development and childrens health.

developmental biology↗

bioRxiv2021

A deep learning approach to capture the essence of Candida albicans morphologies

We present deep learning-based approaches for exploring the complex array of morphologies exhibited by the opportunistic human pathogen C. albicans. Our system entitled Candescence automatically detects C. albicans cells from Differential Image Contrast microscopy, and labels each detected cell with one of nine vegetative, mating-competent or filamentous morphologies. The software is based upon a fully convolutional one-stage object detector and exploits a novel cumulative curriculum-based learning strategy that stratifies our images by difficulty from simple vegetative forms to more complex filamentous architectures. Candescence achieves very good performance on this difficult learning set which has substantial intermixing between the predicted classes. To capture the essence of each C. albicans morphology, we develop models using generative adversarial networks and identify subcomponents of the latent space which control technical variables, developmental trajectories or morphological switches. We envision Candescence as a community meeting point for quantitative explorations of C. albicans morphology.

microbiology↗

bioRxiv2021

A metagenomic-based stufy of two sites from the Barbadian reef system

We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community in addition to their proximity to urban development and runoffs from inland watersheds. The composition of the microbial community was estimated using whole genome DNA shotgun sequencing. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangmans Bay) is strongly concentrated with phototrophs. In comparison, the more urbanized location (Bellairs Research Institute) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Overall, our samples and associated measurements of chemical and environmental qualities of the water are in line with previous marine microbiome profiles of warm ocean surface waters. This suggests our approach captures salient information regarding the state of each coral reef site and sets the stage for larger longitudinal studies of coral reef dynamics in Barbados.

microbiology↗

bioRxiv2020

Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs that facilitate the evolution of drug resistance

We developed a modified protocol for nanolitre droplet-based single cell sequencing appropriate for fungal settings, and used it to transcriptionally profiled several thousands cells from a prototrophic Candida albicans population and several drug exposed colonies (incl. fluconazole, caspofungin and nystatin). Thousands of cells from each colony were profiled both at early and late time points post-treatment in order to infer survival trajectories from initial drug tolerance to drug resistance. We find that prototrophic C. albicans populations differentially and stochastically express cytoprotective epigenetic programs. For all drugs, there is evidence that tolerant individuals partition into distinct subpopulations, each with a unique survival strategy involving different regulatory programs. These responses are weakly related to changes in morphology (shift from white to opaque forms, or shift from yeast to filamentous forms). In turn, those subpopulations that successfully reach resistance each have a distinct multivariate epigenetic response that coordinates the expression of efflux pumps, chaperones, transport mechanisms, and cell wall maintenance. Live cell fluorescent imaging was used to validate predictions of which molecular responses most often led to survival after drug exposure. Together our findings provide evidence that C. albicans has a robust toolkit of short-term epigenetic cytoprotective responses designed to "buy time" and increase the chance of acquiring long-term resistance.

genomics↗

bioRxiv2020

The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans

Zinc cluster transcription factors are essential fungal specific regulators of gene expression. In the dimorphic pathogen Candida albicans, they control processes ranging from metabolism and stress adaptation to mating, virulence, and antifungal resistance. Here, we have identified the gene CaORF19.1604 as encoding a zinc cluster transcription factor that acts as a regulator of filament development. Hyperactivation of CaORF19.1604, which we have named RHA1 for Regulator of Hyphal Activity, leads to a wrinkled colony morphology under non-hyphal growth conditions, to pseudohyphal growth and filament formation, to invasiveness and enhanced biofilm formation. Cells with activated Rha1 are sensitive to cell wall modifying agents such as Congo red and the echinocandin drug caspofungin but show normal sensitivity to fluconazole. RNA-sequencing-based transcriptional profiling of the activated Rha1 strain reveals the up-regulation of genes for core filamentation and cell-wall-adhesion-related proteins such as Als1, Als3, Ece1, and Hwp1. Upregulation is also seen for the genes for the hyphal-inducing transcription factors Brg1 and Ume6 and genes encoding several enzymes involved in arginine metabolism, while downregulation is seen for the hyphal repressor Nrg1. The deletion of BRG1 blocks the filamentation caused by activated Rha1, while null mutants of UME6 result in a partial block. Deletion of RHA1 can partially reduce healthy hyphal development triggered by environmental conditions such as Spider medium or serum at 37{degrees}C. In contrast to the limited effect of either single mutant, the double rha1 ume6 deletion strain is totally defective in both serum and Spider medium stimulated hyphal development. While the loss of Brg1 function blocks serum-stimulated hyphal development, this block can be significantly bypassed by Rha1 hyperactivity, and the combination of Rha1 hyperactivity and serum addition can generate significant polarization in even brg1 ume6 double mutants. Our results thus suggest that in response to external signals, Rha1 functions to facilitate the switch from an Nrg1 controlled yeast state to a Brg1/Ume6 regulated hyphal state. Author SummaryCandida albicans is the predominant human fungal pathogen, generating a mortality rate of 40% in systemically infected patients. The ability of Candida albicans to change its morphology is a determinant of its tissue penetration and invasion in response to variant host-related stimuli. The regulatory mechanism for filamentation includes a complex network of transcription factors that play roles in regulating hyphae associated genes. We identify here a new regulator of filamentation from the zinc cluster transcription factor family. We present evidence suggesting that this transcription factor assists the Nrg1/Brg1 switch regulating hyphal development.

microbiology↗

bioRxiv2019

Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits

Mutations in the ATRX chromatin remodeler are associated with syndromic and non-syndromic intellectual disability. Emerging evidence points to key roles for ATRX in preserving neuroprogenitor cell genomic stability, whereas ATRX function in differentiated neurons and memory processes are still unresolved. Here, we show that Atrx deletion in mouse forebrain glutamatergic neurons causes distinct hippocampal structural defects identified by magnetic resonance imaging. Ultrastructural analysis revealed fewer presynaptic vesicles and an enlarged postsynaptic area at CA1 apical dendrite-axon junctions. These synaptic defects are associated with impaired long-term contextual memory in male, but not female mice. Mechanistically, we identify ATRX-dependent and sex-specific alterations in synaptic gene expression linked to Mir137 levels, a known regulator of presynaptic processes and spatial memory. We conclude that ablation of Atrx in excitatory forebrain neurons leads to sexually dimorphic outcomes on miR-137 and on spatial memory, identifying a promising therapeutic target for neurological disorders caused by ATRX dysfunction.\n\nSummary statementAblation of the ATRX chromatin remodeler specifically in forebrain excitatory neurons of mice causes male-specific deficits in long-term spatial memory associated with miR-137 overexpression, transcriptional changes and structural alterations corresponding to pre- and post-synaptic abnormalities.

neuroscience↗

bioRxiv2018

Reproducible Data Analysis Pipelines for Precision Medicine

Precision medicine brings the promise of more precise diagnosis and individualized therapeutic strategies from analyzing a cancers genomic signature. Technologies such as high-throughput sequencing enable cheaper data collection at higher speed, but rely on modern data analysis platforms to extract knowledge from these high dimensional datasets. Since this is a rapidly advancing field, new diagnoses and therapies often require tailoring of the analysis. These pipelines are therefore developed iteratively, continuously modifying analysis parameters before arriving at the final results. To enable reproducible results it is important to record all these modifications and decisions made during the analysis process.\n\nWe built a system, walrus, to support reproducible analyses for iteratively developed analysis pipelines. The approach is based on our experiences developing and using deep analysis pipelines to provide insights and recommendations for treatment in an actual breast cancer case. We designed walrus for the single servers or small compute clusters typically available for novel treatments in the clinical setting. walrus leverages software containers to provide reproducible execution environments, and integrates with modern version control systems to capture provenance of data and pipeline parameters.\n\nWe have used walrus to analyze a patients primary tumor and adjacent normal tissue, including subsequent metastatic lesions. Although we have used walrus for specialized analyses of whole-exome sequencing datasets, it is a general data analysis tool that can be applied in a variety of scientific disciplines. We have open sourced walrus along with example data analysis pipelines at github.com/uit-bdps/walrus.

bioinformatics↗

bioRxiv2018

Candidate SNP analyses integrated with mRNA expression and hormone levels reveal influence on mammographic density and breast cancer risk

Introduction Introduction Materials and methods Results Discussion Globaltest Conclusion Competing interests Authors contributions Reference List Mammographic density (MD) is a well-documented risk factor for breast cancer[1-9], and thus a promising target for early detection of the disease. Based on mammographic results, the breast is given a percent density (PDEN) score ranging from 0-100% with 0 being the least dense (primarily adipose tissue). It is estimated that the risk of developing breast cancer is four to six times higher in women with an MD score of at least 75% [2,9] and that one-third of breast cancers occur in patients with PDEN scores of at least 50% [2]. MD is ...

genomics↗