Biology subjects

Brunet, A.

Publications and source records attributed to Brunet, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Sexual reproduction impacts vertebrate organ aging

Sexual reproduction is a central component of life. Yet, an unanswered question remains: how does sexual reproduction shape physiology and health across an individual's lifetime? Unlike other external factors such as diet and exercise, the impact of sexual reproduction on organ health during aging is far less studied, particularly in vertebrates. Here, we develop the short-lived killifish as a vertebrate model to study how lifelong mating affects organ aging. We discover that mating regulates liver aging in a cell-type and sex-specific manner. In old female livers, mating dampened hepatocyte inflammation and reduced myeloid cell levels, and machine-learning models predicted that mating led to a 'younger' transcriptomic age in several liver cell types. Functionally, mating reduced hepatic accumulation of several lipid classes and was associated with enhanced female resilience against the liver toxin acetaminophen. More broadly, mating induced anti-inflammatory and metabolic rewiring transcriptomic signatures in the brain and gut, indicating that mating may affect vertebrate organ aging more globally. Using publicly available human datasets and plasma proteomics aging clocks, we observed an association between sexual experience and a 'younger' plasma proteomic age of several cell types, including hepatocytes. Our work provides evidence that lifelong mating reshapes the physiological context during aging in a vertebrate, highlighting an understudied connection between vertebrate sexual history, health, and aging.

genomics↗

bioRxiv2026

Somatic mutations reveal the ontogeny of human microglia

Microglia are the resident hematopoietic cells of the central nervous system1. In mice, microglia seed the brain during embryogenesis and can be maintained throughout life with minimal input from adult hematopoiesis2-4. The origins of human microglia are less clear, but recent evidence suggests that marrow-derived cells may be able to supplement the human microglial pool in certain individuals5,6. Here, to investigate the ontogeny of human microglia, we develop a method that uses the collection of accumulated somatic mutations which uniquely labels each clone of cells to track the infiltration of marrow-derived cells into the human brain. Applying this method to 20 aged individuals, we find evidence of an influx of marrow-derived cells into the brain in all examined individuals. Single cell analysis, including single cell lineage tracing using mitochondrial DNA variants, demonstrates that these infiltrating cells are nearly identical to microglia and can comprise a large fraction of the microglial pool. Analysis of large-scale sequencing cohorts demonstrates a protective association between most types of clonal hematopoiesis and Alzheimers disease. In sum, this work uncovers a widespread influx of myeloid cells into the healthy human brain which serves to reinforce the pool of human microglia and becomes common with aging.

immunology↗

bioRxiv2026

Engulfment by brain macrophages in a short-lived vertebrate

Engulfment by macrophages is critical for waste clearance in the vertebrate brain. Understanding clearance mechanisms may open new therapeutic possibilities to counter brain aging and neurodegenerative diseases. However, few in vivo models exist to study engulfment in the brain and characterize this process during aging and across species. Here we present a genetic model for secretion of a fluorescent protein by neurons in the brain of the African turquoise killifish, the shortest-lived vertebrate that can be bred in captivity. We use this model to identify a population of brain macrophages in the killifish responsible for engulfment of material from the brain extracellular space. Intriguingly, many of these cells bear similarities to mammalian border-associated and monocyte-derived macrophages, rare subsets of macrophages in mouse and human brains noted for their engulfment capabilities. We also find that in our model, killifish brain macrophages decline in engulfment capacity with age. This work highlights how vertebrate brain macrophages, particularly those at brain border regions, can play a critical role in clearance and provides an opportunity to test interventions that can boost engulfment by these macrophages to promote brain resilience in old age and disease.

cell biology↗

bioRxiv2025

SpatialProp: tissue perturbation modeling with spatially resolved single-cell transcriptomics

Perturbational studies are the gold standard for identifying causal relationships between components of biological systems. Recent technological advances, including Perturb-seq and related assays, have enabled high-throughput screening of genetic perturbation effects on single cells. Several machine learning tools have also been developed to infer the effect of single-cell perturbations. However, both approaches are generally limited to dissociated cells, and the effect of genetic perturbations on neighboring cells within intact tissue has not yet been explored. Here we introduce a computational framework using graph neural networks for predicting the effect of multi-gene, multi-cell type perturbations on cells in whole tissue sections. We leverage the natural heterogeneity in tissue microenvironments across spatially resolved single-cell transcriptomics datasets to train SpatialProp (Spatial Propagation of Single-cell Perturbations). We show that SpatialProp can predict gene expression from the tissue microenvironment and map fine-grained steering of tissue microenvironments to new target states. To assess for causal enrichment in spatial perturbation predictions, we propose CausalInteractionBench, a bidirectional benchmarking approach using curated cell-cell interactions. Under this benchmark, we evaluate the causal utility of SpatialProp in predicting the spatial effects of different perturbations. SpatialProp provides a framework towards rapid hypothesis generation and in silico perturbation experiments, particularly in the study of spatially patterned tissue biology.

bioinformatics↗

bioRxiv2025

Life-long behavioral screen reveals an architecture of vertebrate aging

Mapping behavior of individual vertebrate animals across lifespan is challenging, but if achieved, could provide an unprecedented view into the life-long process of aging. We created the first platform for high-resolution continuous behavioral tracking of a vertebrate animal across natural lifespan from adolescence to death--here, of the African killifish. This behavioral screen revealed that animals follow distinct individual aging trajectories. The behaviors of long-lived animals differed markedly from those of short-lived animals, even relatively early in life, and were linked to organ-specific transcriptomic shifts. Machine learning models accurately predicted age and even forecasted an individuals future lifespan, given only behavior at a young age. Finally, we found that animals progressed through adulthood in a sequence of stable and stereotyped behavioral stages with abrupt transitions suggesting a novel structure for the architecture of vertebrate aging.

animal behavior and cognition↗

bioRxiv2025

Age-related microbiome metabolites modulate splicing and chromatin accessibility in the brain

The gut microbiome generates diverse metabolites that can enter the bloodstream and alter host biology, including brain function. Hundreds of physiologically relevant, gut-brain signaling molecules likely exist; however, there has been no systematic, high-throughput effort to identify and validate them. Here, we integrate computational, in vitro, and in vivo approaches to pinpoint microbiome-derived metabolites whose blood levels change during aging, and that induce molecular changes in the mouse brain. First, we mine large-scale metabolomics datasets from human cohorts (each n [≥] 1200) to identify 30 microbiome-associated metabolites whose blood levels change with age. We then screen this panel in an in vitro transcriptomic assay to identify metabolites that perturb genes linked to age-related neurodegeneration. To assess in vivo relevance, we then test four metabolites in male mice by acute exposure, using multi-omic approaches to evaluate the metabolites impact on cellular functions in the brain. With RNA-seq, we confirm known effects of trimethylamine N-oxide (TMAO), including changes in mitochondrial pathways, and further discover its effects on the pathways of glycolysis, GABAergic signaling, and RNA splicing. Additionally, using both RNA- and ATAC-seq, we identify glycodeoxycholate (GDCA), a microbiome-derived secondary bile acid, as a potent regulator of chromatin accessibility and of genes involved in protecting the brain from age-related stressors. GDCA also acutely reduces locomotion in male but not female mice. In summary, we present a generalizable framework for identifying microbiome metabolites that impact host biology, and apply it to identify age-related microbial metabolites that affect processes related to brain aging and neurodegeneration.

neuroscience↗

bioRxiv2025

Engineering single-AAV CRISPR-Cas13 RNA base editors for treatment of inherited retinal diseases

Site-directed RNA editing, especially RNA base editing, allows for specific manipulation of RNA sequences, making it a useful approach for the correction of pathogenic mutations. Correction of RNA transcripts allows therapeutic gene editing in a safe and reversible manner and avoids permanent alterations in the genome. RNA-targeting CRISPR-Cas nucleases (e.g., CRISPR-Cas13) enable delivery within a single adeno-associated virus (AAV) vector for RNA base editing, making the approach clinically feasible. Here, we used the inactive CRISPR-Cas13bt3 (also known as Cas13X.1) fused to the ADAR2 deaminase domain (ADAR2DD) for targeted correction of inherited retinal disease (IRD) mutations. First, we show in vitro that dCas13bt3-ADAR2DD can efficiently correct a pathogenic nonsense mutation (c.130C>T [p.R44X]) found in the mouse Rpe65 gene and recover protein expression in retinal pigment epithelium cells (RPEs). Across clinically reported RPE65 mutations, we observed editing efficiencies ranging from 0% to 60%. In the Rpe65-deficient mouse model of retinal degeneration (rd12), we observed that RNA base editing can recover Rpe65 expression in RPEs and rescue retinal function with no observable adverse effects. We further employed our RNA base editor against the large USH2A gene to assess the promise of RNA base editing for addressing untreatable IRDs caused by genes too large for AAV gene delivery. Against the human USH2A in vitro, we observed up to 60% on-target efficiency. We further found that gRNA mismatches, domain-inlaid ADAR2DD design and nucleocytoplasmic shuttling of the RNA base editor optimised on-target and bystander editing for a highly precise base editor. Against the mouse Ush2a in vitro, we similarly observed up to 60% on-target editing in mammalian cells, while in the Ush2aW3947X mice, we observed [~]12% on-target editing, with no impact on retinal structure or function, or transcriptome-wide editing. Overall, our findings demonstrate dCas13bt3-ADAR2DD as a potent tool for gene therapy against IRDs, addressing a significant unmet clinical need in ophthalmology.

bioengineering↗

bioRxiv2025

Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish

Aging is associated with progressive tissue dysfunction, leading to frailty and mortality. Characterizing aging features, such as changes in gene expression and dynamics, shared across tissues or specific to each tissue, is crucial for understanding systemic and local factors contributing to the aging process. We performed RNA-sequencing on 13 tissues at 6 different ages in the African turquoise killifish, the shortest-lived vertebrate that can be raised in captivity. This comprehensive, sex-balanced atlas dataset reveals the varying strength of sex-age interactions across killifish tissues and identifies age-altered biological pathways that are evolutionarily conserved. Demonstrating the utility of this resource, we discovered that the killifish head kidney exhibits a myeloid bias during aging, a phenomenon more pronounced in females than in males. In addition, we developed tissue-specific transcriptomic clocks and identified biomarkers predictive of chronological age. We show the importance of sex-specific clocks for selected tissues and use the tissue clocks to evaluate a dietary intervention in the killifish. Our work provides a comprehensive resource for studying aging dynamics across tissues in the killifish, a powerful vertebrate aging model.

genomics↗

bioRxiv2024

CREB3 gain of function variants protect against ALS

Amyotrophic lateral sclerosis (ALS) is a fatal and rapidly evolving neurodegenerative disease that arises from the loss of glutamatergic corticospinal neurons (CSN) and cholinergic motoneurons (MN). The disease is mostly sporadic, but genetics is expected to highly contribute to disease onset and progression. Genome wide association studies identified a few genetic disease modifiers, mostly associated with a negative outcome, and demonstrated that ALS is primarily a disease of excitatory glutamatergic neurons. Here, we reasoned that at least a subpart of genetic disease modifiers may directly modulate the molecular pathways selectively activated in vulnerable neurons as the disease progresses, and concentrated on CSN for their selective vulnerability and glutamatergic identity. We implemented comparative cross-species transcriptomics using snRNAseq data from postmortem motor cortex of ALS patients and controls, and longitudinal RNAseq data from anatomically defined CSN purified from the Sod1G86R mouse model of ALS. We report that disease vulnerable neuronal populations undergo ER stress and altered mRNA translation, and identify the transcription factor CREB3 and its regulatory network as a resilience marker of neuronal dysfunction in ALS. Using genetic and epidemiologic analyses we further identify the rare variant CREB3R119G (rs11538707) as a new disease modifier in ALS. Through gain of function, CREB3R119G decreases both the risk of developing ALS and the progression rate of ALS patients. This study reveals novel genetic variants that protect against ALS and highlights the benefice of combining transcriptomics and genetics to identify new disease modifiers and therapeutic targets.

genomics↗

bioRxiv2024

Spatiotemporal transcriptomic profiling and modeling of mouse brain at single-cell resolution reveals cell proximity effects of aging and rejuvenation

Old age is associated with a decline in cognitive function and an increase in neurodegenerative disease risk1. Brain aging is complex and accompanied by many cellular changes2-20. However, the influence that aged cells have on neighboring cells and how this contributes to tissue decline is unknown. More generally, the tools to systematically address this question in aging tissues have not yet been developed. Here, we generate spatiotemporal data at single-cell resolution for the mouse brain across lifespan, and we develop the first machine learning models based on spatial transcriptomics ( spatial aging clocks) to reveal cell proximity effects during brain aging and rejuvenation. We collect a single-cell spatial transcriptomics brain atlas of 4.2 million cells from 20 distinct ages and across two rejuvenating interventions--exercise and partial reprogramming. We identify spatial and cell type-specific transcriptomic fingerprints of aging, rejuvenation, and disease, including for rare cell types. Using spatial aging clocks and deep learning models, we find that T cells, which infiltrate the brain with age, have a striking pro-aging proximity effect on neighboring cells. Surprisingly, neural stem cells have a strong pro-rejuvenating effect on neighboring cells. By developing computational tools to identify mediators of these proximity effects, we find that pro-aging T cells trigger a local inflammatory response likely via interferon-{gamma} whereas pro-rejuvenating neural stem cells impact the metabolism of neighboring cells possibly via growth factors (e.g. vascular endothelial growth factor) and extracellular vesicles, and we experimentally validate some of these predictions. These results suggest that rare cells can have a drastic influence on their neighbors and could be targeted to counter tissue aging. We anticipate that these spatial aging clocks will not only allow scalable assessment of the efficacy of interventions for aging and disease but also represent a new tool for studying cell-cell interactions in many spatial contexts.

neuroscience↗

bioRxiv2024

Plasma proteomics in the UK Biobank reveals youthful brains and immune systems promote healthspan and longevity

Organ-derived plasma protein signatures derived from aptamer protein arrays track organ-specific aging, disease, and mortality in humans, but the robustness and clinical utility of these models and their biological underpinnings remain unknown. Here, we estimate biological age of 11 organs from 44,526 individuals in the UK Biobank using an antibody-based proteomics platform to model disease and mortality risk. Organ age estimates are associated with future onset of heart failure (heart age HR=1.83), chronic obstructive pulmonary disease (lung age HR=1.39), type II diabetes (kidney age HR=1.58), and Alzheimers disease (brain age HR=1.81) and sensitive to lifestyle factors such as smoking and exercise, hormone replacement therapy, or supplements. Remarkably, the accrual of aged organs progressively increases mortality risk while a youthful brain and immune system are uniquely associated with disease-free longevity. These findings support the use of plasma proteins for monitoring organ health and the efficacy of drugs targeting organ aging disease.

molecular biology↗

bioRxiv2024

Playing with the ploidy level enables to switch on and off the strict recombination control even in the vicinity of Brassica centromeres

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates novel genetic diversity at each generation. However, due to its importance in chromosome segregation and genomic stability, crossovers are highly regulated in both frequency and distribution. We previously demonstrated that this strict regulation is not a fatality and that it can be naturally modified (3.6-fold increased frequency and altered distribution) in an allotriploid Brassica hybrid (2n=3x=29; AAC), resulting from a cross between B. napus (2n=4x=38; AACC) and B. rapa (2n=2x=20; AA). Taking advantage of the recently updated Brassica napus genome assembly, which now includes the pericentromeric regions, we unambiguously demonstrated that crossovers occur in these normally cold regions in allotriploids, with the presence of crossovers as close as 375 kb from the centromere. We deciphered that this modified recombination landscape (both frequency and distribution) can be maintained in successive generations of allotriploidy, with even a slight increase of crossover frequency. We also showed that this deregulated meiotic behavior may revert back to a strictly regulated one when recovering an allotetraploid progeny in the second generation. Overall, we provide here for the first time a practical and natural way to switch on and off the tight recombination control in a polyploid crop. We also discuss the potential role of this modified regulation of recombination in polyploid speciation success.

genetics↗

bioRxiv2022

CRTC-1 Balances Histone Trimethylation and Acetylation to Promote Longevity

Loss of function during ageing is accompanied by transcriptional drift, altering gene expression and contributing to a variety of age-related diseases. CREB-regulated transcriptional coactivators (CRTCs) have emerged as key regulators of gene expression that might be targeted to promote longevity. Here, we define the role of the Caenorhabditis elegans CRTC-1 in the epigenetic regulation of longevity. Endogenous CRTC-1 binds chromatin factors, including components of the COMPASS complex, which trimethylates lysine 4 on histone H3 (H3K4me3). CRISPR editing of endogenous CRTC-1 reveals that the CREB-binding domain in neurons is specifically required for H3K4me3-dependent longevity. However, this effect is independent of CREB but instead acts via the transcription factor AP-1. Strikingly, CRTC-1 also mediates global histone acetylation levels, and this acetylation is essential for H3K4me3-dependent longevity. Indeed, overexpression of an acetyltransferase enzyme is sufficient to promote longevity in wild-type worms. CRTCs, therefore, link energetics to longevity by critically fine-tuning histone acetylation and methylation to promote healthy ageing.

genetics↗

bioRxiv2022

Lipidomic profiling reveals age-dependent changes in complex plasma membrane lipids that regulate neural stem cell aging

The aging brain exhibits a decline in the regenerative populations of neural stem cells (NSCs), which may underlie age-associated defects in sensory and cognitive functions1-6. While mechanisms that restore old NSC function have started to be identified7-23, the role of lipids - especially complex lipids - in NSC aging remains largely unclear. Using lipidomic profiling by mass spectrometry, we identify age-related lipidomic signatures in young and old quiescent NSCs in vitro and in vivo. These analyses reveal drastic changes in several complex membrane lipid classes, including phospholipids and sphingolipids in old NSCs. Moreover, poly-unsaturated fatty acids (PUFAs) strikingly increase across complex lipid classes in quiescent NSCs during aging. Age-related changes in complex lipid levels and side chain composition are largely occurring in plasma membrane lipids, as revealed by lipidomic profiling of isolated plasma membrane vesicles. Experimentally, we find that aging is accompanied by modifications in plasma membrane biophysical properties, with a decrease in plasma membrane order in old quiescent NSCs in vitro and in vivo. To determine the functional role of plasma membrane lipids in aging NSCs, we performed genetic and supplementation studies. Knockout of Mboat2, which encodes a phospholipid acyltransferase, exacerbates age-related lipidomic changes in old quiescent NSCs and impedes their ability to activate. As Mboat2 expression declines with age, Mboat2 deficiency may drive NSC decline during aging. Interestingly, supplementation of plasma membrane lipids derived from young NSCs boosts the ability of old quiescent NSCs to activate. Our work could lead to lipid-based strategies for restoring the regenerative potential of NSCs in old individuals, which has important implications for countering brain decline during aging.

molecular biology↗

bioRxiv2022

Rapid and precise genome engineering in a naturally short-lived vertebrate

The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci, to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.

genetics↗

bioRxiv2022

Identification of protein aggregates in the aging vertebrate brain with prion-like andphase separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms mislocalized cytoplasmic aggregates in the brains of old killifish and mice. Interestingly, DDX5s prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the proteins ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.

neuroscience↗

bioRxiv2022

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate

Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue-specific, and not simply driven by protein expression differences. Experimental interrogation, combined with machine learning, indicates that this specificity is linked to both protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during aging and reveal strong, tissue-specific associations with dysfunction and disease. HIGHLIGHTSO_LITissue-specific protein aggregation is prevalent during vertebrate aging C_LIO_LIBoth protein biophysical properties and tissue-specific protein homeostasis patterns impact aggregation C_LIO_LIA segmental progeria model with accelerated aging exhibits selectively increased protein aggregation in affected tissues C_LIO_LIMany aggregates that accumulate during physiological aging are linked to disease C_LI

systems biology↗

bioRxiv2022

Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain

Aging manifests as progressive dysfunction culminating in death. The diversity of cell types is a challenge to the precise quantification of aging and its reversal. Here we develop a suite of aging clocks based on single cell transcriptomic data to characterize cell type-specific aging and rejuvenation strategies. The subventricular zone (SVZ) neurogenic region contains many cell types and provides an excellent system to study cell-level tissue aging and regeneration. We generated 21,458 single-cell transcriptomes from the neurogenic regions of 28 mice, tiling ages from young to old. With these data, we trained a suite of single cell-based regression models (aging clocks) to predict both chronological age (passage of time) and biological age (fitness, in this case the proliferative capacity of the neurogenic region). Both types of clocks perform well on independent cohorts of mice. Genes underlying the single cell-based aging clocks are mostly cell-type specific, but also include a few shared genes in the interferon and lipid metabolism pathways. We used these single cell-based aging clocks to measure transcriptomic rejuvenation, by generating single cell RNA-seq datasets of SVZ neurogenic regions for two interventions - heterochronic parabiosis (young blood) and exercise. Interestingly, the use of aging clocks reveals that both heterochronic parabiosis and exercise reverse transcriptomic aging in the niche, but in different ways across cell types and genes. This study represents the first development of high-resolution aging clocks from single cell transcriptomic data and demonstrates their application to quantify transcriptomic rejuvenation.

genomics↗