Biology subjects

Bonnin, A.

Publications and source records attributed to Bonnin, A..

11 recordsLinked to original sources

bioRxiv2026

Efficient murine cardiac phenotyping by combining synchrotron-based phase-contrast micro-CT, histology, immunofluorescence and spatial transcriptomics

1.Congenital heart disease is commonly studied using genetically modified mouse models, but characterization of complex three-dimensional (3D) cardiac anomalies remains technically challenging. Histology of fixed paraffin-embedded samples, typically used for structural and molecular analysis, is limited to two dimensions (2D). Synchrotron radiation-based phase-contrast micro-computed tomography (SRPC-{micro}CT) enables rapid, high-resolution, 3D imaging but had yet to be fully integrated with molecular tissue analysis. Importantly, SRPC-{micro}CT is nondestructive and compatible with paraffin-embedded tissue, potentially allowing integration with downstream molecular analyses such as multiplexed spatial transcriptomic profiling on tissue sections. Here, we present a pipeline combining SRPC-{micro}CT with complementary molecular approaches for rapid and accurate phenotyping of mouse hearts and for investigating disease mechanisms. We demonstrate the successful integration of high-resolution 3D imaging with spatial transcriptomics, fluorescent stainings, and histochemistry. Notably, all 2D modalities were applied sequentially to a single tissue section and registered within the 3D volume. This multimodal framework provides a powerful approach for linking structural and molecular information that is broadly applicable across biomedical research.

developmental biology↗

bioRxiv2026

Placental prostaglandin signaling disrupts barrier integrity and relays an acute inflammatory signal to the fetus.

Maternal inflammation during pregnancy is a major risk factor for adverse neurodevelopmental outcomes, yet the mechanisms linking maternal immune activation (MIA) to placenta-fetal brain axis dysfunction remain unclear. Using a poly-(I:C) mouse model, we show that MIA rapidly disrupts placental-blood barrier (PBB) integrity by disrupting pericyte-endothelium coupling within 48 hours, leading to increased placental permeability detected by in vivo MRI. We identify a prostaglandin E2 (PGE2)-dependent pathway involving cyclooxygenase-2 (COX2) and prostaglandin E-synthase (mPGES1) as a key mediator of this effect. Pharmacological inhibition of COX2 prevented MIA-induced structural and functional changes. In vitro explant studies confirmed that PGE2 acts via the EP3 receptor to disrupt pericyte-endothelium interactions, while ex vivo perfusion demonstrated that in addition to its local effects on PBB structure, placenta-derived PGE2 enters the fetal circulation. Finally, similar vascular alterations were observed in human placentas from pregnancies with severe maternal inflammation. These findings reveal a conserved inflammatory mechanism that compromises PBB integrity and may relay signals to the fetal brain, highlighting potential therapeutic targets for neuroprotection during prenatal inflammation. One Sentence SummaryMaternal immune activation during pregnancy disrupts placental vascular integrity through a COX2-dependent prostaglandin E2 pathway, which compromises the placenta-blood barrier and relays inflammatory signals to the fetus, identifying potential therapeutic targets for neuroprotection.

developmental biology↗

bioRxiv2025

Structure-Function Mapping of Olfactory Bulb Circuits with Synchrotron X-ray Nanotomography

Information is routed between brain areas via parallel streams. Neurons may share common inputs yet convey distinct information to different downstream targets. Here, we leverage the anatomical organisation of the mouse olfactory bulb (OB), where dozens of projection neurons (mitral and tufted cells, M/TCs) affiliate with a single input unit, a glomerulus1-3. To link functional properties of M/TCs to their anatomical glomerular association at scale, we combine in vivo two-photon (2P) imaging with synchrotron {micro}CT4-6 anatomical analysis and targeted X- ray nano-holotomography (XNH)7,8. Improving XNH resolution for mm3 volumes enables us to reliably identify subcellular features, automatically segment >80,000 cell nuclei in individual experiments, and delineate several hundred functionally imaged projection neurons and their detailed morphology, including up to 20 M/TCs per individual glomerulus ("sister" cells). In over 2400 sister cell pairs, we consistently find that odour response amplitudes to a panel of 47 monomolecular odours are conserved between sister cells, with, however, distinct responses to individual odours. Responses correlated with anatomical features such as cell body position and lateral dendritic arborisation. Thus, sister cells neither simply relay glomerular inputs nor are they dominated by network activity. Instead, they show a "balanced diversity" in their responses, enabling efficient encoding of odour stimuli whilst retaining the overall structure of odour space. Thus, synchrotron X-ray tomography can reliably link subcellular anatomy to function in a non-destructive way across the mm3 scale. With recent advances in X-ray optics9 and the emergence of 4th generation synchrotrons10,11, it becomes conceivable to extend this highly accessible approach to entire brain regions with increasing resolution.

neuroscience↗

bioRxiv2025

Deep learning-based 3D spatial transcriptomics with X-Pression

Spatial transcriptomics technologies currently lack scalable and cost-effective options to profile tissues in three dimensions. Technological advances in microcomputed tomography enabled non-destructive volumetric imaging of tissue blocks with sub-micron resolution at a centimetre scale. Here, we present X-Pression, a deep convolutional neural network-based frame-work designed to reconstruct 3D expression signatures of cellular niches from volumetric microcomputed tomography data. By training on a singular 2D section of a paired spatial transcriptomics experiment, X-Pression achieves high accuracy and is capable of generalising to out-of-sample examples. We utilised X-Pression to demonstrate the benefit of 3D examination of tissues on a paired SARS-CoV-2 vaccine efficacy spatial transcriptomics and microcomputed tomography cohort of a recently developed live attenuated SARS-CoV-2 vaccine. By applying X-Pression to the entire mouse lung, we visualised the sites of viral replication at the organ level and the simultaneous collapse of small alveoli in their vicinity. In addition, we assessed the immunological response following vaccination and virus challenge infection. X-Pression offers a valuable and cost-effective addition to infer expression signatures without the need for consecutive 2D sectioning and reconstruction, providing new insights into transcriptomic profiles in three dimensions.

bioinformatics↗

bioRxiv2024

Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture

Thoracic aortic aneurysm and dissection (TAAD) associates with a high mortality rate. Despite the existence of different mouse models for TAAD, the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical aortic diameters as current pharmacological interventions are unable to stop disease progression. In humans, loss of function (LOF) of SMAD3 and SMAD6 impairs vascular homeostasis, increasing the risk for TAAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. At 10 days post fertilization, we found an increased diameter of the ventral aorta in smad3a-/-;smad3b-/- double knockout zebrafish, while smad6a-/-;smad6b-/- double knockout zebrafish have a reduced aortic diameter associated with early mortality. We discovered that a smad3a-/-;smad3b-/-;smad6a-/-;smad6b-/- quadruple knockout (qKO) zebrafish model is viable and survives to adulthood, although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta shows medial elastolysis, aortic dissections and ruptures at sites exposed to high biomechanical stress. RNA-sequencing of 5 days post fertilization qKO zebrafish indicates a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis, a previously unaddressed pathway in this pathology. We confirm that pharmacological modulation of tyrosinase, the enzyme responsible for the production of melanin, influences aortic morphology. Overall, the qKO mutant, thus far the only known zebrafish model of thoracic aortic dissection and rupture, reveals novel SMAD3/6-dependent pathways that impact thoracic aortic homeostasis, in this way opening avenues for the development of novel treatments in TAAD.

developmental biology↗

bioRxiv2024

SARS-COV-2 induces blood-brain barrier and choroid plexus barrier impairments and vascular inflammation in mice

The coronavirus disease of 2019 (COVID-19) pandemic that has led to more than 700 million confirmed cases and near 7 million deaths. Although Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus mainly infects the respiratory system, neurological complications are widely reported in both acute infection and long-COVID cases. Despite the success of vaccines and antiviral treatments, neuroinvasiveness of SARS-CoV-2 remains as an important question, which is also centered on the mystery whether the virus is capable of breaching the barriers into the central nervous system. By studying the K18-hACE2 infection model, we observed clear evidence of microvascular damage and breakdown of the blood-brain barrier (BBB). Mechanistically, SARS-CoV-2 infection caused pericyte damage, tight junction loss, endothelial activation and vascular inflammation, which together drive microvascular injury and BBB impairment. In addition, the blood-cerebrospinal fluid barrier at the choroid plexus was also impaired after infection. Therefore, cerebrovascular and choroid plexus dysfunctions are important aspects of COVID-19 and may contribute to the neurological complications both acutely and in long COVID.

neuroscience↗

bioRxiv2023

A Practical Approach to Estimating the Effect of Synchrotron Radiation on Sperm Motility and Viability

Studying the dynamics of sperm tail beating in 3D is important for understanding decreasing fertility trends related to motility. Syn-chrotron X-ray tomography (SXRT) shows promising results for imaging live biological samples in 3D and time, making it a candidate for imaging sperm tail beating patterns. However, the dose of ionizing radiation (IR) that the cells would receive during image acquisition is of concern as this is likely to affect essential cellular functions. The effect of IR on motility at the dose rates encountered in a synchrotron has never been assessed. Here, results are presented of analyzing the movement and viability of sperm cells exposed at varying durations at the TOMCAT beamline (Swiss Light Source (SLS)) which has the field of view and spatial resolution needed to reconstruct sperm cells coupled with sub-second exposure times. The results indicate that motility is affected long before viability and that sperm cell dynamics are affected very quickly by the beam.

biophysics↗

bioRxiv2022

Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy

Integrating physiology with structural insights of the same neuronal circuit provides a unique approach to understanding how the mammalian brain computes information. However, combining the techniques that provide both streams of data represents an experimental challenge. When studying glomerular column circuits in the mouse olfactory bulb, this approach involves e.g. recording the neuronal activity with in vivo 2-photon (2P) calcium imaging, retrieving the circuit structure with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT) and/or serial block-face electron microscopy (SBEM) and correlating these datasets. Sample preparation and dataset correlation are two key bottlenecks in this correlative workflow. Here, we first quantify the occurrence of different artefacts when staining tissue slices with heavy metals to generate X-ray or electron contrast. We report improvements in the staining procedure, ultimately achieving perfect staining in [~]67% of the 0.6 mm thick olfactory bulb slices that were previously imaged in vivo with 2P. Secondly, we characterise the accuracy of the spatial correlation between functional and structural datasets. We demonstrate that direct, single-cell precise correlation between in vivo 2P and SXRT tissue volumes is possible and as reliable as correlating between 2P and SBEM. Altogether, these results pave the way for experiments that require retrieving physiology, circuit structure and synaptic signatures in targeted regions. These correlative function-structure studies will bring a more complete understanding of mammalian olfactory processing across length scales and time.

neuroscience↗

bioRxiv2021

Micrometer-resolution reconstruction and analysis of whole mouse brain vasculature by synchrotron-based phase-contrast tomographic microscopy

Nervous tissue metabolism is mainly supported by the dense thread of blood vessels which mainly provides fast supplies of oxygen and glucose. Recently, the supplying role of the brain vascular system has been examined in major neurological conditions such as the Alzheimers and Parkinsons diseases. However, to date, fast and reliable methods for the fine level microstructural extraction of whole brain vascular systems are still unavailable. We present a methodological framework suitable for reconstruction of the whole mouse brain cerebral microvasculature by X-ray tomography with the unprecedented pixel size of 0.65 m. Our measurements suggest that the resolving power of the technique is better than in many previous studies, and therefore it allows for a refinement of current measurements of blood vessel properties. Relevant insights emerged from analyses characterizing the regional morphology and topology of blood vessels. Specifically, vascular diameter and density appeared non-homogeneously distributed among the brain regions suggesting preferential sites for high-demanding metabolic requirements. Also, topological features such as the vessel branching points were non-uniformly distributed among the brain districts indicating that specific architectural schemes are required to serve the distinct functional specialization of the nervous tissue. In conclusion, here we propose a combination of experimental and computational method for efficient and fast investigations of the vascular system of entire organs with submicrometric precision.

neuroscience↗

bioRxiv2021

Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy

Attributing in vivo neurophysiology to the brains ultrastructure requires a large field of view containing contextual anatomy. Electron microscopy (EM) is the gold standard technique to identify ultrastructure, yet acquiring volumes containing full mammalian neural circuits is challenging and time consuming using EM. Here, we show that synchrotron X-ray computed tomography (SXRT) provides rapid imaging of EM-prepared tissue volumes of several cubic millimetres. Resolution was sufficient for distinguishing cell bodies as well as for tracing apical dendrites in olfactory bulb and hippocampus, for up to 350 m. Correlating EM with SXRT allowed us to associate dendritic spines on pyramidal cell apical dendrites in the stratum radiatum to their corresponding soma locations. Superficial pyramidal neurons had larger spine apparatus density compared to deeper ones, implying differential synaptic plasticity for superficial and deeper cells. Finally, we show that X-ray tomography and volume EM can be reliably correlated to prior in vivo imaging. Thus, combining functional measurements with multiscale X-ray microscopy and volume EM establishes a correlative workflow that enables functional and structural investigation of subcellular features in the context of cellular morphologies, tissues and ultimately whole organs.

neuroscience↗

bioRxiv2019

UDCT: Unsupervised data to content transformation with histogram-matching cycle-consistent generative adversarial networks

The segmentation of images is a common task in a broad range of research fields. To tackle increasingly complex images, artificial intelligence (AI) based approaches have emerged to overcome the shortcomings of traditional feature detection methods. Owing to the fact that most AI research is made publicly accessible and programming the required algorithms is now possible in many popular languages, the use of such approaches is becoming widespread. However, these methods often require data labeled by the researcher to provide a training target for the algorithms to converge to the desired result. This labeling is a limiting factor in many cases and can become prohibitively time consuming. Inspired by Cycle-consistent Generative Adversarial Networks (cycleGAN) ability to perform style transfer, we outline a method whereby a computer generated set of images is used to segment the true images. We benchmark our unsupervised approach against a state-of-the-art supervised cell-counting network on the VGG Cells dataset and show that it is not only competitive but can also precisely locate individual cells. We demonstrate the power of this method by segmenting bright-field images of cell cultures, a live-dead assay of C.Elegans and X-ray-computed tomography of metallic nanowire meshes.

bioengineering↗