Biology subjects

El Amki, M.

Publications and source records attributed to El Amki, M..

7 recordsLinked to original sources

bioRxiv2026

Brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneity

Brain capillary pericytes are essential components of the neurovascular unit, yet the extent of their molecular heterogeneity within intact vascular networks remains poorly understood. Here, we combined spatial imaging with reanalysis of independent single-cell transcriptomic datasets to investigate the molecular organization of adult mouse brain pericytes. We identified spatial organization of pericyte molecular heterogeneity associated with anatomical region and position within the vascular network, including recurrent differences in ACE2, CASQ2, Igf2, and OPN expression. Moreover, pericyte molecular phenotypes varied with aging, acute ischemia, and circadian phase. Notably, light-dark phase emerged as a major axis of transcriptional variation, with pericytes exhibiting distinct circadian phase-associated molecular states. Together, these data demonstrate that adult brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneity associated with vascular and physiological context.

neuroscience↗

bioRxiv2026

Streak-Aware Localization Microscopy Enables High-Throughput Brain Imaging Across Platforms

Optical, ultrasound, and optoacoustic localization microscopy based on microparticle tracking has enabled surpassing the resolution limits imposed by ultrasound diffraction and optical diffusion in tissues. However, its reliance on high-speed (kilohertz) data acquisition systems for precise emitter localization and tracking substantially increases methodological complexity and data storage demands, limiting scalability and applicability beyond specialized benchtop platforms. Here, we present streak-aware localization microscopy (SALM) that employs localization- and tracking-free deep learning model to convert motion-blurred streaks originating from low frame rate recordings of flowing emitters into super-resolved structural and functional readouts. In optical implementations, SALM exploits streaks captured by low-speed cameras to recover capillary-level cerebrovascular maps across a variety of benchtop, miniaturized, and second near-infrared preclinical imaging platforms, achieving over 30-fold reduction in the reconstruction time compared to conventional localization pipelines. We further introduce three coded excitation strategies that embed finer time-varying vectorial flow signatures into individual streaks, enabling single-frame velocimetry and video-rate hemodynamic imaging. Extending SALM to ultrasound imaging enables high-fidelity vascular imaging with centimeter-scale penetration in rhesus macaque and rat brains while reducing plane-wave compounding frame rates by up to one order of magnitude. By overcoming long-standing trade-offs between spatiotemporal resolution and hardware complexity, SALM offers a flexible and scalable framework for next-generation super-resolution microscopy.

neuroscience↗

bioRxiv2025

Loss of Cerebral Autoregulation After Stroke Drives Abnormal Perfusion Patterns

Cerebral autoregulation stabilizes cerebral blood flow (CBF) in response to variations in blood pressure, primarily through dynamic adjustments in arterial caliber. However, the impact of autoregulation mechanisms on local vascular responses and microcirculatory perfusion remains poorly understood. Given that impaired autoregulation is common in pathologies such as ischemic stroke, quantifying vessel-level responses can help to inform clinical strategies. Here, we present a novel in silico model that incorporates static myogenic and endothelial regulatory mechanisms to simulate CBF in large microvascular networks derived from realistic surface vasculatures of mice with and without leptomeningeal collaterals (LMCs). We assessed the role of autoregulation mechanisms under three conditions: i) healthy autoregulation, ii) ischaemic stroke and reperfusion with altered vascular reactivity, and iii) chronic autoregulation dysfunction after stroke. For healthy autoregulation, our model reproduced the classic static autoregulation curve and identified the dominant contribution of surface arteries in buffering pressure changes. Networks with lower descending arteriole density exhibited more extensive arterial dilations, reflecting the topological influence on vessel diameter changes. During reperfusion after stroke, we investigated the interplay between LMCs and parameters governing the vasoreactive response. While LMCs play a crucial role in maintaining residual perfusion in adjacent regions during MCA occlusion, our results suggest that their extent alone does not substantially influence perfusion after recanalization. Instead, alterations in myogenic reactivity emerged as the key contributor to hyperperfusion, underscoring the importance of regulatory mechanisms in determining reperfusion outcomes. To mimic chronic autoregulatory dysfunction, we progressively impaired regulatory capacity in arteries on the middle cerebral artery (MCA) side, reflecting the territory previously affected by stroke. The loss of autoregulation in proximal vessels significantly disrupts capillary perfusion and alters the autoregulation curve. To our knowledge, this is the first in silico study to explore cerebral autoregulation at the microvascular level under both physiological and pathological conditions. Our findings provide mechanistic insight into how individual vessel behavior shapes global flow regulation and highlight myogenic tone as a potential therapeutic target to reduce reperfusion-related complications in stroke.

physiology↗

bioRxiv2025

ECgo: All-Optical Induction of Single Endothelial Cell Injury and Capillary Occlusion in the Brain

The ability to induce endothelial cell (EC) damage in the mouse brain with high spatial precision is invaluable for mechanistic studies of brain capillary injury and repair. Here, we introduce an optical method, termed ECgo, that utilizes a new two-photon-excitable porphyrin-based photosensitizer (Ps2P) to selectively obliterate single ECs within the brain microvascular network. Using the developed approach, we were able to induce occlusions of single capillaries with high spatiotemporal control, while preserving the surrounding tissue. Combined with longitudinal two-photon imaging, ECgo enables studies of morphological and functional consequences of targeted single capillary EC injury in vivo under healthy and diseased conditions. SIGNIFICANCE STATEMENTBrain capillary injury is a common feature of aging and many neurological disorders. While a single capillary lesion may appear inconsequential, the cumulative effect of repeated and spatially dispersed capillary insults can lead to substantial brain dysfunction. Understanding how single capillary injuries contribute cumulatively to long-term brain damage requires tools that can precisely target individual capillaries in the living brain. Here, we introduce an optical method that uses a new light-activatable compound to selectively injure single brain capillaries with high spatial accuracy. Our method enables detailed, longitudinal studies of capillary repair, blood flow recovery, local oxygen dynamics, and glial responses following microvascular injury.

neuroscience↗

bioRxiv2023

Transcranial cortex-wide imaging of murine ischemic perfusion with large-field multifocal illumination fluorescence microscopy

Ischemic stroke is a common cause of death worldwide and a main cause of morbidity. Presently, computed tomography and magnetic resonance imaging are the mainstay for stroke diagnosis and therapeutic monitoring. These modalities are often limited in terms of accessibility as well as their ability to map brain perfusion with sufficient spatial and temporal resolution, particularly in the context of preclinical studies, thus calling for development of new brain perfusion techniques featuring rapid imaging speed, cost-effectiveness, and ease of use. Herein, we report on cortex-wide perfusion imaging in murine ischemic stroke with large-field multi-focal illumination fluorescence microscopy (LMI). We attained quantitative readings of hemodynamic and structural changes in cerebral vascular network and pial vessels at capillary level resolution and 80 Hz frame rate fully transcranially. The in vivo perfusion maps accurately delineated the ischemic core and penumbra, further exhibiting strong correlation with ex vivo triphenyl tetrazolium chloride staining. Interestingly, monitoring of therapeutic effects of thrombolysis in stroke has revealed that early recanalization could effectively save the penumbra whilst reducing the infarct area. Furthermore, cross-strain comparison of perfusion dynamics affirmed that C57BL/6 mice, benefiting from more extensive pial collateral recruitment, feature a larger penumbra and smaller infarct core as compared to BALB/c mice which have few or no collaterals. Finally, we apply LMI to show that sensory stimulation-based treatment enhances blood flow and abolish perfusion deficit in the ischemic core and penumbra regions. The simple, cost-effective and minimally invasive nature of the proposed approach offers new venues for brain perfusion research under various disease conditions such as stroke, neurodegeneration or epileptic seizures.

neuroscience↗

bioRxiv2023

Leptomeningeal collaterals regulate reperfusion in ischemic stroke

Recanalization is the mainstay of ischemic stroke treatment. However, even with timely clot removal, many stroke patients recover poorly. Leptomeningeal collaterals (LMCs) are pial anastomotic vessels with yet unknown functions. Utilizing a thrombin-based mouse model of stroke and the gold standard fibrinolytic treatment rt-PA, we here show that LMCs play a critical role in preserving vascular function in ischemic territories. We applied laser speckle contrast imaging, ultrafast ultrasound, and two-photon microscopy, to show that after thrombolysis, LMCs allow for gradual reperfusion resulting in small infarcts. On the contrary, in mice with poor LMCs, distal segments of recanalized arteries collapse and deleterious hyperemia causes hemorrhage and mortality. Accordingly, in stroke patients with poor collaterals undergoing thrombectomy, rapid reperfusion resulted in hemorrhagic transformation and unfavorable recovery. Thus, we identify LMCs as key components regulating reperfusion after stroke. Future therapeutic interventions should aim to enhance collateral function, allowing for gradual reperfusion of ischemic tissues after stroke.

neuroscience↗

bioRxiv2023

Acoustic trapping and navigation of microrobots in the mouse brain vasculature

Many cerebrovascular and neurodegenerative diseases are currently challenging to treat due to the complex and delicate anatomy of the brain. The use of microrobots can create new opportunities in brain research due to their ability to access hard-to-reach regions and empower various biological applications; however, little is known about the functionality of microrobots in the brain, owing to their limited imaging modalities and intravascular challenges such as high blood flow velocities, osmotic pressures, and cellular responses. Here, we present an acoustic, non-invasive, biocompatible microrobot actuation system, for in vivo navigation in the bloodstream, in which microrobots are formed by lipid-shelled microbubbles that aggregate and propel under the force of acoustic irradiation. We investigated their capacities in vitro within a microfluidic 3D setup and in vivo in a living mouse brain. We show that microrobots can self-assemble and navigate upstream in the brain vasculature. Our microrobots achieved upstream velocities of up to 1.5 m/s and overcame blood flows of ~10 mm/s. Our results prove that microbubble-based microrobots are scalable to the complex 3D living milieu. Significance StatementNumerous brain diseases, including ischemic stroke, Alzheimers disease, and glioblastoma, may benefit from local and targeted therapies. Although they show great promise, microrobots have not yet demonstrated successful in vivo navigation inside the brain, as the challenging flow conditions and the complex 3D vascular network in the brain pose fundamental limitations. Here, we apply acoustically driven microrobots with the capacity for self-assembly and real-time navigation, including navigation against blood flow up to 10 mm/s, used for the first time inside the brain vasculature of a living mouse. The ultrasound manipulation of microrobots inside animal models provides a much-needed pathway for the advancement of preclinical research.

bioengineering↗