Biology subjects

Nouraein, S.

Publications and source records attributed to Nouraein, S..

8 recordsLinked to original sources

bioRxiv2026

Monitoring Gene Expression in Retina with Synthetic Serum Markers

Gene expression underlies retinal development, function, and pathogenesis. However, monitoring retinal gene expression in vivo is challenging. In this study, we apply synthetic serum markers, called Released Markers of Activity, or RMAs, to quantify gene expression in an intact retina through a simple blood test. We show that RMAs can quantify transduction of multiple retinal cell-types and monitor cell implantation or cell loss. We found RMAs are sensitive enough to measure transduction of rare cell populations, such as retinal ganglion cells and could detect transplantation of as few as 100 stem cells. Expression of RMAs showed no evidence of cell loss or immune activation in the retina. Overall, these findings demonstrate that RMAs are highly sensitive, tissue non-destructive gene expression reporters that can continuously track gene delivery and cell survival in intact retina through a simple blood test.

bioengineering↗

bioRxiv2025

Noninvasive Control of Seizure Threshold with Acoustically Targeted Chemogenetics

Many neurological and psychiatric diseases are characterized by pathological neuronal activity. Current treatments involve drugs, surgeries, and implantable devices to modulate or remove the affected region. However, none of these methods can be simultaneously non-invasive and possess site- and cell type specificity. Here, we apply a non-invasive neuromodulation approach called Acoustically-Targeted Chemogenetics, or ATAC, to increase the seizure threshold. Here, the ATAC approach used a multi-point focused ultrasound to transiently open the blood-brain barrier of the whole hippocampus and transduce pyramidal neurons with engineered G-protein-coupled receptors to inhibit their activity. To express the engineered receptors in the mouse hippo-campus, we used a recently engineered viral vector optimized for ultrasound-based gene delivery to the brain, AAV.FUS.3. In a mouse flurothyl seizure model, we showed successful gene delivery throughout the hippocampus, a significant neuronal activity inhibition as evidence by an increase in seizure threshold. Finally, we benchmarked these effects against a clinically prescribed drug that acts without spatial precision.

bioengineering↗

bioRxiv2025

Erasable Synthetic Serum Markers

Gene expression in the brain is typically evaluated using invasive biopsy or postmortem histology. Serum markers provide an alternative way to monitor the brain, but relatively few such markers exist. Additionally, the origin of serum markers often cannot be localized to a specific cell population, and monitoring dynamic changes in their gene expression is compromised by the same factor that makes the markers detectable - long serum half-life. Here we propose a paradigm to improve the sensitivity of serum marker measurement by modifying the markers in vivo, called erasable serum markers, or ESM. As a proof of concept, we use a well-controlled system with known half-life and tunable serum levels. This system, released markers of activity, or RMAs enable measurement of transgene expression in the brain through a simple blood test. RMAs are stable in blood, with a half-life of >100 h and can detect expression from as few as 12 neurons in mice. However, their long serum half-life also generates long-lasting background signals when RMA are used to track temporal changes in gene expression. By engineering on-demand erasable RMAs and injecting an intravenous targeted protease, we reduced RMA background signal by more than an order of magnitude without compromising the detection sensitivity. Similarly to previous RMA iteration, our approach showed a 65,000-fold increase in their signal over the baseline when expressed in a single brain region. Furthermore, we demonstrated that this erasable RMA system improves the dynamic range of detection for low-level promoter activity that is driven by physiological levels of c-Fos.

bioengineering↗

bioRxiv2025

Site-Specific Noninvasive Delivery of Retrograde Viral Vectors to the Brain

Neuronal activity underlies the brain function. Different behaviors, physiological processes, and disorders depend on which neurons are active at a given moment. Treating brain disorders without side effects will require exclusive control of disease-relevant neurons. Traditionally, small molecule drugs could control a subset of neurons that express a molecularly specific receptor. Local noninvasive therapies such as delivery of neuromodulatory agents with focused ultrasound blood-brain barrier opening (FUS-BBBO) also added spatial precision allowing one to control specific brain regions without surgery. However, the final characteristic of neurons, which other neurons they connect to, remains underexplored as a therapeutic target. If targeting neurons based on their connectivity was possible noninvasively, it would open the doors to broadly deployable precise therapies that can target selected subgroups of neurons within a brain region. Such delivery could be achieved with retrograde-tracing adeno-associated viral vectors (AAVs). For noninvasive delivery with FUS-BBBO, AAV9 has emerged as the most promising serotype. However, its retrograde-tracing version, the AAV9.retro, has not been evaluated for FUS-BBBO delivery. Here, we show that following such noninvasive delivery AAV9.retro can safely transduce neuronal projections with comparable efficiency to a direct intracranial injection. Compared to AAV8, a naturally occurring vector with low retrograde transduction, AAV9.retro offers superior retrograde transduction and comparable transduction at the site of delivery. Overall, we show that AAV9.retro is a valuable FUS-BBBO gene delivery vector, while also highlighting the surprising possibility of improved specificity of transduction of projections compared to invasive delivery.

bioengineering↗

bioRxiv2024

Monitoring in vivo transcription with synthetic serum markers

Understanding transcription profiles of living tissues is critical for biology and medicine. However, measurement of the transcript levels is typically done in homogenized tissues post-mortem. Here, we present a new platform that enables non-invasive monitoring of specific mRNA levels in vivo, without tissue destruction. We achieved this by combining two cutting-edge tools - synthetic serum markers, called Released Markers of Activity (RMAs), and RNA-based sensors of transcription. We call this platform IN-vivo Tracking of ACtive Transcription, or INTACT. In INTACT, when the target mRNA is expressed, the RNA sensor detects it and triggers the production and release of RMA reporters into the blood. Once in blood, the RMAs can be easily measured through a simple blood draw. Our data shows that INTACT can measure transcription of transgenes, as well as endogenous transcripts, such as c-Fos or Arc, both in vivo in the brain and in tissue culture. INTACT enables simple measurement of transcript level histories in genetically-targetable cell populations of living animals.

bioengineering↗

bioRxiv2023

Engineering Regionally-Activated Drugs for Neuroscience

The brain is comprised of multiple regions performing distinct functions. Within each of these regions, there are multiple cell types that can affect brain physiology. Finally, within each cell there are multiple signaling pathways, that, when activated or inhibited, control the cells activity, and consequently the brain function. For these reasons, methods that can control the brain with regional, cell-type, and molecular precision have been widely used in neuroscience. However, so far, achieving sustained control over a brain region with that level of specificity relied either on gene delivery or placement of invasive devices. While gene therapy holds great promise, the risks of genomic integration, vector toxicity, vector-directed immune response, high cost, and gene delivery to the brain pose significant challenges. On the other hand, invasive devices enable site-specific delivery of drugs but can also surgically damage the modulated brain region, carrying risks of infection and hemorrhage. Here, we present a new approach that can provide multi-day, noninvasive, site-specific control over specific cell types in the brain without the need to use invasive devices or gene delivery. To achieve this, we introduce a new paradigm called Regionally Activated Interstitial Drugs, or RAID, which delivers a protein-based catalytic centers, or RAID enzymes, to the brain using focused ultrasound blood-brain barrier opening. This catalytic center is designed to attach to the interstitial space in the brain where it remains for days after initial delivery. While the catalytic center is present in the brain, it can locally process an inert BBB permeable prodrug into an active drug, resulting in localized therapy. Our proof-of concept studies demonstrated that the engineered RAID enzymes can retain activity in the brain parenchyma for several days, allowing for noninvasive site-specific induction of neuronal activity that was sufficiently potent to elicit behavioral effects. Overall, the RAID paradigm enabled noninvasive, tunable, temporally-re-solved, site-specific, non-genetic, neuromodulation over multiple days. The RAID paradigm is versatile and can be applied to any enzyme and prodrug pair to control various aspects of central nervous system physiology.

bioengineering↗

bioRxiv2023

Acoustically Targeted Noninvasive Gene Therapy in Large Brain Regions

Focused Ultrasound Blood-Brain Barrier Opening (FUS-BBBO) can deliver adeno-associated viral vectors (AAVs) to treat genetic disorders of the brain. However, such disorders often affect large brain regions. Moreover, the applicability of FUS-BBBO in the treatment of brain-wide genetic disorders has not yet been evaluated. Herein, we evaluated the transduction efficiency and safety of opening up to 105 sites simultaneously. Increasing the number of targeted sites increased gene delivery efficiency at each site. We achieved transduction of up to 60% of brain cells with comparable efficiency in the majority of the brain regions. Furthermore, gene delivery with FUS-BBBO was safe even when all 105 sites were targeted simultaneously without negative effects on animal weight, neuronal loss, or astrocyte activation. To evaluate the application of multi-site FUS-BBBO for gene therapy, we used it for gene editing using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, and found effective gene editing, but also a loss of neurons at the targeted sites. Overall, this study provides a brain-wide map of transduction efficiency and the first example of gene editing after site-specific noninvasive gene delivery to a large brain region.

bioengineering↗

bioRxiv2022

Engineered Serum Markers for Noninvasive Monitoring of Gene Expression in the Brain

Noninvasive efforts to map brain gene expression have been hampered by low sensitivity and limited access to the brain. Here, we introduce a new platform that enables multiplexed, noninvasive, and site-specific monitoring of brain gene expression through a novel class of engineered reporters called Released Markers of Activity (RMAs). Instead of detecting gene expression in the less accessible brain, RMA reporters exit from a known brain region into the blood, where they can be easily measured with biochemical techniques. Expressing RMAs at a single brain site, typically covering [~]1% of the brain volume, provides up to a 39,000-fold signal increase over the baseline in vivo. Further, expression of RMAs in as few as several hundred neurons was sufficient for their reliable detection. When placed under a promoter upregulated by neuronal activity, RMAs could be used to measure neuronal activity in specific brain regions with a simple blood draw. We found that chemogenetic activation of cells expressing Fos-responsive RMA increased serum levels of RMA over 4-fold compared to non-activated controls. By contrast, a control RMA expressed under a constitutive neuronal promoter did not show such upregulation, demonstrating multiplexed ratiometric measurement with RMAs and proving specificity of neuronal activity discrimination. Together, our study pioneers a new noninvasive paradigm for repeatable and multiplexed monitoring of gene expression in an intact brain with sensitivity that is currently unavailable through other noninvasive gene expression reporter systems.

neuroscience↗