Biology subjects

Ji, R.

Publications and source records attributed to Ji, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparison of sodium azide- and cooling-based immobilization methods for Caenorhabditis elegans chemotaxis assays

Chemotaxis assays are widely used to quantify sensory-driven behavioral responses in Caenorhabditis elegans. Sodium azide is commonly used to immobilize animals at assay endpoints, although concerns have been raised that diffusion beyond the endpoint region could affect behavior before a choice is completed. We compared sodium azide-mediated immobilization with post-assay cooling using the repellent 1-octanol and attractant diacetyl. Wild-type animals showed robust avoidance of 30% 1-octanol and attraction to 0.5% diacetyl with either method, across multiple assay durations, and with or without worm food Escherichia coli OP50. These results support post-assay cooling as an alternative endpoint-scoring method.

animal behavior and cognition↗

bioRxiv2026

Benchmarking single-cell foundation models for aging biology

Single cell foundation models (scFMs) provide representations of cellular states, but their utility across biological questions in aging research remains unclear. We established a benchmark of cellular representations for aging research, evaluating ten general-purpose scFMs, three aging-specific models and conventional methods across five biological questions using more than 2.5 million single cell transcriptomes. Using frozen pretrained representations, Geneformer performed best among scFMs for chronological age prediction and age pseudotime concordance, although 2,000 highly variable genes achieved higher mean performance. Several scFMs captured positive molecular age shifts across three disease contexts, consistent with reported aging-associated changes. SCimilarity performed well for rare cellular state identification across out-of-distribution datasets, exceeding aging specific models and conventional baselines. At the gene level, scGPT showed the highest recovery of reference TF target interactions, including aging-related regulatory hubs. Overall, scFMs supported diverse aging analyses, but performance depended on the biological question, highlighting their utility for rare cellular state identification and regulatory analysis.

bioinformatics↗

bioRxiv2026

Pervasive Backdoor Vulnerabilities in Genomic Foundation Models

Genomic foundation models are increasingly used to interpret and design DNA sequences, yet their susceptibility to training-data manipulation remains poorly understood. Here we systematically evaluate backdoor poisoning across three model families, seven parameter scales ranging from 50 million to 7 billion, and 18 genomic classification tasks. We introduce two complementary 48-nucleotide triggers: a composition-matched synthetic sequence and a biologically grounded trigger derived from transposon terminal inverted repeats. Poisoning 5% of the training data induced high attack success rates across all tested models, with model-level median values ranging from 91.4% to 100%. Increasing parameter scale did not consistently improve resistance, whereas poisoning rate and trigger length had stronger effects on attack efficacy. Performance on unmodified sequences was generally preserved, with 79.4% of model - task - trigger configurations changing by no more than two percentage points, although larger task-specific losses occurred. We further developed a two-stage defense that combines single-nucleotide mutation-sensitivity screening with reference-database validation. Across 28 evaluated configurations, the method achieved 100% precision and a median recall of 92.95%, while localizing the trigger in nearly all detected poisoned sequences. These findings establish training-data poisoning as a pervasive and difficult-to-detect vulnerability in genomic foundation models and motivate stronger data-provenance controls, adversarial evaluation and post-training security auditing.

bioinformatics↗

bioRxiv2026

Kinetic model of a determinate legume root nodule reveals plant metabolic characteristics for more efficient nitrogen fixation symbiosis

While nitrogen fertilizers are widely used in agricultural production, their application incurs significant environmental and energetic costs. In contrast, some crops are less dependent on these fertilizers because they engage in symbioses with rhizobia, nitrogen-fixing bacteria provide ammonium to the plant in exchange for carbon. However, the carbon cost associated with nitrogen fixation can negatively impact crop yields. Improving the efficiency of this metabolic process could alleviate this impact on crop productivity. Mathematical models can help us quantitatively explore metabolic behavior and identify potential targets for metabolic engineering. In this work, we developed a kinetic model of determinate root nodule metabolism, where this symbiotic exchange of carbon from the plant and nitrogen from the bacteria occurs. We used this model to evaluate how the predicted metabolic behavior differs between inefficient and efficient nodules, and to identify potential engineering targets for improving nitrogen fixation efficiency and rate. We show that the enzymes phosphoenolpyruvate carboxylase and pyruvate kinase have significant influence on the predicted rate and efficiency of nitrogen fixation, especially when their expression is varied in combination with oxidative Pentose Phosphate Pathway enzymes like glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase. The model predicts that pairing a 3-fold decrease in glucose-6-phosphate dehydrogenase activity along with either a 3-fold increase in phosphoenolpyruvate carboxylase activity or decrease in pyruvate kinase activity could increase nitrogen fixation rate by 5.51% while improving nitrogen fixation efficiency by 7.74%.

plant biology↗

bioRxiv2026

Polyclonal-Monoclonal Transition in Lung Squamous Cell Carcinoma Evolution

The evolutionary trajectory of lung squamous cell carcinoma (LUSC) remains poorly defined, hindering the development of effective therapies. By integrating genomic and transcriptomic sequencing from human LUSC specimens, we delineated a polyclonal-to-monoclonal evolutionary trajectory during LUSC progression. This evolutionary pattern was corroborated by single-cell RNA sequencing, which revealed consistent tumor cell heterogeneity. Specifically, the SBS5 mutational signature was enriched and correlated with poor prognosis independent of tumor stage. By further utilizing the spontaneous LUSC mouse model to identify key genomic and genetic events in LUSC progression, we observed that the JNK pathway was inhibited and that cytoskeleton-related pathways were dysregulated during LUSC development, and identified the mutations in the JNK pathway (e.g., DACT1) and cytoskeletal regulators (e.g., KIF26A). Collectively, these findings established a polyclonal-monoclonal evolution paradigm for LUSC, potentially regulated by JNK pathways, which could benefit LUSC precision therapeutics.

genomics↗

bioRxiv2026

Pharmacological recruitment of a VTA glutamatergic arousal circuit by the natural product BN3 drives broad-spectrum emergence from general anesthesia

Pharmacological control of emergence from general anesthesia remains strikingly limited. Clinically available antagonists are largely drug-class specific, leaving recovery dependent on anesthetic clearance rather than to an actively programmable switch in brain state. Through phenotypic screening of a structurally diverse natural-product library, we identified BN3 (L-(-)-camphor) as a broad-spectrum emergence agent. BN3 robustly shortened recovery from propofol anesthesia across species--from mice and rats to rabbits, dogs, and rhesus monkeys--and remained effective after continuous infusion. In rodents, BN3 also accelerated emergence from mechanistically distinct anesthetics, including etomidate, remimazolam, sodium {gamma} - hydroxybutyrate, midazolam, ketamine, sodium pentobarbital, and isoflurane. EEG recordings revealed a rapid cortical shift from slow-wave dominance to a wake-like high-frequency spectrum. Mechanistically, BN3 preferentially recruited ventral tegmental area (VTA) glutamatergic neurons: chemogenetic silencing abolished the BN3-evoked EEG spectral shift and strongly attenuated behavioral acceleration of emergence, whereas optogenetic activation of these neurons was sufficient to promote recovery. BN3 increased glutamate release in the nucleus accumbens and medial prefrontal cortex, and projection-specific inhibition of VTA[->]NAc or VTA[->]mPFC outputs blunted BN3-induced emergence. These findings define a VTA-centered glutamatergic arousal circuit that can be pharmacologically recruited as a common gateway for anesthetic-independent emergence.

neuroscience↗

bioRxiv2026

Targeting FGFR signaling overcomes therapeutic resistance and immune evasion in oncogenic PIK3CA-driven serous-like endometrial cancer

Serous endometrial cancer (SEC) is an aggressive subtype of endometrial cancer (EC) with poor prognosis and limited treatment options. Here, we developed a clinically relevant, immunocompetent serous-like mouse model incorporating oncogenic PIK3CA mutation, Trp53 loss, and MYC overexpression. Using this model together with human EC cell lines, patient-derived organoids (PDOs), xenografts, and patient datasets, we investigated mechanisms underlying resistance to PI3K-targeted therapy. Single-cell profiling reveals that FGFR1/2 upregulation associates with intrinsic resistance, whereas FGFR3 characterizes acquired resistance. Dual FGFR and PI3K inhibition produced superior tumor control compared with either agent alone. Mechanistically, FGFR signaling promotes immune evasion by downregulating MHC-I/HLA-mediated antigen presentation and enriching M2-type tumor-associated macrophages. FGFR inhibition reversed these changes and synergized with anti-PD-1 therapy to enhance antitumor immune responses and establish durable immune memory. Collectively, these findings identify FGFR signaling as a key driver of therapeutic resistance and immune escape in SEC and support FGFR-targeted combination strategies.

cancer biology↗

bioRxiv2025

Modeling patient tissues at molecular resolution with Eva

Tissue structure is essential to function and homeostasis in all organs, and disruptions to structure usually indicate disease. Modeling relationships between structural, molecular, and clinical aspects of tissues could advance new diagnostics and treatment strategies. Although profiling techniques like spatial proteomics can capture these relationships, the data remain challenging to extract insight from. Here, we present Eva, a foundation model for tissue imaging data that learns multi-scale spatial representations of tissues at the molecular, cellular, and sample level. Eva uses a novel vision transformer architecture and is pre-trained on masked reconstruction of over 40 million matched spatial proteomics and histopathology images. We show that Eva excels at a variety of tasks, including cross-modal inference from H&E to proteomics stains, quality control, data annotation, zero-shot retrieval, survival modeling, and patient stratification. Extensive evaluations on held-out validation data demonstrate the versatility and generalizability of the learned embeddings. We anticipate that Eva will accelerate translational science by bridging basic research and clinical practice.

bioinformatics↗

bioRxiv2025

Predicting and Designing Red Fluorescent Protein Variants Using Sequence-to-Function Machine Learning Models

Fluorescent proteins (FPs) are widely used reporters for visualizing cellular structures and processes. Traditional wet-lab strategies for FP engineering (rational design and directed evolution) have enabled substantial improvements in photophysical performance but are limited by their requirement for deep expert knowledge or labor-intensive screening. AI-driven approaches have recently gained traction for engineering variants of green FPs, yet applications to red fluorescent proteins (RFPs) remain scarce. Here, we applied machine learning models to an RFP sequence-function dataset and trained these models to predict functional single-mutation variants of the state-of-the-art RFP mScarlet-I3. Guided by model predictions, we identified variants exhibiting red-shifted emission peaks, large Stokes shifts, or brightness comparable to the parental protein. Our findings show that even lightweight, data-efficient models can extract actionable design principles for improving RFPs. This work demonstrates the feasibility of AI-guided design for RFPs and provides a reliable benchmark for future development of more powerful AI-driven strategies for FP engineering.

molecular biology↗

bioRxiv2025

IRG1/itaconate/NRF2/GSH axis in tumor-associated macrophages drives therapy resistance and immune evasion in BRCA1-deficient breast cancer

Tumor-associated macrophages (TAMs) are major contributors to immunosuppression and therapeutic resistance, including resistance to PARP inhibitors (PARPi) in BRCA1-deficient breast cancer. However, the mechanisms underlying TAM-mediated PARPi resistance remain unclear. Here, we demonstrate that TAM-derived glutathione (GSH) impairs the efficacy of PARPi by protecting tumor cells from DNA damage and ferroptosis while suppressing STING-mediated immune activation. Mechanistically, STAT5-driven upregulation of the IRG1/itaconate axis in TAMs rewires mitochondrial metabolism and activates NRF2-dependent GSH biosynthesis. GSH is subsequently released into the tumor microenvironment, where it is taken up by tumor cells, protecting them from PARPi-induced cytotoxicity and dampening immune responses. Pharmacological inhibition of IRG1 reverses these effects, restoring PARPi sensitivity and enhancing anti-tumor immunity in BRCA1-deficient tumor models. Collectively, these findings uncover a TAM-specific immunometabolic program that limits PARPi efficacy and highlight the IRG1/NRF2/GSH axis as a promising therapeutic target to improve treatment outcomes in BRCA1-associated breast cancer.

cancer biology↗

bioRxiv2025

Spatially variable growth responses to warming in Atlantic Sea Scallops (Placopecten magellanicus)

Atlantic sea scallop is an important commercial species in the U.S., and its growth rate is strongly modulated by temperature. In this study, we quantified the interannual variations in scallop growth rate and thermal stress intensity in the Mid-Atlantic Bight (MAB) from 2000 to 2018. The results showed that the scallop growth rate variations were overall synchronized between the shallow (< 60 m) and deep ([≥] 60 m) MAB prior to 2015. The response of growth rate to warming in 2015 and 2016 showed marked spatial heterogeneity: scallops in the shallow subregions grew more slowly in the warm years, whereas higher temperature contributed to elevated growth rates in the deep subregions. We developed a dynamic energy budget model to explain the distinct growth rate response to warming at different depths. The model results showed that, in 2016, bottom temperatures in the shallow subregions exceeded the optimal range, limiting the energy available for growth. In contrast, warming created more favorable thermal conditions in the deep habitats. This work reveals the spatiotemporal patterns of scallop growth rates in the MAB and contributes a quantitative understanding of thermal stress and the development of science-based management strategies under future warming.

ecology↗

bioRxiv2025

Probing the CaV1.2 interactome in heart failure identifies a positive modulator of inotropy and lusitropy

BackgroundMaladaptive changes in the function, expression and localization of proteins involved in calcium-handling worsen the impaired contractility of systolic heart failure (HF). Standard proteomics techniques require cell lysis and so are unable to characterize changes specific to the critical sub-cellular domain bounded by the T-tubule and the sarcoplasmic reticulum, known as the cardiac dyad. Traditional approaches are also less likely to capture low-affinity protein-protein interactions on lipid membranes. To improve our understanding of heart failure pathophysiology, we applied proximity proteomics to the cardiac dyad of mice with ischemic cardiomyopathy. MethodsUsing two lines of transgenic mice expressing fusion proteins of the engineered ascorbate peroxidase APEX2 with subunits of the cardiac voltage gated calcium channel, CaV1.2, we labeled the dyad proteome of live, intact myocytes from healthy mice (N=6) and mice with coronary artery ligation HF (N=5) by peroxidase-catalyzed biotinylation. Quantitative mass spectrometry with isobaric tandem mass tags (TMT) was used to assess alterations in the local dyad proteome in myocytes from mice with chronic, remodeled HF. We subsequently generated a mouse with inducible cardiac overexpression of Galectin-1 to examine the effects of this protein on cardiac function and more specifically on the calcium-handling properties of mature myocytes, using cellular electrophysiology, calcium imaging, and echocardiography. ResultsFrom mice with HF, we found significant enrichment of 43 proteins defined by their abundance and proximity to transgenic CaV1.2 1C channels, and a significant reduction in 22 proteins, out a of a total of 2326 proteins quantified. We also significantly enriched 286 proteins, and saw a reduction in 13 proteins, defined by proximity and abundance to CaV1.2 {beta}2B-subunits, out of a total 2236 proteins identified. Pathway analysis revealed HF is associated with increased abundance of components of the 26s proteasome and microtubules in the dyad, as well as the dimerizing, carbohydrate binding protein Galectin-1. Cardiac specific overexpression of Galectin-1 in healthy mice increases activation of CaV1.2 and the Ryanodine receptor and accelerates myocyte relaxation through phosphorylation of Phospholamban. ConclusionsUsing proximity proteomics to examine the effects of HF in vivo, we find increased localization of Galectin-1 to the cardiac dyad, and that overexpression of Galectin-1 accelerates calcium kinetics in the heart.

cell biology↗

bioRxiv2025

De novo Design of a Peptide Modulator to Reverse Sodium Channel Dysfunction Linked to Cardiac Arrhythmias and Epilepsy

Ion channels orchestrate electrical signaling in excitable cells. In nature, ion channel function is customized by modulatory proteins that have evolved to fulfill distinct physiological needs. Yet, engineering synthetic modulators that precisely tune ion channel function is challenging. One example involves the voltage-gated sodium (NaV) channel that initiates the action potential, and whose dysfunction amplifies late/persistent sodium current (INaL), a commonality that underlies various human diseases including cardiac arrhythmias and epilepsy. Here, using a computational protein design platform, we engineered a de novo peptide modulator, ELIXIR, that binds NaV channels with submicromolar affinity. Functional analysis revealed an unexpected selectivity in inhibiting pathogenic INaL and confirmed its effectiveness in reversing NaV dysfunction linked to both cardiac arrhythmias and epilepsy in cellular and murine models. These findings exemplify the efficacy of de novo protein design for engineering synthetic ion channel modulators and sets the stage for rational design of future therapeutic approaches.

biophysics↗

bioRxiv2025

Portable transcranial therapeutic ultrasound enhances targeted gene delivery for Parkinson's disease: from rodent models to non-human primates

Gene therapy for neurodegenerative diseases faces significant challenges due to the blood-brain barrier (BBB), which limits drug delivery to the central nervous system (CNS). While clinical trials for Parkinsons disease (PD) have progressed, administration of vectors expressing enzymatic or neurotrophic factor transgenes have required extensive optimization of the delivery method to achieve potentially therapeutic levels of transgene expression. Focused ultrasound (FUS) combined with microbubbles has emerged as a promising non-invasive strategy to transiently open the BBB for targeted gene delivery via viral nanocarriers including recombinant adeno-associated viruses (AAVs). However, key factors influencing FUS-mediated AAV delivery, including dose distribution and therapeutic efficacy, remain underexplored in non-human primates (NHPs). Here, we evaluated the feasibility of AAV9-CAG-GFP delivery using two portable therapeutic ultrasound modalities: ultrasound-guided, spherically-focused FUS (USgFUS) and a novel low-frequency linear array configuration for imaging and therapy called theranostic ultrasound (ThUS). In mice, FUS-sonicated regions exhibited a 25-fold increase in AAV9 biodistribution compared to systemic injection alone. Extending this approach to NHPs, we observed up to a 200-fold increase in AAV9 DNA in treated brain regions, including PD-relevant structures. In assessing the translational therapeutic potential of this technique, ThUS-mediated AAV9-hSyn-hNTRN (human neurturin) delivery in a toxin mouse model of PD facilitated the rescue of up to 80% and 75% of degenerated dopaminergic neurons in the substantia nigra and striatum, respectively. These findings demonstrate that portable ultrasound technologies can non-invasively enhance AAV9 delivery to targeted brain regions in both mice and NHPs relative to what can be achieved with intravenous (IV) delivery of the same capsid alone. With further development, these approaches may offer a clinically viable, non-invasive alternative for gene therapy in neurodegenerative diseases. One sentence summaryBBB opening with portable therapeutic ultrasound non-invasively increased viral gene delivery to the brain after systemic AAV vector administration in mice and rhesus macaques.

bioengineering↗

bioRxiv2025

Metabolic modeling reveals synergistic growth benefits of engineering maize symbiosis with rhizobia and arbuscular mycorrhizal fungi

Engineering a novel N2-fixing rhizobia symbiosis in cereal crops is a strategy being pursued to improve agricultural sustainability. However, if such a symbiosis were introduced, it would have to be economically viable in the context of existing nutrient acquisition strategies, including the existing symbiosis with arbuscular mycorrhizal fungi (AMF) that the vast majority of plants already engage in. This raises the question of how the metabolic costs and benefits from these separate symbioses that have partially overlapping functions might impact nutrient status and subsequent plant growth. To address this, we developed metabolic models describing how the relative growth rate of Zea mays is impacted by the AMF Rhizophagus irregularis and a hypothetical N2-fixing symbiosis with Bradyrhizobium diazoefficiens both in isolation and in tandem. To validate the AMF component of our model, we conducted field evaluation of mutant AMF-incompatible maize hybrids and found that the empirically measured AMF-mediated growth benefit agreed well with our models predictions. Our model of the rhizobium symbiosis predicted that the lower N content of cereal crops makes the relative growth rate cost associated with acquiring nitrogen from N2-fixing rhizobia smaller than in legumes. Finally, our model also predicted positive synergies between rhizobia and AMF under nutrient-limited conditions but negative synergies under nutrient, particularly phosphorus, replete conditions. These findings indicate that these bioengineering strategies could improve cereal crop yields and may achieve greater gains in tandem, but soil nutrient status of target sites as well as the nitrogen requirements of specific varieties should be considered.

systems biology↗

bioRxiv2025

Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions

Focused ultrasound (FUS) with microbubbles opens the blood-brain barrier (BBB) to allow targeted drug delivery into the brain. The mechanisms by which endothelial cells (ECs) respond to either low acoustic pressures known to open the BBB transiently, or high acoustic pressures that cause brain damage, remain incompletely characterized. Here, we use a mouse strain where tight junctions between ECs are labelled with eGFP and apply FUS at low (450 kPa) and high (750 kPa) acoustic pressures, after which mice are sacrificed at 1 or 72 hours. We find that the EC response leading to FUS-mediated BBB opening at low pressures is localized primarily in arterioles and capillaries, and characterized by a transient loss and reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting that it is driven primarily by transient dismantlement and reorganization of tight junctions. In contrast, BBB opening at high pressures is associated with obliteration of EC tight junctions that remain unrepaired even after 72 hours, allowing continuous fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing of arteriole, capillary and venule ECs from FUS mice reveals that the transcriptomic responses of ECs exposed to high pressure are dominated by genes belonging to the stress response and cell junction disassembly at both 1 and 72 hours, while lower pressures induce primarily genes responsible for intracellular repair responses in ECs. Our findings suggest that at low pressures transient reorganization of tight junctions and repair responses mediate safe BBB opening for therapeutic delivery. Significance StatementFocused ultrasound with microbubbles is used as a noninvasive method to safely open the BBB at low acoustic pressures for therapeutic delivery into the CNS, but the mechanisms mediating this process remain unclear. Kugelman et al., demonstrate that FUS-mediated BBB opening at low pressures occurs primarily in arterioles and capillaries due to transient reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting a transcellular route-independent mechanism. At high unsafe pressures, cell junctions are obliterated and remain unrepaired even after 72 hours, allowing fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing supports cell biological findings that safe, FUS-mediated BBB opening may be driven by transient reorganization and repair of EC tight junctions.

bioengineering↗

bioRxiv2025

Characterization of Microbubble Cavitation in Theranostic Ultrasound-mediated Blood-Brain Barrier Opening and Gene Delivery

RationaleThe characterization of microbubble activity has proven critical in assessing the safety and efficacy of ultrasound-mediated blood-brain barrier (BBB) opening and drug and gene delivery. In this study, we build upon our previous work on theranostic ultrasound (ThUS)-mediated BBB opening (ThUS-BBBO) and conduct for the first time a comprehensive characterization of the role of microbubble cavitation in ThUS-BBBO, as well as its impact on gene delivery with adeno-associated viruses (AAV). MethodsA repurposed imaging phased array was used throughout the study to generate focused transmits and record microbubble activity through high-resolution power cavitation imaging (PCI). The cavitation of microbubbles under ThUS pulses was first characterized in flow phantom using pulse lengths ranging from 1.5 to 20 cycles and under varying microbubble flow rates using a separate single-element transducer a passive cavitation detector (PCD). A comprehensive in vivo study in mice was then conducted to characterize the in vivo microbubble activity under ThUS and correlate the resulting cavitation with AAV-mediated transgene delivery and expression. The transcranial microbubble activity was first detected in two mice using a PCD, to confirm the findings of the flow phantom study. Next, three mouse studies were conducted to evaluate the relationship between cavitation and AAV delivery; one with three different microbubble size distributions using polydisperse and size-isolated microbubbles, one with variable burst length and burst repetition frequency, and one with different AAV serotypes and injection doses. Electronic beam steering was used to induce bilateral BBB opening with 1.5 cycle on the left and 10 cycles on the right hemisphere. Cavitation dose was correlated with BBB opening volume, AAV transgene expression was evaluated with immunofluorescence staining and histological safety was assessed with T2* imaging and Hematoxylin and Eosin staining. ResultsFrequency domain analysis in the phantoms revealed a broadband-cavitation dominance at the shorter pulse lengths, while harmonic cavitation components are significantly increased for longer pulses. The PCD was better at detecting higher frequency harmonics, while the signal received by the theranostic array was more broadband dominated. Analysis of signals in the time domain showed that the longer pulses induce higher microbubble collapse compared to short pulses. In the transcranial in vivo experiments, the PCD was able to detect increased harmonic cavitation for 10-cycle pulses. The microbubble study showed that 3-5 m microbubbles resulted in the largest cavitation doses, BBBO volumes and AAV transgene expression compared to the smaller microbubble sizes. The burst sequence study revealed that the sequences with shorter bursts and faster burst repetition frequencies induce larger BBBO volumes and AAV transduction due to faster microbubble replenishment in the focal volume. Increased erythrocyte extravasation was observed on the hemisphere sonicated with 10-cycle pulses. Transgene expression was also increased with injection dose, without notable side effects during the three-week survival period. Finally, AAV9 was shown to be the serotype with the highest transduction efficiency compared to AAV2 and AAV5 at the same injected dose. ConclusionsThis is the first comprehensive study into the microbubble cavitation under theranostic ultrasound. The phantom and in vivo studies show that the mechanism of ThUS-BBBO is mainly transient cavitation dominant, as microbubble collapse increases with pulse length despite the increased harmonic frequency response. Increased cavitation dose resulted in larger BBBO volumes and transgene expression in vivo. While ThUS induced microhemorrhage for most of the studied conditions, it did not have an impact on the survival and behavior of the mice.

bioengineering↗

bioRxiv2024

Low hemoglobin causes hematoma expansion and poor intracerebral hemorrhage outcomes

ObjectivesAlthough lower hemoglobin levels associate with worse intracerebral hemorrhage (ICH) outcomes, causal drivers for this relationship remain unclear. We investigated the hypothesis that lower hemoglobin relates to increased hematoma expansion (HE) risk and poor outcomes using human observational data and assessed causal relationships using a translational murine model of anemia and ICH. MethodsICH patients with baseline hemoglobin measurements and serial CT neuroimaging enrolled between 2010-2016 to a multicenter, prospective observational cohort study were studied. Patients with systemic evidence of coagulopathy were excluded. Separate regression models assessed relationships of baseline hemoglobin with HE ([≥]33% and/or [≥]6mL growth) and poor long-term neurological outcomes (modified Rankin Scale 4-6) after adjusting for relevant covariates. Using a murine collagenase ICH model with serial neuroimaging in anemic vs. non-anemic C57/BL6 mice, intergroup differences in ICH lesion volume, ICH volume changes, and early mortality were assessed. ResultsAmong 1190 ICH patients analyzed, lower baseline hemoglobin levels associated with increased odds of HE (adjusted OR per -1g/dL hemoglobin decrement: 1.10 [1.02-1.19]) and poor 3-month clinical outcomes (adjusted OR per -1g/dL hemoglobin decrement: 1.11 [1.03-1.21]). Similar relationships were seen with poor 6 and 12-month outcomes. In our animal model, anemic mice had significantly greater ICH lesion expansion, final lesion volumes, and greater mortality, as compared to non-anemic mice. ConclusionsThese results, in a human cohort and a mouse model, provide novel evidence suggesting that anemia has causal roles in HE and poor ICH outcomes. Additional studies are required to clarify whether correcting anemia can improve these outcomes.

pathology↗