Biology subjects

Liang, N.

Publications and source records attributed to Liang, N..

At least 19 recordsLinked to original sources

bioRxiv2026

The effects of DNA repair factor-Cas9 fusions on homing drive performance

CRISPR-based homing gene drives achieve super-Mendelian inheritance by converting wild-type alleles into drive alleles through homology-directed repair (HDR). However, competing end-joining repair can generate resistance alleles that limit drive spread. Although fusing Cas9 to DNA repair-associated proteins has improved HDR in conventional genome editing systems, its effectiveness in gene drives remains unclear. Here, we systematically evaluated in Drosophila melanogaster eight Cas9 fusion constructs previously reported to improve HDR in other systems. Although none of the fusion constructs significantly increased HDR-associated signals in S2 cells, several candidates retained relatively high activity comparable to standard Cas9. These candidates were then tested in vivo across multiple split drive systems, regulatory elements, target loci, and parental sexes. Cas9-POLD3 significantly increased female drive inheritance in contexts with low baseline efficiency or substantial nonfunctional resistance formation, likely by increasing effective cutting rate and potentially also by biasing repair outcomes toward drive conversion. Cas9-Geminin degron generally maintained germline drive performance while reducing embryo resistance. Together, these findings identify Cas9-POLD3 and Cas9-Geminin degron as complementary, context-specific tools for enhancing drive conversion and limiting embryo resistance, respectively. These results highlight the importance of matching fusion modules to the regulatory and genetic context of individual drive systems.

genetics↗

bioRxiv2026

Rac1 and CHK1 Converge on Abi-1 to Regulate DNA Repair Dependency and Treatment Response in Human Cancers

Radiation therapy (RT) resistance remains a major clinical challenge, yet biomarkers guiding precision radiosensitization are lacking. We previously demonstrated that Rac1 promotes RT resistance in glioblastoma (GBM) by inducing Abi-1-S323 dephosphorylation and enhancing non-homologous end joining (NHEJ). Here, we identify Abi-1-S323 as a key regulator of DNA repair states and a determinant of therapeutic efficacy in human cancers. Clinically, loss of Abi-1-S323 phosphorylation was associated with poor outcomes in patients with RT-treated GBM. Bioinformatic analyses revealed that non-small cell lung cancer (NSCLC) and head and neck cancer (HNC) are among the cancers with frequent RAC1 amplification, suggesting that these tumor types may have increased Rac1-Abi-1 signaling activity. Loss of Abi-1-S323 phosphorylation also predicted poor outcomes in patients with RT-treated HNC. Consistent with these clinical observations, high Rac1 activity and low Abi-1-S323 phosphorylation were associated with enhanced DNA double-strand break repair and radioresistance in NSCLC and HNC models, whereas genetic or pharmacological inhibition of this signaling impaired DNA repair and radiosensitized tumors in vitro and in vivo. Mechanistically, we identified CHK1 as a kinase that phosphorylates Abi-1 at S323 and defines an alternative homologous recombination (HR)-dependent repair state. Tumors with high Rac1-Abi-1 signaling exhibited elevated NHEJ capacity and were selectively radiosensitized by Rac1 inhibition, whereas tumors with low Rac1-Abi-1 signaling displayed high CHK1 activity, preferentially relied on HR, and were selectively radiosensitized by CHK1 inhibition. These findings establish Abi-1-S323 as a biomarker defining therapeutically distinct DNA repair states and provide a framework for precision radiosensitization.

cancer biology↗

bioRxiv2026

CNS diseases cerebrospinal fluid single-cell atlas reveals immune characteristics of neuropsychiatric systemic lupus erythematosus

Neuropsychiatric systemic lupus erythematosus (NPSLE) is a potentially severe complication of systemic lupus erythematosus (SLE), yet its pathogenesis remains largely elusive. By jointly probing the immune dynamics of subjects cerebrospinal fluid (CSF) and peripheral blood, we showed that both innate and adaptive immune responses jointly contribute to the pathogenesis of NPSLE. In particular, we found the remarkable enrichment of BAM-CCL3, a subtype of border-associated macrophages with strong recruitment capacity, implicating its potential role in central nervous system (CNS) inflammation. We also observed pronounced activation of memory B cells and CD4+ regulatory T cells in NPSLE CSF, along with the preferential blood-to-CSF migration and subsequent within-CSF clonal expansion of CD8+ effector memory T cells in NPSLE patients, suggesting a persistent CNS-localized adaptive immune dysregulation. Finally, we developed the single-cell CNS disease CSF-Blood Atlas (scCDCB), a comprehensive collection for CSF and peripheral blood of multiple CNS diseases, which is publicly available at (https://sccdcb.gao-lab.org) to serve as a reference for future research on CNS diseases.

genomics↗

bioRxiv2025

Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance

Gene drive can control pathogen transmission or suppress vector populations by spreading drive alleles with super-Mendelian inheritance. CRISPR homing drive currently represents the most powerful type, and regulating Cas9 expression with specific promoters has been effective for improving drive performance. However, selecting these is often a major challenge. Here, we evaluated 35 Cas9 constructs driven by distinct promoters in different gene drive systems and identified associations between drive performance and single-cell RNA expression patterns of the promoter-associated genes. Our results indicate that higher drive conversion is significantly associated with elevated expression of the promoter-associated gene in the respective reproductive cells, but embryo resistance allele formation correlates with excessive female germline expression. For males, early germline expression produces superior performance. Thus, we find that optimal drive performance requires restricting Cas9 expression to a tight quantitative and spatiotemporal window. In addition, found that in situ integrated rhino-Cas9 constructs significantly reduce somatic expression, underscoring the importance of genomic locus. On the basis of these results, we propose criteria for selecting promoters, providing a theoretical rationale and practical guidance for optimization of promoter elements in homing gene drive systems.

genetics↗

bioRxiv2025

A simple growth model for tumor spheroids

Mathematical models of tumor spheroid growth provide essential insights into avascular tumor dynamics, hypoxia development, and treatment response. Here, we present a simple biophysically motivated growth model that integrates energy conservation, oxygen diffusion, and necrosis formation into a unified framework. The model captures the key features of spheroid development, including initial exponential growth, deceleration due to diffusion limitation, and growth inhibition mediated by necrotic tissue. Using published growth data from human colon carcinoma (HCC1), mouse colon carcinoma (MCC26), V79 fibroblasts, and EMT6-Ro spheroids, we demonstrate that the model accurately reproduces observed growth kinetics across multiple phases. Importantly, the model predicts viable rim thickness and oxygen distribution over time, in agreement with theoretical expectations. Fitted parameters further enable estimation of single-cell mass, oxygen consumption rate, and the energetic cost of cell production. By linking geometry, metabolism, and growth regulation, this minimal model offers a transparent yet quantitative description of tumor spheroid behavior, with potential applications in radiobiology and therapy modeling.

biophysics↗

bioRxiv2025

A systematic delineation of 3'UTR regulatory elements and their contextual associations

The 3'UTR encodes regulatory information that shapes transcript abundance and subcellular distribution, yet the underlying sequence rules remain incompletely defined. Using SEERS, we quantified the effects of [~]2 million synthetic 3'UTR inserts in A549 and HCT116 cells on RNA output and nuclear-cytoplasmic partitioning. We identify a broad repertoire of short (2[~]8 nt) elements whose effects largely align along a major coupled axis that links high expression with cytoplasmic enrichment and low expression with nuclear enrichment, and contribute predominantly in an additive manner. A context-aware deep learning model (TALE) captures most of this behavior while revealing that strong context dependence is uncommon and emerges mainly in rare, extreme contexts consistent with higher-order constraints. Applying TALE to ClinVar 3'UTR variants prioritizes a subset of pathogenic SNVs with aberrant predicted effects, frequently explained by creation or disruption of splice-site-like U1 telescripting signals, highlighting a potent route to 3'UTR-driven disease mechanisms.

genomics↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗

bioRxiv2025

An autonomous AI agent for universal behavior analysis

Behavior analysis across species represents a fundamental challenge in neuroscience, psychology, and ethology, typically requiring extensive expert knowledge and labor-intensive processes that limit research scalability and accessibility. We introduce BehaveAgent, an autonomous multimodal AI agent designed to automate behavior analysis from video input without retraining or manual intervention. Unlike conventional methods that require manual behavior annotation, video segmentation, task-specific model training, BehaveAgent leverages the reasoning capabilities of multimodal large language models (LLM) to generalize across novel behavioral domains without need for additional training. It integrates LLMs, vision-language models (VLMs), and large-scale visual grounding modules, orchestrated through a multimodal context memory and goal-directed attention mechanism, to enable robust zero-shot visual reasoning across species and experimental paradigms, including plants, insects, rodents, primates, and humans. Upon receiving a video input, BehaveAgent autonomously identifies the correct analysis strategy and performs end-to-end behavior analysis and interpretation without human supervision. Leveraging vision-language representations, it performs general-purpose tracking, pose estimation and segmentation. We demonstrate BehaveAgents universal applicability to autonomously (1) identify the behavioral paradigm and develop an action plan specialized for the identified paradigm, (2) identify relevant subjects and objects, (3) track those features, (4) identify behavioral sequences with explicit reasoning, (5) generate and execute code for targeted analysis and (6) generate comprehensive research reports that integrate behavioral findings with relevant scientific literature. Through interpretable agentic reasoning, BehaveAgent makes its internal decision-making process transparent, clarifying why particular features are tracked or behaviors inferred. By reducing the time and expertise required for behavior analysis, BehaveAgent introduces a scalable, generalizable, and explainable paradigm for advancing biological and behavioral research.

neuroscience↗

bioRxiv2025

Whey Protein Phospholipid Concentrate Supplementation Prevents High-Fat Diet Induced Cognitive Impairment in Wistar Rats by Promoting Brain Neuronal Connectivity and Sphingolipid Clearance

Whey protein phospholipid concentrate (WPPC), a byproduct of whey protein processing, is high in phospholipids and glycoconjugates which serve as substrates for fatty acids and sugar monomers (e.g. sialic acid) critical to neuronal myelin synthesis in the brain. This led us to hypothesize that WPPC will improve cognitive impairment induced by a high fat (HF) diet by promoting myelin turnover and improving myelin-dependent processes associated with encoding and storing memory. Male Wistar rats were randomized to one of four diets starting at weaning to [~]6.5 months on age: a low-fat (LF) diet containing 10% fat by weight, a HF diet containing 45% fat by weight to induce cognitive impairment, and a HF diet containing either 1.6% or 10% WPPC by weight (n=12 per diet). Rats were subjected to cognitive testing after 2 and 4 months of dietary intervention and then implanted with chronic bipolar electrodes to measure axonal evoked responses within the entorhinal cortex-hippocampal circuitry. Phospholipid and sphingolipid components of myelin were quantified in the hippocampus. There were no significant differences in cognition measured by novel object recognition after 2 months of supplementation. At 4 months, rats on the HF diet performed significantly worse than rats on the LF, HF1.6 and HF10 diets. The beneficial effects of WPPC on cognition were due to a partial reversal in evoked response impairments in hippocampal memory storage. Additionally, hippocampus sphingolipids were higher in rats on the HF diet compared to the LF, HF1.6 and HF10 groups. These findings demonstrate that WPPC prevented cognitive impairment induced by a HF diet by regulating entorhinal cortex-hippocampal circuitries associated with memory storage, though modulating myelin turnover.

neuroscience↗

bioRxiv2025

Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo

Spatial transcriptomics has revolutionized our understanding of tissue organization by simultaneously capturing gene expression and spatial localization within intact tissues. However, analyzing these increasingly complex datasets requires specialized expertise across computational biology, statistics, and biological context. To address this challenge, we introduce the Spatial Transcriptomics AI Agent (STAgent), an autonomous multimodal agentic AI that integrates multimodal large language models (LLMs) with specialized computational tools to transform weeks-long analysis tasks into minutes of automated processing. Unlike conventional machine learning approaches that are limited to narrow, predefined tasks, STAgent leverages the emergent capabilities of multimodal LLMs - such as flexible reasoning, contextual understanding, and cross-modal integration - which allow it to adapt to novel data, execute multi-step analyses, and generate biologically meaningful insights with minimal human input. STAgent enables autonomous deep research through integrated capabilities, including dynamic code generation for complex analytical workflows, visual reasoning for interpreting spatial patterns, real-time retrieval of relevant peer-reviewd scientific literature, and synthesis of comprehensive, actionable reports. We applied STAgent to investigate the in vivo maturation of human stem cell-derived pancreatic cells (SC-pancreas) transplanted into immunodeficient mice. We generated single-cell spatial transcriptomics data spanning multiple developmental timepoints. STAgent autonomously (1) identified the maturation of initially scattered endocrine cells into well-defined islet-like structures, with predominantly peripheral -cells surrounding {beta}-cell cores supported by an expanding mesenchymal network; (2) revealed strengthening endocrine-endocrine cell interactions over time and, through context-aware gene set analysis, uncovered spatially resolved biological processes driving maturation; (3) unlike traditional analytical approaches, STAgent offers mechanistic explanations of spatial patterns, contextualizing findings with relevant literatures and developing cohesive insights into human pancreatic development. This agentic approach establishes a new paradigm in spatial transcriptomics analysis by substantially lowering the expertise barrier and reducing analysis time, accelerating biological and biomedical discovery.

genomics↗

bioRxiv2025

Metabolic Alteration in Oxylipins and Endocannabinoids Point to an Important Role for Soluble Epoxide Hydrolase and Inflammation in Alzheimer's Disease - Finding from Alzheimer's Disease Neuroimaging Initiative.

Mounting evidence implicates inflammation as a key factor in Alzheimers disease (AD) development. We previously identified pro-inflammatory soluble epoxide hydrolase (sEH) metabolites to be elevated in plasma and CSF of AD patients and to be associated with lower cognition in non-AD subjects. Soluble epoxide hydrolase is a key enzyme converting anti-inflammatory epoxy fatty acids to pro-inflammatory diols, reported to be elevated in multiple cardiometabolic disorders. Here we analyzed over 700 fasting plasma samples from the baseline of Alzheimers Disease Neuroimaging Initiative (ADNI) 2/GO study. We applied targeted mass spectrometry method to provide absolute quantifications of over 150 metabolites from oxylipin and endocannabinoids pathway, interrogating the role for inflammation/immune dysregulation and the key enzyme soluble epoxide hydrolase in AD. We provide further insights into the regulation of this pathway in different disease stages, APOE genotypes and between sexes. Additionally, we investigated in mild cognitive impaired (MCI) patients, metabolic signatures that inform about resilience to progression and conversion to AD. Key findings include I) confirmed disruption in this key central pathway of inflammation and pointed to dysregulation of sEH in AD with sex and disease stage differences; II) identified markers of disease progression and cognitive resilience using sex and ApoE genotype stratified analysis highlighting an important role for bile acids, lipid peroxidation and stress response hormone cortisol. In conclusion, we provide molecular insights into a central pathway of inflammation and links to cognitive dysfunction, suggesting novel therapeutic approaches that are based on targeting inflammation tailored for subgroups of individuals based on their sex, APOE genotype and their metabolic profile.

neuroscience↗

bioRxiv2025

LINC01503-MP is a Mitochondrial Microprotein That Promotes Cell Proliferation and Oxidative Metabolism.

Long non-coding RNAs (lncRNAs) are well-established as key regulators of gene expression. However, emerging evidence reveals that some lncRNAs can also encode functional microproteins. In this study, we report the identification of an evolutionarily young microprotein encoded by LINC01503, expressed across several human tissues. This microprotein, designated as LINC01503-MP, localises to the mitochondria and exerts a proliferative effect on HCT116 colorectal cancer (CRC) cells. Functional studies reveal that LINC01503-MP regulates mitochondrial oxygen consumption rate, linking its activity to enhanced metabolic functions and cell proliferation. Interactome analyses identified multiple mitochondrial metabolism-related proteins as potential interaction partners. Our findings show that LINC01503-MP plays a role in the proliferative phenotype associated with LINC01503 upregulation in CRC, suggesting the functional significance of evolutionarily young, lncRNA-derived microproteins in cancer progression.

molecular biology↗

bioRxiv2025

APOE Genotype Influences on The Brain Metabolome of Aging Mice - Role for Mitochondrial Energetics in Mechanisms of Resilience in APOE2 Genotype.

Alzheimers disease (AD) risk and progression are significantly influenced by APOE genotype with APOE4 increasing and APOE2 decreasing susceptibility compared to APOE3. While the effect of those genotypes was extensively studied on blood metabolome, less is known about their impact in the brain. Here we investigated the impacts of APOE genotypes and aging on brain metabolic profiles across the lifespan, using human APOE-targeted replacement mice. Biocrates P180 targeted metabolomics platform was used to measure a broad range of metabolites probing various metabolic processes. In all genotypes investigated we report changes in acylcarnitines, biogenic amines, amino acids, phospholipids and sphingomyelins during aging. The decreased ratio of medium to long-chain acylcarnitine suggests a reduced level of fatty acid {beta}-oxidation and thus the possibility of mitochondrial dysfunction as these animals age. Additionally, aging APOE2/2 mice had altered branch-chain amino acids (BCAA) profile and increased their downstream metabolite C5 acylcarnitine, indicating increased branched-chain amino acid utilization in TCA cycle and better energetic profile endowed by this protective genotype. We compared these results with human dorsolateral prefrontal cortex metabolomic data from the Religious Orders Study/Memory and Aging Project, and we found that the carriers of APOE2/3 genotype had lower markers of impaired BCAA katabolism, including tiglyl carnitine, methylmalonate and 3-methylglutaconate. In summary, these results suggest a potential involvement of the APOE2 genotype in BCAA utilization in the TCA cycle and nominate these humanized APOE mouse models for further study of APOE in AD, brain aging, and brain BCAA utilization for energy. We have previously shown lower plasma BCAA to be associated with incident dementia, and their higher levels in brain with AD pathology and cognitive impairment. Those findings together with our current results could potentially explain the AD-protective effect of APOE2 genotype by enabling higher utilization of BCAA for energy during the decline of fatty acid {beta}-oxidation.

systems biology↗

bioRxiv2025

Spike sorting AI agent

Spike sorting is a fundamental process for decoding neural activity, involving preprocessing, spike detection, feature extraction, clustering, and validation. However, conventional spike sorting methods are highly fragmented, labor-intensive, and heavily reliant on expert manual curation, limiting their scalability and reproducibility. This challenge has become more pressing with advances in neural recording technology, such as high-density Neuropixels for large-scale neural recording or flexible electrodes for long-term stable recording over months to years. The volume and complexity of these datasets make manual curation infeasible, requiring an automated and scalable solution. Here, we introduce SpikeAgent, a multimodal large language model (LLM)-based AI agent that automates and standardizes the entire spike sorting pipeline. Unlike traditional approaches, SpikeAgent integrates multiple LLM backends, coding functions, and established algorithms, autonomously performing spike sorting with reasoning-based decision-making and real-time interaction with intermediate results. It generates interpretable reports, providing transparent justifications for each sorting decision, enhancing transparency and reliability. We benchmarked SpikeAgent against human experts across various neural recording technology, demonstrating its versatility and ability to achieve curation consistency that are equal to, or even higher than human experts. It also drastically reduces the expertise barrier and accelerates the curation and validation time by orders of magnitude. Moreover, it enables automated interpretability of the neural spiking data, which cannot be achieved by any conventional methods. SpikeAgent presents a paradigm shift in processing signals for neuroscience and brain-computer interfaces, while laying the ground for AI agent-augmented science across various domains.

neuroscience↗

bioRxiv2024

Quantify genetic variants' regulatory potential via a hybrid sequence-oriented model

Understanding how noncoding DNA determines gene expression is critical for decoding the functional genome. Leveraging a hybrid sequence-oriented architecture, we developed SVEN to model (and predict) tissue-specific transcriptomic impacts for large-scale structural variants across over 200 tissues and cell lines. We expect that SVEN will enable more effective in silico analysis and interpretation of human genome-wide disease-related genetic variants.

bioinformatics↗

bioRxiv2023

A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance

CRISPR homing gene drive is a potent technology with considerable potential for managing populations of medically and agriculturally significant insects. It induces a bias in the inheritance of the drive allele in progeny, rapidly spreading desired genes throughout the population. Homing drives operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome. However, resistance alleles formed by end-joining repair pose a significant obstacle to the spread of the drive. To address this challenge, we created a homing drive targeting the essential but haplosufficient hairy gene. Our strategy involves spreading the drive construct through the homing process, eliminating nonfunctional resistance, which are recessive lethal, while rescuing drive-carrying individuals with a recoded version of hairy. This strategy eliminates resistance more slowly than a previous strategy targeting haplolethal genes, but it may be easier to construct in non-model organisms. Our drive inheritance rate was moderate, and multigenerational cage studies showed quick drive spread to 96-97% of the population. However, the drive failed to reach the whole population due to the formation of functional resistance alleles, despite use of four gRNAs, a strategy that previously was successful at preventing functional resistance. Sequencing showed that these alleles had a large deletion and must have utilized an alternate start codon. The resistance allele had a modest fitness advantage over the drive in a cage study, which could prevent long-term persistence of the drive, especially if cargo genes had an additional fitness cost. Thus, revised design strategies targeting more essential regions of a target gene may often be necessary to avoid such functional resistance, even when using multiplexed gRNAs.

synthetic biology↗

bioRxiv2023

Piezo inhibition prevents and rescues scarring by targeting the adipocyte to fibroblast transition

While past studies have suggested that plasticity exists between dermal fibroblasts and adipocytes, it remains unknown whether fat actively contributes to fibrosis in scarring. We show that adipocytes convert to scar-forming fibroblasts in response to Piezo-mediated mechanosensing to drive wound fibrosis. We establish that mechanics alone are sufficient to drive adipocyte-to- fibroblast conversion. By leveraging clonal-lineage-tracing in combination with scRNA-seq, Visium, and CODEX, we define a "mechanically naive" fibroblast-subpopulation that represents a transcriptionally intermediate state between adipocytes and scar-fibroblasts. Finally, we show that Piezo1 or Piezo2-inhibition yields regenerative healing by preventing adipocytes activation to fibroblasts, in both mouse-wounds and a novel human-xenograft-wound model. Importantly, Piezo1-inhibition induced wound regeneration even in pre-existing established scars, a finding that suggests a role for adipocyte-to-fibroblast transition in wound remodeling, the least-understood phase of wound healing. Adipocyte-to-fibroblast transition may thus represent a therapeutic target for minimizing fibrosis via Piezo-inhibition in organs where fat contributes to fibrosis.

cell biology↗

bioRxiv2022

Pro-resolving lipid mediators within brain esterified lipid pools are reduced in female rats chronically exposed to traffic-related air pollution or genetically susceptible to Alzheimer's Disease phenotype

Traffic-related air pollution (TRAP) is a risk factor for Alzheimers disease (AD) where neuroinflammation underlies disease progression and pathogenesis. Unresolved inflammation in AD is known to be exacerbated by brain deficits in unesterified pro-resolving lipid mediators enzymatically synthesized from polyunsaturated fatty acids. Recently, we reported that in the brain, unesterified pro-resolving lipid mediators which are bioactive, can also be supplied from less bioactive esterified lipid pools such as neutral lipids (NLs) and phospholipids (PLs). It is not known whether esterified pro-resolving lipid mediators are affected by AD pathology and exacerbated by TRAP exposure. In the present study we addressed this data gap using TgF344-AD male and female rats that express human AD risk genes and their wildtype littermates exposed to filtered air (FA) or TRAP from 1 to 15 months of age. Esterified lipid mediators within NLs and PLs were quantified by mass-spectrometry. We observed a significant reduction in pro-resolving lipid mediators in both NLs and PLs of female TgF344-AD rats compared to wildtype controls. TRAP exposure also reduced pro-resolving lipids in the female brain, mainly in PL pools, but did not exacerbate changes observed in TgF344-AD rats. Minimal changes were observed in males. Our findings indicate that AD genotype and chronic TRAP exposure result in sex-specific deficits in brain esterified pro-resolving lipid mediators, the pool that supplies free and bioactive lipid mediators. These data provide new information on lipid-mediated mechanisms regulating impaired inflammation resolution in AD, and show for the first time that chronic TRAP exposure targets the same lipid network implicated in AD.

neuroscience↗