Biology subjects

Ji, H.

Publications and source records attributed to Ji, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Nrf2 orchestrates epigenetic regulations and serves as the master regulator of KLF4 expression and activity during arsenic-induced transformation

Emerging evidence suggests that Nrf2 plays a pro-carcinogenic role in cancer. Our previous study showed that arsenic-induced Nrf2 activation triggers metabolic reprogramming, leading to the formation of cancer stem-like cells. Here, we further demonstrated that KLF4, a key pluripotency factor, is a direct transcriptional target of Nrf2 in arsenic-exposed human bronchial epithelial cells. ChIP-seq analysis identified multiple Nrf2 binding peaks at the Klf4 gene locus, which overlap with the enhancer markers H3K4me1 and H3K27Ac. Nrf2 knockout reduced both KLF4 expression and enhancer marker enrichment, accompanied by a global decrease in KLF4 binding across the genome. In wild-type (WT) cells, arsenic treatment increased KLF4 binding on genes involved in oncogenic pathways such as STAT3, SOX2, Nrf2, cell growth, Hedgehog, and EMT. We also found that KLF4 engages in a self-feedback loop in response to Nrf2 signaling. Lastly, our data showed that the co-occupancy of Nrf2 and KLF4 is crucial for establishing active enhancer hubs in the genome. These findings suggest that Nrf2s oncogenic effects are, in part, mediated by Nrf2 dependent self-amplification of KLF4 expression and function. Thus, targeting both Nrf2 and KLF4 could be a promising therapeutic strategy for eliminating cancer stem-like cells.

cancer biology↗

bioRxiv2024

Developmental trajectory of thalamus topography during the late preterm and perinatal period in normal development, after premature birth and in congenital heart defects

The thalamus plays a critical role in neural circuit maturation and brain connectivity. It is well known to show a characteristic topographical organization of local and long-range connectivity, yet developmental changes in this topography remains incompletely understood. Our study aims to first validate the use of diffusion MRI for the topographic delineation of thalamic subdivisions (nuclei), to characterize thalamic topography during development and assess the impact of congenital heart defects (CHD) on thalamus development. We used local fiber orientation distribution functions, derived from diffusion MRI (dMRI) data, to subdivide the thalamus into seven clusters. We first evaluated the within-subject reproducibility of a dMRI based clustering method across 30 adults scan-rescan datasets (n = 30) using K-means clustering, achieving reproducible segmentation of the thalamus into seven parts. This was applied to a large developmental cohort comprising normally developing infants from the term-born dHCP cohort (n = 68, gestational age [GW] at MRI scan ranging from 37.4 to 44.8 weeks, mean {+/-} SD: 41.4 {+/-} 2.1 weeks) and the Zurich cohort (n = 42, GW at MRI ranging from 39.0 to 48.7 weeks, mean {+/-} SD: 42.55 {+/-} 1.96 weeks). The cohort also included preterm-born dHCP cohort (n = 48, GW at MRI scan ranging from 29.3 to 37.4 corrected gestational weeks, mean {+/-} SD: 34.4 {+/-} 2.02 weeks) and one case of a postmortem fetal specimen (n = 1, GW at MRI = 21 weeks). Cluster volumes were analyzed as a function of age using multivariate linear regression. Differences in cluster volumes between control subjects (n = 42, GW at MRI ranging from 39.0 to 48.7 weeks, mean {+/-} SD: 42.55 {+/-} 1.96 weeks) and newborns with congenital heart disease (CHD) (n = 49, GW at MRI ranging from 37.6 to 42.9 weeks, mean {+/-} SD: 40.23 {+/-} 1.30 weeks) were analyzed using variance analysis, controlling for sex and age at MRI scan. The clustering on average had a within-subject overlap of 0.811 (Dice overlap metric). While absolute thalamus volumes increased with age, their relative volumes remained stable in the studied developmental period. CHD infants shown reduced absolute volumes in six of the seven thalamic nuclei, with significant increasing in the relative volume of the cluster overlapping with the mediodorsal nucleus. While the perinatal period comprises rapid developmental events including the maturation of white matter, the topography of thalamic circuitry remains stable. Our study highlights alterations in thalamic topology and potential impacts on brain connectivity in CHD infants. By leveraging local diffusion properties from diffusion MRI, our validated segmentation technique offers a robust, data-centric approach to thalamic delineation.

neuroscience↗

bioRxiv2024

A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing

BackgroundSelecting highly variable features is a crucial step in most analysis pipelines of single-cell RNA-sequencing (scRNA-seq) data. Despite numerous methods proposed in recent years, a systematic understanding of the best solution is still lacking. ResultsHere, we systematically evaluate 47 highly variable gene (HVG) selection methods, consisting of 21 baseline methods developed based on different data transformations and mean-variance adjustment techniques and 26 hybrid methods developed based on mixtures of baseline methods. Across 19 diverse benchmark datasets, 18 objective evaluation criteria per method, and 5,358 analysis settings, we observe that no single baseline method consistently outperforms the others across all datasets and criteria. However, hybrid methods as a group robustly outperform individual baseline methods. Based on these findings, a new HVG selection approach, mixture HVG selection (mixHVG), that incorporates top-ranked features from multiple baseline methods is proposed as a better solution to HVG selection. An open source R package mixhvg is developed to enable convenient use of mixHVG and its integration into users data analysis pipelines. ConclusionOur benchmark study not only provides a systematic comparison of existing methods, leading to a better HVG selection solution, but also creates a pipeline and resource consisting of diverse benchmark data and criteria for evaluating new methods in the future.

bioinformatics↗

bioRxiv2024

Functional analysis of conserved C. elegans bHLH family members uncovers lifespan control by a peptidergic hub neuron

Throughout the animal kingdom, several members of the basic helix-loop-helix (bHLH) family act as proneural genes during early steps of nervous system development. Roles of bHLH genes in specifying terminal differentiation of postmitotic neurons have been less extensively studied. We analyze here the function of five C. elegans bHLH genes, falling into three phylogenetically conserved subfamilies, which are continuously expressed in a very small number of postmitotic neurons in the central nervous system. We show (a) that two orthologs of the vertebrate bHLHb4/b5 genes, called hlh-17 and hlh-32, function redundantly to specify the identity of a single head interneuron (AUA), as well as an individual motor neuron (VB2), (b) that the PTF1a ortholog hlh-13 acts as a terminal selector to control terminal differentiation and function of the sole octopaminergic neuron class in C. elegans, RIC, and (c) that the NHLH1/2 ortholog hlh-15 controls terminal differentiation and function of the peptidergic AVK head interneuron class, a known neuropeptidergic signaling hub in the animal. Strikingly, through null mutant analysis and cell-specific rescue experiments, we find that loss of hlh-15/NHLH in the peptidergic AVK neurons and the resulting abrogation of neuropeptide secretion causes a substantially expanded lifespan of the animal, revealing an unanticipated impact of a central, peptidergic hub neuron in regulating lifespan, which we propose to be akin to hypothalamic control of lifespan in vertebrates. Taken together, our functional analysis reveals themes of bHLH gene function during terminal differentiation that are complementary to the earlier lineage specification roles of other bHLH family members. However, such late functions are much more sparsely employed by members of the bHLH transcription factor family, compared to the function of the much more broadly employed homeodomain transcription factor family.

neuroscience↗

bioRxiv2024

Macroscopic label-free biomedical imaging withshortwave infrared Raman scattering

Shortwave infrared (SWIR) imaging provides enhanced tissue penetration and reduced autofluorescence in clinical and pre-clinical applications. However, existing applications often lack the ability to probe chemical composition and molecular specificity without the need for contrast agents. Here, we present a SWIR imaging approach that visualizes spontaneous Raman scattering with remarkable chemical contrast deep within tissue across large fields of view. Our results demonstrate that Raman scattering overcomes autofluorescence as the predominant source of endogenous tissue background at illumination wavelengths as short as 892 nm. We highlight the versatility of SWIR Raman imaging through in vivo monitoring of whole-body tissue composition dynamics and non-invasive detection of fatty liver disease in mice, and identification of calcification and lipids in unfixed human atherosclerotic plaques. Moreover, our approach facilitates the visualization of nerves embedded in fatty tissue, a major advancement for surgical applications. With a simple wide-field setup orthogonal to fluorescence, SWIR Raman imaging holds promise for rapid adoption by clinicians and biologists. This technique opens new possibilities for contrast agent-free visualization of pathophysiology in whole animals and intraoperative imaging in humans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/597863v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@394289org.highwire.dtl.DTLVardef@13f3289org.highwire.dtl.DTLVardef@ee6f7org.highwire.dtl.DTLVardef@5d7399_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

OSBA: An open neonatal neuroimaging atlas and template for spina bifida aperta

We present the Open Spina Bifida Aperta (OSBA) atlas, an open atlas and set of neuroimaging templates for spina bifida aperta (SBA). Traditional brain atlases may not adequately capture anatomical variations present in pediatric or disease-specific cohorts. The OSBA atlas fills in this gap by representing the computationally averaged anatomy of the neonatal brain with SBA after fetal surgical repair. The OSBA atlas was constructed using structural T2-weighted and diffusion tensor MRI of 28 newborns with SBA who underwent prenatal surgical correction. The corrected gestational age at MRI was 38.1 {+/-} 1.1 weeks (mean {+/-} SD). The OSBA atlas consists of T2-weighted and fractional anisotropy templates, along with 9 tissue prior maps and region of interest (ROI) delineations. The OSBA atlas offers a standardized reference space for spatial normalization and anatomical ROI definition. Our image segmentation and cortical ribbon definition is based on a human-in-the-loop approach including manual segmentation. The precise alignment of the ROIs was achieved by a combination of manual image alignment and automated, non-linear image registration. By providing a dedicated neonatal atlas for SBA, we enable more accurate spatial standardization and support advanced analyses such as diffusion tractography and connectomic studies in newborns affected by this condition.

neuroscience↗

bioRxiv2024

Chemical Space Localization for Unknown Metabolite Annotation via Semantic Similarity of Mass Spectral Language

Untargeted analysis using liquid chromatography{square}mass spectrometry (LC-MS) allows quantification of known and unknown compounds within biological systems. However, in practical analysis of complex biological system, the majority of compounds often remain unidentified. Here, we developed a novel deep learning-based compound annotation approach via semantic similarity analysis of mass spectral language. This approach enables the prediction of structurally related compounds for unknowns. By considering the chemical space, these structurally related compounds provide valuable information about the potential location of the unknown compounds and assist in ranking candidates obtained from molecular structure databases. Validated with two independent benchmark datasets obtained by chemical standards, our method has consistently demonstrated superior performance compared to existing compound annotation methods. A case study of the tomato ripening process indicates that DeepMASS has significant potential for metabolic biomarker identification in real biological systems. Overall, the presented method shows considerable promise in annotating metabolites, particularly in revealing the "dark matter" in untargeted analysis.

bioinformatics↗

bioRxiv2024

BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

Bioinformatics plays a crucial role in understanding biological phenomena, yet the exponential growth of biological data and rapid technological advancements have heightened the barriers to in-depth exploration of this domain. Thereby, we propose Bio-Informatics Agent (BIA), an intelligent agent leveraging Large Language Models (LLMs) technology, to facilitate autonomous bioinformatic analysis through natural language. The primary functionalities of BIA encompass extraction and processing of raw data and metadata, querying both locally deployed and public databases for information. It further undertakes the formulation of workflow designs, generates executable code, and delivers comprehensive reports. Focused on the single-cell RNA sequencing (scRNA-seq) data, this paper demonstrates BIAs remarkable proficiency in information processing and analysis, as well as executing sophisticated tasks and interactions. Additionally, we analyzed failed executions from the agent and demonstrate prospective enhancement strategies including selfrefinement and domain adaptation. The future outlook includes expanding BIAs practical implementations across multi-omics data, to alleviating the workload burden for the bioinformatics community and empowering more profound investigations into the mysteries of life sciences. BIA is available at: https://github.com/biagent-dev/biagent.

bioinformatics↗

bioRxiv2024

Cholestasis alters polarization and suppressor function of hepatic regulatory T cells.

Fibrosing cholangiopathies, including biliary atresia and primary sclerosing cholangitis, involve immune-mediated bile duct epithelial injury and hepatic bile acid (BA) retention (cholestasis). Regulatory T-cells (Tregs) can prevent auto-reactive lymphocyte activation, yet the effects of BA on this CD4 lymphocyte subset are unknown. Gene regulatory networks for hepatic CD4 lymphocytes in a murine cholestasis model revealed Tregs are polarized to Th17 during cholestasis. Following bile duct ligation, Stat3 deletion in CD4 lymphocytes preserved hepatic Treg responses. While pharmacological reduction of hepatic BA in MDR2-/- mice prompted Treg expansion and diminished liver injury, this improvement subsided with Treg depletion. A cluster of patients diagnosed with biliary atresia showed both increased hepatic Treg responses and improved 2-year native liver survival, supporting that Tregs might protect against neonatal bile duct obstruction. Together, these findings suggest liver BA determine Treg function and should be considered as a therapeutic target to restore protective hepatic immune responses.

immunology↗

bioRxiv2024

Host-derived Interleukin 1α induces an immunosuppressive tumor microenvironment via regulating monocyte-to-macrophage differentiation

Tumor-associated macrophages exhibit high heterogeneity and contribute to the establishment of an immunosuppressive tumor microenvironment (TME). Although numerous studies have demonstrated that extracellular factors promote macrophage proliferation and polarization, the regulatory mechanisms governing the differentiation process to generate phenotypically, and functionally diverse macrophage subpopulations remain largely unexplored. In this study, we examined the influence of interleukin 1 (IL-1) on the development of an immunosuppressive TME using orthotopic transplantation murine models of breast cancer. Deletion of host Il1 led to the rejection of inoculated congenic tumors. Single-cell sequencing analysis revealed that CX3CR1+ macrophage cells were the primary sources of IL-1 in the TME. The absence of IL-1 reprogrammed the monocyte-to-macrophage differentiation process within the TME, characterized by a notable decrease in the subset of CX3CR+ ductal-like macrophages and an increase in iNOS-expressing inflammatory cells. Comparative analysis of gene signatures in both human and mouse macrophage subsets suggested that IL-1 deficiency shifted the macrophage polarization from M2 to M1 phenotypes, leading to enhanced cytotoxic T lymphocyte activity in the TME. Importantly, elevated levels of IL-1 in human cancers were associated with worse prognosis following immunotherapy. These findings underscore the pivotal role of IL-1 in shaping an immune-suppressive TME through the regulation of macrophage differentiation and activity, highlighting IL-1 as a potential target for breast cancer treatment. TeaserInterleukin 1 dictates macrophage behavior, influencing an immunosuppressive microenvironment in breast cancer, suggesting it as a treatment target.

cancer biology↗

bioRxiv2024

Efficient differentiation of human retinal pigment epithelium cells from chemically induced pluripotent stem cells

Human induced pluripotent stem cells (hiPSCs) hold considerable promise for autologous cellular therapies, particularly in ocular disease treatment, because of the low numbers of cells required for transplantation and the non-invasive nature of graft monitoring. However, the use of hiPSCs in ocular disease treatment faces challenges because the production of clinical-grade autologous hiPSCs via genetic techniques remains expensive, time-consuming, and subject to safety concerns. Here, we utilize a recently reported chemical method to derive human chemically induced pluripotent stem cells (hCiPSCs), demonstrating that hiPSC lines can be generated using small molecules in a simple and robust manner. Moreover, we show that these cell lines can be efficiently differentiated into retinal pigment epithelium (RPE) cells, which may aid in the treatment of age-related macular degeneration (AMD). Our study provides a foundation for cost-effective, fast, and safe methods that enable efficient production of autologous retinal cell types for ocular disease treatment.

cell biology↗

bioRxiv2024

Multi-gradient Permutation Survival Analysis Identifies Mitosis and Immune Signatures Steadily Associated with Cancer Patient Prognosis

The inconsistency of the association between genes and cancer prognosis is often attributed to many variables that contribute to patient survival. Whether there exist the Genes Steadily Associated with Prognosis (GEARs) and what their functions are remain largely elusive. Here we developed a novel method named "Multi-gradient Permutation Survival Analysis " (MEMORY) to screen the GEARs by using RNA-seq data from the TCGA database. We employed a network construction approach to identify hub genes from GEARs, and utilized them for cancer classification. In the case of lung adenocarcinoma (LUAD), the GEARs were found to be related to mitosis. Our analysis suggested that LUAD cell lines carrying PIK3CA mutations exhibit increased drug resistance. For breast invasive carcinoma (BRCA), the GEARs were related to immunity. Further analysis revealed that CDH1 mutation might regulate immune infiltration through the EMT process. Moreover, we explored the prognostic relevance of mitosis and immunity through their respective scores and demonstrated it as valuable biomarkers for predicting patient prognosis. In summary, our study offered significant biological insights into GEARs and highlights their potentials as robust prognostic indicators across diverse cancer types.

cancer biology↗

bioRxiv2024

Automated multimodal imaging of Caenorhabditis elegans behavior in multi-well plates

Assays of behavior in model organisms play an important role in genetic screens, drug testing, and the elucidation of gene-behavior relationships. We have developed an automated, high-throughput imaging and analysis method for assaying behaviors of the nematode C. elegans. We use high-resolution optical imaging to longitudinally record the behaviors of 96 animals at a time in multi-well plates, and computer vision software to quantify the animals locomotor activity, behavioral states, and egg laying events. To demonstrate the capabilities of our system we used it to examine the role of serotonin in C. elegans behavior. We found that egg-laying events are preceded by a period of reduced locomotion, and that this decline in movement requires serotonin signaling. In addition, we identified novel roles of serotonin receptors SER-1 and SER-7 in regulating the effects of serotonin on egg laying across roaming, dwelling, and quiescent locomotor states. Our system will be useful for performing genetic or chemical screens for modulators of behavior.

neuroscience↗

bioRxiv2024

Segmentation-free measurement of locomotor frequency in Caenorhabditis elegans using image invariants

An animals locomotor rate is an important indicator of its motility. In studies of the nematode C. elegans, assays of the frequency of body bending waves have often been used to discern the effects of mutations, drugs, or aging. Traditional manual methods for measuring locomotor frequency are low in throughput and subject to human error. Most current automated methods depend on image segmentation, which requires high image quality and is prone to errors. Here, we describe an algorithm for automated estimation of C. elegans locomotor frequency using image invariants, i.e., shape-based parameters that are independent of object translation, rotation, and scaling. For each video frame, the method calculates a combination of 8 Hus moment invariants and a set of Maximally Stable Extremal Regions (MSER) invariants. The algorithm then calculates the locomotor frequency by computing the autocorrelation of the time sequence of the invariant ensemble. Results of our method show excellent agreement with manual or segmentation-based results over a wide range of frequencies. We show that compared to a segmentation-based method that analyzes a worms shape and a method based on video covariance, our technique is more robust to low image quality and background noise. We demonstrate the systems capabilities by testing the effects of serotonin and serotonin pathway mutations on C. elegans locomotor frequency.

neuroscience↗

bioRxiv2023

Inhibition of KLK8 promotes pulmonary endothelial repair by restoring VE-cadherin/Akt/FOXM1 pathway

The tissue kallikrein-related peptidases (KLKs) are secreted serine proteases deeply involved in angiogenesis. However, whether KLKs are involved in the regulation of endothelial regeneration during sepsis remains unknown. By comparing the mRNA levels of 15 KLKs, we found that KLK8 was the highest induced KLK member in lung tissues or primary isolated mouse lung vascular endothelial cells (MLVECs) exposed to lipopolysaccharide (LPS). Adenovirus-mediated overexpression of KLK8 caused endothelial hyperpermeability both in vitro and in vivo. Inhibition of KLK8, by either gene knockout or KLK8 neutralizing antibodies, alleviated sepsis-induced endothelial hyperpermeability, acute lung injury and mortality. Mechanistically, transcription profiling of KLK8-overexpressed endothelial cells revealed a central role of forkhead box M1 (FOXM1) downregulation in mediating the pro-injury and anti-proliferation effects of KLK8. KLK8 cleaved VE-cadherin and consequently suppressed FOXM1 expression by inactivation of the VE-cadherin/Akt pathway. KLK8 deficiency or blockade rescued VE-cadherin/Akt/FOXM1 pathway, thus promoting endothelium regeneration. This study reveals a critical role for KLK8-induced inactivation of VE-cadherin/Akt/FOXM1 pathway in mediating the impairment of endothelial regeneration and the consequent lung vascular leakiness in response to sepsis. HighlightsO_LIUpregulated KLK8 mediates lung endothelial barrier dysfunction during sepsis C_LIO_LIKLK8 inactivates VE-cadherin/Akt/FOXM1, thus impairing endothelium regeneration C_LIO_LIKLK8 deficiency or blockade rescues VE-cadherin/Akt/FOXM1 signaling pathway C_LIO_LIKLK8 deficiency or blockade promotes endothelium regeneration during sepsis C_LIO_LIKLK8 deficiency or blockade attenuates sepsis-induced acute lung injury and mortality C_LI

physiology↗

bioRxiv2023

Sprr1 and miR-130b contribute to the senescence-like phenotype in aging

Aging is an inevitable process with senescence being one of its hallmarks. Recent advances have indicated that the elimination of senescent cells can reduce the signs of aging and increase healthy life span. Here, we identify a negative modulator of aging, Sprr1a, and in turn a negative modulator of Sprr1a, miR-130b. We show that reductions in Sprr1a levels, including via miR-130b expression, promotes cell senescence-like phenotype. We find that mediators of senescence, such as inflammatory cytokines and cell cycle regulators, are modulated by the miR-130b and Sprr1a-related pathway. For example, the levels of p16, p53 and p21 become decreased or increased upon the respective expression of Sprr1a versus miR-130b. Further, as shown in relation to p16 levels and {beta}-galactosidase levels, cells expressing Sprr1a exhibit significant protection from senescence-inducing factors such as radiation or Doxorubicin, suggesting that Sprr1a might contribute to protection against age-related pathologies. Taken together, we introduce two modulators of properties associated with senescence-like phenotype.

molecular biology↗

bioRxiv2023

SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia

Age is a major risk factor for coronavirus disease (COVID-19)-associated severe pneumonia and mortality; however, the underlying mechanism remains unclear. Herein, we investigated whether age-related deregulation of RNAi components and RNA splicing factors affects COVID-19 severity. Decreased expression of RNAi components (Dicer and XPO5) and splicing factors (SRSF3 and hnRNPA3) correlated with increased severity of COVID-19 and SARS-CoV-2 nucleocapsid (N) protein-induced pneumonia. N protein induced autophagic degradation of Dicer, XPO5, SRSF3, and hnRNPA3, repressing miRNA biogenesis and RNA splicing and inducing DNA damage, proteotoxic stress, and pneumonia. Dicer, XPO5, SRSF3, and hnRNPA3 were downregulated with age in mouse lung tissues. Older mice experienced more severe N protein-induced pneumonia than younger mice. However, treatment with a poly(ADP-ribose) polymerase inhibitor (PJ34) or aromatase inhibitor (anastrozole) relieved N protein-induced pneumonia by restoring Dicer, XPO5, SRSF3, and hnRNPA3 expression. These findings will aid in developing improved treatments for SARS-CoV-2-associated pneumonia.

microbiology↗

bioRxiv2023

Suppression of HIV and cocaine-induced neurotoxicity and inflammation by cell penetrable itaconate esters

HIV-associated neurological disorder (HAND) is a serious complication of HIV infection, marked by neurotoxicity induced by viral proteins like Tat. Substance abuse exacerbates neurocognitive impairment in people living with HIV. There is an urgent need for effective therapeutic strategies to combat HAND comorbid with Cocaine Use Disorder (CUD). Our analysis of the HIV and cocaine-induced transcriptomes in primary cortical cultures revealed a significant overexpression of the macrophage-specific gene, aconitate decarboxylase 1 (Acod1), caused by the combined insults of HIV and cocaine. ACOD1 protein converts the tricarboxylic acid intermediate cis-aconitate into itaconate during the activation of inflammation. The itaconate produced facilitates cytokine production and subsequently activates anti-inflammatory transcription factors, shielding macrophages from infection-induced cell death. While the role of itaconate in limiting inflammation has been studied in peripheral macrophages, its immunometabolic function remains unexplored in HIV and cocaine-exposed microglia. We assessed in this model system the potential of 4-octyl-itaconate (4OI), a cell-penetrable esterified form of itaconate known for its potent anti-inflammatory properties and potential therapeutic applications. We administered 4OI to primary cortical cultures exposed to Tat and cocaine. 4OI treatment increased the number of microglial cells in both untreated and Tat{+/-}Cocaine-treated cultures and also reversed the morphological altercations induced by Tat and cocaine. In the presence of 4OI, microglial cells also appeared more ramified, resembling the quiescent microglia. Consistent with these results, 4OI treatment inhibited the secretion of the proinflammatory cytokines IL-1, IL-1{beta}, IL-6, and MIP1- induced by Tat and cocaine. Transcriptome profiling further determined that Nrf2 target genes such as NAD(P)H quinone oxidoreductase 1 (Nqo1), Glutathione S-transferase Pi (Gstp1), and glutamate cysteine ligase catalytic (Gclc), were most significantly activated in Tat-4OI treated cultures, relative to Tat alone. Further, genes associated with cytoskeleton dynamics in inflammatory microglia were downregulated by 4OI treatment. Together, the results strongly suggest 4-octyl-itaconate holds promise as a potential candidate for therapeutic development aimed at addressing HAND coupled with CUD comorbidities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/559154v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@bfffa8org.highwire.dtl.DTLVardef@129ad8dorg.highwire.dtl.DTLVardef@1412ea2org.highwire.dtl.DTLVardef@5cb968_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Model of 4OI-mediated neuroprotection against Tat-Cocaine toxicity Tat and Tat-Cocaine treatment induce neuronal damage, which is mitigated by 4OI through microglia cells. This cartoon shows the reduction of harmful effects such as proinflammatory cytokine release, upregulation of P2R, PDE, and Acod1 by the presence of 4OI. This ester modified itaconate triggers anti-inflammatory responses and activates antioxidant pathways. C_FIG

neuroscience↗