Genome Research Articles

Genome Sequence Resource of Neopestalotiopsis cubana, a Pathogen to Guava

The pestalotiopsis-like taxa, inclusive of Pseudopestalotiopsis, Pestalotiopsis, and Neopestalotiopsis, constitute a well-recognized fungal family. Recently, species within the Neopestalotiopsis genus have been identified as plant pathogens affecting crops and fruits. However, there is currently a paucity of reference genome data for Neopestalotiopsis cubana in germplasm resource evaluation research. In this study, we present a chromosome-level reference genome of N. cubana, constructed using DNBSEQ platform and PacBio RS II platform. The assembled genome spans a total length of 50,399,148 bp, with a GC content of 50.17%. Furthermore, the reference genome contains annotations for a total of 15,709 protein-coding genes and 657 non-coding RNAs (ncRNAs). The availability of this genome sequence data enhances our understanding of the lifestyle strategy and pathogenesis of Neopestalotiopsis species. Our study significantly contributes to the species richness of Neopestalotiopsis spp. and provides a foundation for future research.

Enhanced Mosquito Larvicidal Efficacy and Dehairing Properties of Bacillus thuringiensis Serovar israelensis Strain VCRC-B649 Isolated from Malabar Coast, India.

In recent years, there has been a global threat from emerging vector-borne diseases (VBD), despite the implementation of several vector control programs. Considering the benefits of bacterial pesticides, the present study aimed to isolate potential mosquitocidal bacteria from the various soil types collected from the Kasaragod (12.5°N, 75.0°E) district of Kerala, India. One bacterial strain was isolated from the coastal alluvium soil and showed promising mosquitocidal activity. The mosquitocidal isolate was identified as Bacillus thuringiensis serovar israelensis strain VCRC-B649 through phylogenetic analysis of whole genome sequence. LC50 values against Culex quinquefasciatus, Aedes aegypti, and Anopheles stephensi larvae were determined as 0.0064, 0.0072, and 0.0101mg/L, and LC90 values were 0.0127, 0.0140, and 0.019mg/L. Comparative analysis of larvicidal activity of this strain has revealed more efficacy than the WHO reference strain of B. thuringiensis var. israelensis (H14) The cry and cyt gene profile of this isolate is found to be similar to WHO reference strain of B. thuringiensis var. israelensis (H14). This new isolate has not shown any adverse effects against aquatic non-target organisms. Further evaluation of its morphological, biochemical characteristics and growth kinetics revealed similarities with already reported B. thuringiensis strains. Sporulated culture at 72h showed maximum (20.6 ± 1.5mm) proteolytic activity and animal skin (goat skin) dehairing property and revealed the industrial applications of this new strain. This is the first report on the isolation of mosquitocidal bacterial strain with enzyme-producing property from the Malabar coastal region and it was proven to be a more suitable alternative biocontrol agent for controlling the disease transmitting mosquito vectors with translational value.

Whole genome sequencing completes the molecular genetic testing workflow of patients with Lynch syndrome

Multigene panel tests (MGPTs) revolutionized the diagnosis of Lynch syndrome (LS), however noncoding pathogenic variants (PVs) can only be detected by complementary methods including whole genome sequencing (WGS). Here we present a DNA-, RNA- and tumor tissue-based WGS prioritization workflow for patients with a suspicion of LS where MGPT detected no LS-related PV. Among the 100 enrolled patients, MGPT detected 28 simple PVs and an additional 3 complex PVs. Among the 69 MGPT-negative patients, the lack of somatic MLH1 promoter methylation in a patient with a distinguished MLH1 allelic imbalance selected this sample for WGS. This returned a germline deep intronic MLH1 variant, with further functional studies confirming its’ pathogenicity. Interestingly, all three complex PVs and the MLH1 deep intronic PV were found to be recurrent at our center. Our straightforward and cost-effective prioritization workflow can optimally include WGS in the genetic diagnosis of LS.

Comparative Analysis of the Probiotic Features of Lysinibacillus and Enterobacter Strains Isolated from Gut Tract of Triploid Cyprinid Fish.

Gut mucosal immunity of teleost is mainly governed by mucosa-associated lymphoid tissues (MALT) and indigenous microbiota on mucosal surfaces of gut tract, which can confer protection against pathogenic invasion. However, the probiotic features of bacterial isolates from gut tract of triploid cyprinid fish (TCF) were largely unclear. In this study, Lysinibacillus and Enterobacter strains were isolated for probiotic identification. Whole genome sequencing (WGS) analysis indicated that Lysinibacillus and Enterobacter isolates possessed a variety of functional genes associated with probiotic features. Biofilm-forming activity (BFA) were one of the most important probiotic features, which can enable probiotic strains to communicate with indigenous microbiota by forming sessile community and then confer protection against stressors and invading pathogens. In this study, Lysinibacillus and Enterobacter isolates displayed high levels of BFA, hydrophobicity as well as aggregating potentials. Moreover, supernatants of probiotic isolates not only decreased pathogenic BFA and growth activity, but also showed high decomposing activity to macronutrients. These results indicated that probiotic isolates from gut tract of TCFs may pose protective roles in health of farmed fish.

Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks

Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.

The FBXO45-GEF-H1 axis controls germinal center formation and B-cell lymphomagenesis.

The role of ubiquitin-mediated degradation mechanisms in the pathogenesis of diffuse large B cell (DLBCL) and follicular lymphoma (FL) is not completely understood. We show that conditional deletion of the E3 ubiquitin ligase Fbxo45 in germinal center B-cells results in B-cell lymphomagenesis in homozygous (100%) and heterozygous (48%) mice. Mechanistically, FBXO45 targets the RHO guanine exchange factor ARHGEF2/GEF-H1 for ubiquitin-mediated degradation. Double genetic ablation of Fbxo45 and Arhgef2 ameliorated lymphoma formation. Transgenic knock-in mice harboring a GEF-H1 mutant unable to bind FBXO45 develop B-cell lymphomas with ~50% penetrance. Genome sequencing in human lymphomas identified mutually-exclusive FBXO45 copy number losses and ARHGEF2 gains, with combined frequencies ranging from 26.32% in FL to 45.12% in DLBCL. Notably, FBXO45 silencing enhances sensitivity to MEK1/2 inhibition. These results identify FBXO45 and ARHGEF2 as a novel tumor-suppressor and oncogene pair involved in the pathogenesis of B-cell lymphomas with significant implications for targeted therapies.

Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient

Immunocompromised patients struggle to adequately clear viral infections, offering the virus the opportunity to adapt to the immune system in the host. Here we present a case study of a patient undergoing allogeneic hematopoietic stem cell transplantation with a 521-day follow-up of a SARS-CoV-2 infection with the BF.7.21 variant. Virus samples from five time points were submitted to whole genome sequencing. Between the first detection of SARS-CoV-2 infection and its clearance, the patient’s virus population acquired 34 amino acid substitutions and 8 deletions in coding regions. With 11 amino acid substitutions in the receptor binding domain of the virus’ spike protein, substitutions were 15 times more abundant than expected for a random distribution in this highly functional region. Amongst them were the substitutions S:K417T, S:N440S, S:K444R, S:V445A, S:G446N, S:L452Q, S:N460K, and S:E484V at positions that are notorious for their resistance-mediating effects. The substitution patterns found indicate ongoing adaptive evolution.

First complete genome sequence of tulip mild mottle mosaic virus (Ophiovirus tulipae)

Tulip mild mottle mosaic disease, caused by tulip mild mottle mosaic virus (TMMMV, species Ophiovirus tulipae), was first reported in Japan in 1979. TMMMV has a negative-sense ssRNA genome and is closely related to ophioviruses such as Mirafiori lettuce big vein virus (MLBVV, Ophiovirus mirafioriense). However, its complete nucleotide sequence has not yet been reported. Therefore, in this study, we determined the complete nucleotide sequences of all four TMMMV segments. The 5′-terminal tetranucleotide sequences were highly conserved, and the five bases at the 5′ end were identical in all segments. Nucleotide sequence comparisons of the four segments showed the highest sequence identity to those of MLBVV (70–76% for the genomic RNA sequences and 81–87% for the amino acid sequences of each ORF, except for ORF2). The amino acid sequences of the coat proteins of TMMMV and MLBVV were found to be 83.1% identical, which is below the 85% threshold for assignment to the same species, indicating that these viruses belong to different species in the same genus.

Identification of a Novel HIV-1 Second-Generation Circulating Recombinant Form (CRF117_0107) in China.

Under the background of the main epidemic HIV strains (CRF01_AE and CRF07_BC) co-circulation in China, more HIV second-generation recombinant (SGR) strains with CRF01_AE and CRF07_BC as the backbone were also emerging. In this study, we characterize a novel HIV-1 second-generation circulating recombinant form (CRF117_0107) consisting of CRF01_AE and CRF07_BC fragments from three epidemiologically unrelated HIV-1-infected individuals. One near full-length genome (NFLG) sequence was amplified, sequenced, and spliced in two halves using RNA extracted from the plasma of a homosexual in Shenzhen, Guangdong Province. Two other NFLG sequences were obtained from the Los Alamos HIV Sequence Database under accession numbers KY201177 and MK397789, which were isolated from men who have sex with men (MSM) in Guangdong Province and Zhejiang Province, respectively. Phylogenetic analysis revealed that these NFLG sequences formed a monophyletic cluster with a high bootstrap value of 1.0. Recombination analysis demonstrated that the genome of CRF117_0107 was separated into three segments by two breakpoints. Further subregional phylogenetic analysis was performed that showed segment I+III (790-5990nt, 8295-9412nt) of CRF117_0107 originated from the CRF07_BC cluster, and Segment I+III (5991-8294nt) originated from the CRF01_AE cluster. The appearance of CRF117_0107 further highlights that HIV-1 SGR strains containing CRF01_AE and CRF07_BC will be generated more frequently and will most likely be more conducive to accelerating the spread of HIV in China. This study suggested it's essential to monitor HIV-1 second-generation CRFs among high-risk populations such as MSM for the epidemic and evolution dynamics of HIV-1 in China.

Sequence analysis and genome organization of a new marafivirus from Leptochloa chinensis.

High-throughput sequencing was used to identify and characterize a novel marafivirus from the weed Leptochloa chinensis, which was tentatively named "Leptochloa chinensis marafivirus" (LcMV). The complete genome of the virus consists of 6,178 base pairs, and its nucleotide sequence is 73.82% identical to that of Sorghum almum marafivirus, which is a member of the genus Marafivirus within the family Tymoviridae. The LcMV genome contains a relatively large open reading frame (ORF) encoding a single polyprotein (220.6 kDa) with five functional domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), which is a characteristic of members of this genus. Furthermore, a 16-nucleotide conserved marafibox sequence was identified at nucleotide positions 5341-5356. The coat protein of LcMV is 68.02% identical to that of Sorghum almum marafivirus. Phylogenetic analysis based on nucleotide and polyprotein sequences showed that LcMV is closely related to members of the genus Marafivirus. Our findings support the classification of LcMV as a member of a new species within this genus. This is the first report of a marafivirus infecting Leptochloa chinensis, a very important weed of rice.

MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model

DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes.

Utilizing Patient-Derived Xenografts to Model Precision Oncology for Biliary Tract Cancer.

Biliary tract cancers, which are rare and aggressive malignancies, are rich in clinically actionable molecular alterations. A major challenge in the field is the paucity of clinically relevant biliary tract cancer models that recapitulate the diverse molecular profiles of these tumors. The purpose of this study was to curate a collection of patient-derived xenograft (PDX) models that reflect the spectrum of genomic alterations present in biliary tract cancers to create a resource for modeling precision oncology. PDXs were derived from biliary tract cancer samples collected from surgical resections or metastatic biopsies. Alterations present in the PDXs were identified by whole-exome sequencing and RNA sequencing. PDXs were treated with approved and investigational agents. Efficacy was assessed by change in tumor volume from baseline. Event-free survival was defined as the time to tumor doubling from baseline. Responses were categorized at day 21: >30% decrease in tumor volume = partial response, >20% increase in tumor volume = progressive disease, and any non-partial response/progressive disease was considered stable disease. Genomic sequencing demonstrated key actionable alterations across this cohort, including alterations in FGFR2, isocitrate dehydrogenase I, ERRB2, PIK3CA, PTEN, and KRAS. RNA sequencing demonstrated fusions and expression of antibody-drug conjugate targets, including TROP2, HER2, and Nectin4. Therapeutic matching revealed objective responses to approved and investigational agents that have been shown to have antitumor activity clinically. In this study, we developed a catalog of biliary tract cancer PDXs that underwent comprehensive molecular profiling and therapeutic modeling. To date, this is one of the largest collections of biliary tract cancer PDX models and will facilitate the development of personalized treatments for patients with these aggressive malignancies.

Returning genetic risk information for hereditary cancers to participants in a population-based cohort study in Japan.

Large-scale population cohort studies that collect genomic information are tasked with returning an assessment of genetic risk for hereditary cancers to participants. While several studies have applied to return identified genetic risks to participants, comprehensive surveys of participants' understanding, feelings, and behaviors toward cancer risk remain to be conducted. Here, we report our experience and surveys of returning genetic risks to 100 carriers of pathogenic variants for hereditary cancers identified through whole genome sequencing of 50 000 individuals from the Tohoku Medical Megabank project, a population cohort study. The participants werecarriers of pathogenic variants associated with either hereditary breast and ovarian cancer (n = 79, median age=41) or Lynch syndrome (n = 21, median age=62). Of these, 28% and 38% had a history of cancer, respectively. We provided information on cancer risk, heritability, and clinical actionability to the participants in person. The comprehension assessment revealed that the information was better understood by younger (under 60 years) females than by older males. Scores on the cancer worry scale were positively related to cancer experiences and general psychological distress. Seventy-one participants were followed up at Tohoku University Hospital; six females underwent risk-reducing surgery triggered by study participation and three were newly diagnosed with cancer during surveillance. Among first-degree relatives of hereditary breast and ovarian cancer carriers, participants most commonly shared the information with daughters. This study showed the benefits of returning genetic risks to the general population and will provide insights into returning genetic risks to asymptomatic pathogenic variant carriers in both clinical and research settings.

Complete genome sequence of Bifidobacterium animalis subsp. lactis BI040, a probiotic strain with multiple health benefits from the NORDBIOTIC collection.

The complete genome of Bifidobacterium animalis subsp. lactis BI040-a human stool isolate, was sequenced using Illumina and Oxford Nanopore technologies. The BI040 genome is composed of a circular 1,944,141-bp chromosome which carries genes potentially involved in vitamin synthesis and gut health.

Characterization of Streptococcus pyogenes Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023—FIRST Detection of M1UK in Bulgaria

Recently a resurgence of Streptococcus pyogenes infections has arisen, with concerns around the highly virulent M1UK lineage. Our aim was to characterize S. pyogenes, the immune responses it causes, and to determine the presence of the M1UK lineage in Sofia, Bulgaria. In our study, the infections were confirmed by culture testing or rapid antigen test. Identification was performed by MALDI-TOF and was followed up by antibiotic susceptibility testing (EUCAST). Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. Out of 82 children, 38 had scarlet fever and the rest had streptococcal pharyngitis. Strains were susceptible to penicillin (β-lactams), macrolides, clindamycin, tetracyclines, co-trimoxazole, fluoroquinolones, and linezolid. Superantigen profiles were identified: SpeA + SpeJ (45%), SpeC, and SpeI + SpeH (27.5% each). A novel Multilocus sequence typing (MLST) haplotype in the mutS gene (d90b) was found in four strains. The M1UK lineage was detected for the first time in Bulgaria. We observed an increase in complement fractions C3 and C4 and a decrease in T lymphocytes. A significant increase in the levels of IFN-γ, IL-6, and IL-10 with corresponding reduction in IL-17A were revealed. In conclusion, the studied S. pyogenes strains were characterized by their susceptibility to antibiotics and the predominance of SpeA superantigen; for the first time in Bulgaria the presence of M1UK and a novel SNP variation in the mutS gene (d90b) were found. A mixed pattern of pro- and anti-inflammatory immune responses in patients was observed.

Genomic characterization of pathotype diversity and drug resistance among generic Escherichia coli isolated from broiler chickens in Canada.

Escherichia coli is a Gram-negative bacterium that is ubiquitous in animals and humans, with some strains capable of causing disease. The aim of this study was to perform a comparative genomic analysis of 2,732 generic E. coli isolates that were recovered from poultry samples collected from six regions in Canada as part of the National Microbiological Baseline study in Broiler Chicken. Isolates were subjected to whole genome sequencing and a subset (1,122/2,732) were tested for phenotypic resistance to fifteen antimicrobials. These E. coli isolates were highly diverse, representing 376 serotypes, 236 Sequence Types and twenty-one pathotypes, of which 19 were hybrid pathotypes. A high concordance (>85%) between resistance phenotype and the presence of antimicrobial resistance genes and point mutations (resistance determinants) was observed for 13/15 antimicrobials. Over 95% of the β-lactam, fluoroquinolone, and phenicol resistance genes were predicted to be plasmid-borne. The number of resistance determinants per genome was highest in Quebec, while resistance genes associated with β-lactam resistance were more frequently detected in isolates from British Columbia. Generic E. coli in Canadian poultry are highly diverse, can carry pathotype-associated virulence factors and resistance determinants of clinical significance with a risk of emerging into pathogenic strains.

Sherlock-Genome: an R Shiny application for genomic analysis and visualization

MotivationNext-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.ResultsWe developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies. Following FAIR principles, Sherlock-Genome provides a platform and guidelines for managing and sharing finalized sample-level WGS analysis results, enabling users to upload results, inspect analyses locally, and perform integrative analyses. It includes modules for major cancer genomic analyses, allowing interactive data visualizations and integrative analyses with other data types. Sherlock-Genome supports both local and cloud deployment, facilitating the sharing of results for related publications. This tool has the potential to be widely adopted in cancer genomics, significantly enhancing the accessibility and usability of sample-level WGS analysis results for comprehensive biological discovery and research advancements.Availability and implementationThe source code and installation instructions for Sherlock-Genome can be accessed via Github https://github.com/xtmgah/Sherlock-Genome. Documentation and data requirements for user project data can also be found on the same GitHub page.

Insights from a Genome-Wide Study of Pantoea agglomerans UADEC20: A Promising Strain for Phosphate Solubilization and Exopolysaccharides Production

The genome sequence of Pantoea agglomerans UADEC20 is presented, which is a strain isolated from agricultural fields in northeast Mexico. The genome was assembled into 13 scaffolds, constituting a total chromosome size of 4.2 Mbp, with two of the scaffolds representing closed plasmids. The strain exhibits activity in phosphate solubilization and exopolysaccharide (EPS) production and secretion; therefore, we explored its biotechnological potential via its genome sequencing and annotation. Genomic analyses showed that a total of 57 and 58 coding sequences (CDSs) related to phosphate solubilization and EPS production were identified within its genome, in addition to a reduced number of CDSs related to drug resistance and phages. The comprehensive set of genes supporting phosphate solubilization, EPS synthesis, and secretion, along with its low virulence and antibiotic resistance levels, justify further research for its potential biotechnological application and possible use as a plant growth-promoting agent in the field. These findings suggest a unique genetic background in the P. agglomerans UADEC20 strain.

A Review of the Molecular Understanding of the Mpox Virus (MPXV): Genomics, Immune Evasion, and Therapeutic Targets

The Mpox virus (MPXV), a zoonotic pathogen from the Orthopoxvirus genus, has emerged as a significant global public health concern, especially after the unprecedented outbreak in 2022. This review synthesizes the MPXV’s molecular features, focusing on its genomic structure, replication mechanisms, immune evasion strategies, and implications for diagnostics and therapeutics. The study examines the virus’s genomic organization utilizing recent peer-reviewed literature, highlighting essential genes like OPG027 and D1L, which contribute to host adaptation, increased transmissibility, and immune evasion. Advances in molecular diagnostics, including real-time PCR and genome sequencing, are reviewed, emphasizing their critical role in outbreak monitoring and control. However, challenges persist, such as diagnostic limitations in resource-constrained settings and the lack of targeted vaccines and antivirals. This review discusses new antiviral candidates, confirmed through computational and in vitro techniques, identifying thymidine kinase and VP39 as key therapeutic targets. Emphasizing the need for genomic surveillance to track adaptive evolution, results show that particular mutations, such as in the OPG027 and D1L genes, increase the transmissibility and immune evasion of the MPXV. These molecular revelations highlight the urgent necessity for better diagnostics catered towards addressing present constraints and developing focused treatments that reduce the effect of the virus. This study emphasizes how these results underscore the need for combined public health plans to handle the changing MPXV epidemiology properly.

Carotid Endarterectomy Ameliorates Cognitive Impairment in Clinical and Experimental Unilateral Carotid Artery Stenosis.

Carotid endarterectomy (CEA) is widely used to treat carotid artery stenosis (CAS). However, the effects of CEA on unilateral CAS-induced cognitive impairment and the underlying mechanism remain poorly understood. Thirteen patients diagnosed with unilateral severe CAS underwent pre- and post-CEA assessments, including 18fluoro-2-deoxy-d-glucose positron emission tomography/magnetic resonance imaging, cognitive assessments, and routine blood tests before and after CEA. Unilateral carotid common artery occlusion and ligation release (reperfusion) surgeries were performed in mice to mimic CAS and CEA. Cognitive function, cerebral blood flow, and white matter damage were evaluated in mice using the Morris water maze test, Doppler flowmetry, laser-speckle imaging, diffusion tensor imaging, Luxol fast blue staining, transmission electron microscopy, and western blot assays post unilateral carotid common artery occlusion and reperfusion. Genomic sequencing of the white matter was performed to explore the potential underlying mechanism. CEA significantly enhanced the Montreal Cognitive Assessment scores in patients with CAS and preoperative cognitive impairment. Moreover, CEA led to notable improvements in cerebral blood flow, energy metabolism, and white matter integrity, while concurrently reducing blood inflammation. In the mouse model, reperfusion surgery alleviated cognitive deficits, increased cerebral blood flow, and alleviated white matter damage following unilateral carotid common artery occlusion. Furthermore, transcriptional surveys have revealed substantial alterations in the upregulation of Nrf2 signaling and metabolic pathways, coupled with the inhibition of neuroinflammation, cellular communication, and immune cell population signaling following reperfusion. CEA ameliorated CAS-induced cognitive dysfunction by improving the cerebral functional structure. These beneficial effects may be attributed to their antioxidant and anti-inflammatory properties.