The transcription factor forkhead box (FOX)M1 regulates β-cell proliferation and insulin secretion. Our previous work demonstrates that expressing a constitutively active form of FOXM1 (FOXM1*) in β-cells increases β-cell function, proliferation, and mass in male mice. However, in contrast to what is observed in males, we demonstrate here that in female mice expression of FOXM1* in β-cells does not affect β-cell proliferation or glucose tolerance. Similarly, FOXM1* transduction of male but not female human islets enhances insulin secretion in response to elevated glucose. We therefore examined the mechanism behind this sexual dimorphism. Estrogen contributes to diabetes susceptibility differences between males and females, and estrogen receptor (ER)α is the primary mediator of β-cell estrogen signaling. Moreover, in breast cancer cells, ERα and FOXM1 work together to drive gene expression. We therefore examined whether FOXM1 and ERα functionally interact in β-cells. FOXM1* rescued elevated fasting glucose, glucose intolerance, and homeostatic model assessment of β-cell function (HOMA-B) in female mice with a β-cell-specific ERα deletion. Furthermore, in the presence of estrogen, the FOXM1 and ERα cistromes exhibit significant overlap in βTC6 β-cells. In addition, FOXM1 and ERα binding sites frequently occur in complex enhancers co-occupied by other islet transcription factors. These data indicate that FOXM1 and nuclear ERα cooperate to regulate β-cell function and suggest a general mechanism contributing to the lower incidence of diabetes observed in women.NEW & NOTEWORTHY Here we investigate why the effects of increasing FOXM1 activity in β-cells observed in male mice are not seen in female mice. ERα likely collaborates with FOXM1 and other transcription factors to enhance gene expression related to β-cell function. Higher estrogen levels in females may contribute to their increased insulin secretion and the more severe consequences of losing transcription factors like FOXM1 in males. Overall, these findings shed light on sex differences in diabetes susceptibility.

Fibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse progression of the disease. To find novel targets for fibrosis therapeutics, we developed a model for the differentiation of monocytes to myofibroblasts that allowed us to screen for proteins involved in myofibroblast differentiation. Inhibition of a novel protein target generated by our model, talin2, reduces myofibroblast-specific morphology, α-smooth muscle actin content, and collagen I content and lowers the pro-fibrotic secretome of myofibroblasts. We find that knockdown of talin2 de-differentiates myofibroblasts and reverses bleomycin-induced lung fibrosis in mice, and further that Tln2-/- mice are resistant to bleomycin-induced lung fibrosis and resistant to unilateral ureteral obstruction-induced kidney fibrosis. Talin2 inhibition is thus a potential treatment for reversing lung and kidney fibroses.

N6-methyladenosine (m6A) is a critical epitranscriptomic regulator of neuronal function. Cerebral ischemia induces m6A hypermethylation due to decreased expression of m6A demethylase fat mass and obesity-associated (FTO) protein. Previously, we showed that cerebral overexpression of FTO with an adeno-associated virus (AAV) 9 protects the post-stroke brain. We presently evaluated the mechanistic basis for FTO-dependent m6A demethylation in post-ischemic neuroprotection using the mice transient middle cerebral artery occlusion model of experimental stroke. Based on the bioinformatic predictions and m6A abundance, pro-apoptotic transcription factor Jun proto-oncogene (c-Jun) with 19 m6A sites was chosen as an exemplary target. FTO overexpression normalized the post-stroke m6A hypermethylation of c-Jun without altering its transcript levels. FTO-dependent m6A demethylation suppressed translation of c-Jun. Consequently, several c-Jun target genes are transcriptionally repressed, and the post-ischemic neuronal apoptosis is decelerated, as seen by decreased cleaved caspase-3 levels and TUNEL+ neurons in the FTO AAV9 treated group compared to the control AAV9 treated group. Moreover, replenishing c-Jun precluded the FTO-mediated post-stroke neuroprotection and functional recovery. Collectively, this study demonstrated that the FTO/m6A/c-Jun axis ameliorates post-stroke neuronal apoptosis and brain damage, leading to better functional outcomes.

Ongoing and predicted range loss of kelp forests in response to climatic stressors is pressing marine managers to look into the adaptive capacity of populations to inform conservation strategies. Characterising how adaptive genetic diversity and structure relate to present and future environmental variation represents an emerging approach to quantifying kelp vulnerability to environmental change and identifying populations with genotypes that potentially confer an adaptive advantage in future ocean conditions. The dominant Australian kelp, Ecklonia radiata, was genotyped from 10 locations spanning 2000 km of coastline and a 9.5°C average temperature gradient along the east coast of Australia, a global warming hotspot. ddRAD sequencing generated 10,700 high-quality single nucleotide polymorphisms (SNPs) and characterized levels of neutral and adaptive genomic diversity and structure. The adaptive dataset, reflecting portions of the genome putatively under selection, was used to infer genomic vulnerability by 2050 under the RCP 8.5 scenario. There was strong neutral genetic differentiation between Australia mainland and Tasmanian populations, but only weak genetic structure among mainland populations within the main path of the East Australian Current. Genetic diversity was highest in the center of the range and lowest in the warm-edge population. The adaptive SNP candidates revealed similar genetic structure patterns, with a spread of adaptive alleles across most warm (northern) populations. The lowest, but most unique, adaptive genetic diversity values were found in both warm and cool population edges, suggesting local adaptation but low evolutionary potential. Critically, genomic vulnerability modeling identified high levels of vulnerability to future environmental conditions in Tasmanian populations. Populations of kelp at range edges are unlikely to adapt and keep pace with predicted climate change. Ensuring the persistence of these kelp forests, by boosting resilience to climate change, may require active management strategies with assisted adaptation in warm-edge (northern) populations and assisted gene flow in cool-edge (Tasmania) populations.

The limitations of Hi-C (high-throughput chromosome conformation capture) profiling in in vitro cell culture include failing to recapitulate disease-specific physiological properties and lacking a clinically relevant disease microenvironment. In this study, we conduct Hi-C profiling in a pilot cohort of 12 breast tissues comprising two normal tissues, five ER+ breast primary tumors, and five tamoxifen-treated recurrent tumors. We demonstrate 3D chromatin-regulated breast tumor heterogeneity and identify a looping-mediated target gene, CA2, which might play a role in driving tamoxifen resistance. The inhibition of CA2 impedes tumor growth both in vitro and in vivo and reverses chromatin looping. The disruption of CA2 looping reduces tamoxifen-resistant cancer cell proliferation, decreases CA2 mRNA and protein expression, and weakens the looping interaction. Our study thus provides mechanistic and functional insights into the role of 3D chromatin architecture in regulating breast tumor heterogeneity and informs a new looping-mediated therapeutic avenue for treating breast cancer.

Obesity, diabetes, and cardiovascular diseases are major health concerns worldwide. In recent times, research has focused on identifying food-derived molecules and their relationship with metabolic diseases. A study was conducted to establish a process for characterizing the biological targets of capsaicinoids found in chili peppers. Capsaicinoids are a group of compounds including Capsaicin, Dihydrocapsaicin, Nordihydrocapsaicin, Homodihydrocapsaicin, Homocapsaicin, and Nonivamide. The study aimed to use bioinformatics tools to analyze these compounds and their effect on metabolic targets. To achieve this, a search was conducted for SMILES sequences of chili pepper capsaicinoids. The 2D and 3D similarity analyses were performed with compounds known to be experimentally active on their protein targets. These ligands were then analyzed, and predictions were made about enriched biological terms and bio-pathways. A protein-protein interaction analysis was performed on metabolic targets. Additionally, pharmacokinetics and CYP450 interaction prediction were analyzed using capsaicinoids. The molecular activity of the identified ligands for the six capsaicinoids were classified as G-protein-coupled receptors, proteases, membrane receptors, oxidoreductases, erasers, electrochemical transporters, cytochrome P450s, and hydrolases. There are several signaling pathways modulated by capsaicinoids, including insulin signaling, insulin resistance, AGE-RAGE signaling in diabetic complications, endocrine resistance, lipid metabolism, and atherosclerosis. The study found that capsaicin interacts more strongly with pathways that are important in metabolic diseases, such as obesity, cancer, diabetes mellitus, and their complications. These findings could be useful in developing strategies to mitigate the impact of metabolic diseases.

Dunyeguanxinning (DYGXN) has been shown to have therapeutic effects in preventing and treating atherosclerosis. However, the active components and anti- atherosclerosis (AS) mechanisms of DYGXN remain to be elucidated.

This study aims to explore the functional mechanisms of Dunyeguanxinning (DYGXN) in the prevention and treatment of atherosclerosis (AS).

The components of DYGXN were identified using UPLC-Q-Orbitrap HRMS technology. Network pharmacology and molecular docking were utilized to explore the functional mechanisms and core targets of DYGXN. An AS mouse model was established to verify the results obtained from network pharmacology.

A total of 20 compounds were identified or tentatively characterized in the DYGXN solution. In total, 149 potential targets of DYGXN and 4,071 AS-related targets were obtained, with 92 overlapping targets between DYGXN and AS. The protein-protein interaction (PPI) network analysis identified 10 key targets, including SRC and STAT3, along with four core subnetworks. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis indicated that these targets were primarily involved in processes such as phosphorylation, positive regulation of cell migration, inflammatory response and pathways such as lipid and atherosclerosis. Molecular docking demonstrated strong binding affinities between DYGXN compounds and core targets. In vivo experiments showed that DYGXN improved blood lipid levels, reduced pro-inflammatory cytokines, downregulated phosphorylation of Src and STAT3, alleviated hepatic lipid accumulation, and inhibited plaque formation in AS model mice.

DYGXN contains multiple saponins that exert anti-AS effects through the regulation of multiple targets and pathways.

Over the past decades, MDV has dramatically evolved towards more virulent strains and remains a persistent threat to the world's poultry industry. We performed genome-wide gene expression analysis in the spleen, thymus, and bursa tissues from MD-resistant line and susceptible line to explore the mechanism of MD resistance and susceptibility. We identified genes and pathways associated with the transcriptional response to MDV infection using the robust RNA sequencing approach. The transcriptome analysis revealed a tissue-specific expression pattern among immune organs when confronting MDV. At pathway and network levels, MDV infections influenced cytokine-cytokine receptor interaction and cellular development in resistant and susceptible chicken lines. Meanwhile, we also observed different genetic responses between the two chicken lines: some pathways like herpes simplex infection and influenza A were found in MD resistant line spleen tissues, whereas metabolic-related pathways and DNA replication could only be observed in MD susceptible line chickens. In summary, our research renders new perceptions of the MD progression mechanism and beckons further gene function studies into MD resistance.

Hepatic fibrosis (HF) is an intermediate stage in the progression of chronic liver disease to cirrhosis and has been shown to be a reversible pathological process. Known evidence suggests that activation of hepatic stellate cells (HSCs) and degradation of their lipid droplets (LDs) play an indispensable role in the process of HF. Jiawei Taohe Chengqi Decoction (JTCD) can inhibit the activation of HSCs in the process of HF, but the exact mechanism remains to be elucidated.

The aim of this study is to determine whether JTCD inhibits lipophagy and to explore the possible mechanisms of its HF effect in HSCs by regulating the PPARα/TFEB axis.

Network pharmacology and molecular docking were firstly applied to predict the potential mechanism of JTCD for the treatment of HF. In vivo, a mouse model of HF was constructed using carbon tetrachloride (CCl4) solution, and the efficacy of JTCD was assessed by staining of pathological sections, oil red O staining, immunofluorescence (IF), immunohistochemistry (IHC) staining, Western blotting and qRT-PCR. The intervention of JTCD was verified in vitro by induction of activated LX-2 cells with TGF-β solution and intervention using agonists and antagonists of PPARα. Finally, transient transfection of cells using TFEB siRNA was performed for validation studies.

JTCD effectively alleviated CCl4-induced HF in mice and reduced the levels of HF markers α-smooth muscle actin (α-SMA) and collagen I (COL1A1), and inhibited PPARα expression and lipophagy process. In vitro, JTCD delayed the degradation of LDs and reduced lipophagy in LX-2 cells, suggesting a mechanism involving PPARα/TFEB axis signaling regulation.

Pollutant particles can penetrate and accumulate in skin, leading to excessive oxidative stress, inflammation, and skin disorders. Reduced glutathione (GSH) is considered as "the master antioxidant" and major detoxification agent.

To characterize the metabolomic changes of skin keratinocytes under the pollutant benzo[a]pyrene (BaP) challenge and investigate the interventional effects of glutathione amino acid precursors (GAP).

Normal human epidermal keratinocytes (NHEKs) were challenged with BaP with or without GAP treatment. GSH/GSSG levels were measured by UPLC-MS/MS. Non-targeted metabolome analysis was conducted with UPLC-QTOF mass spectrometry. Transcriptomics analysis was performed using RNA-seq. DNA damage biomarker γ-H2AX was analyzed by western blot. Reconstructed pigmented skin equivalent models (pLSE) were used for evaluating phenotypical changes.

One micromolar BaP exposure induced widespread metabolic reprogramming in in vitro NHEKs with over-represented differential metabolites in pathways including purine and pyrimidine nucleotide metabolism, xenobiotic metabolism, methylation, and RNA modification, etc. GAP co-treatment improved GSH/GSSG ratio, reduced reactive BaP metabolites, and partially reversed BaP induced metabolic and transcriptomic alterations. Western blotting further confirmed that GAP treated samples showed reduced γ-H2AX staining. In pLSE models, GAP treatment significantly ameliorated BaP induced skin darkness and hyperpigmentation.

In summary, GAP shows in vitro protective effects against BaP by maintaining GSH homeostasis, helping metabolic detoxification, reducing DNA damage, and is effective in preventing hyperpigmentation of skin models under pollution challenge.

The effectiveness of Sanhuang Shu'ai decoction (SSD), a traditional Chinese medicine used to treat diarrhea and colitis, especially ulcerative colitis (UC), is not well understood regarding how its chemical components work.

This research used ultra-high-performance liquid chromatography (UHPLC)-tandem mass spectrometry (MS), network pharmacology, and molecular docking to understand the active substances and potential mechanisms of SSD in treating UC.

UHPLC and MS analyses identified 710 active components in SSD extracts (ZYTQY) and 387 in SSD-containing serum (HYXQ), with 35 active compounds found in both ZYTQY and HYXQ and 67 active compounds from SSDD (SSD compound obtained directly from the database), along with 6 metabolites that may be key components in its function. Subsequently, we used PubChem, DrugBank, and TTD to identify 108 potential targets from SSDD, and 27 hub genes were found by constructing the PPI network. GO and KEGG pathway analyses confirmed that SSDD may be effective in treating UC through the PI3K/AKT and HIF-1 signaling pathways. The pathway analysis of 4 metabolites in SSD highlights the continued importance of the PI3K/AKT pathway. Molecular docking and simulations indicate that baicalein, oroxylin A, quercetin, and wogonin may aid in treating UC by regulating the MAPK3 and NFKB1 genes. Baicalein interacts with several specific targets, including EGFR, MAPK1, MAPK3, NFKB1, PTGS2, and TP53.

SSD treats UC through various compounds and pathways targeting multiple areas, whereas baicalein specifically promotes intestinal repair in UC by modulating EGFR-PI3K/AKT/NFκB, EGFR/PI3K/AKT-/TP53, and EGFR/PI3K/A KT/MAPK signaling pathways.

Hypertensive disorders of pregnancy are important risk factors for later-life cardiovascular diseases. SGLT2 (sodium-glucose cotransporter-2) inhibition improves outcomes in heart failure, a later-life risk that disproportionately affects those with preeclampsia superimposed on chronic hypertension. SGLT2 inhibition during pregnancy and the postpartum period has not been effectively modeled or tested in superimposed preeclampsia as a potential cardiovascular risk-reducing intervention.

This study aimed to (1) confirm the phenotype of superimposed preeclampsia in the BPH/2J mouse model, (2) test the short- and long-term obstetrical and cardiovascular effects of administering an SGLT2 inhibitor (dapagliflozin) in pregnancy and the immediate postpartum period in this model, and (3) identify molecular effects of SGLT2 inhibition in cardiovascular tissues during and after a treated pregnancy.

We established the BPH/2J model of superimposed preeclampsia and then randomly assigned pregnant BPH/2J mice with implanted telemetry devices to dapagliflozin-enriched chow or control chow starting early in gestation through 21 days after delivery. Maternal cardiovascular and obstetrical outcomes including circulating plasma protein markers, urine studies, obstetrical ultrasounds, and tissue histopathology were compared between the groups. Hearts and aortae were analyzed using serial echocardiography and spatial transcriptomics in late gestation or at 6 months postpartum.

BPH/2J mice had baseline chronic hypertension that worsened in pregnancy with the development of proteinuria and elevated plasma sFlt-1 levels, consistent with superimposed preeclampsia. Mid-gestation systolic blood pressures were higher in the untreated group than the dapagliflozin-treated group (+2.87 mm Hg; P<.001). There were no differences in the number of pups or estimated fetal pup weights between the groups, whereas amniotic fluid volume, placental size, and markers of placental perfusion were improved in the dapagliflozin-treated group. The untreated group had higher aortic peak velocities in late pregnancy compared with the dapagliflozin-treated group (748.1 vs 561.9 mm/s; P=.004×10-3). One maternal death occurred in the untreated group, with no events in the dapagliflozin-treated group. In late life, the untreated group had significant loss of left ventricular function relative to their prepregnancy baseline, whereas dapagliflozin-treated mice had relatively preserved left ventricular function (-20.0% vs -7.6% change; P=.004×10-3; 49.0%±6.34% untreated-baseline to 30.5%±6.78% untreated-aged; 44.9%±8.63% treated-baseline to 36.5%±6.39% treated-aged). Tissue transcriptomic analyses and Masson's trichrome staining demonstrated attenuation of cardiac fibrosis and extracellular remodeling processes with SGLT2 inhibition.

In a murine model of superimposed preeclampsia, dapagliflozin treatment during pregnancy and the puerperium improved physiological cardiovascular parameters during gestation and cardiac function later in life. This may be related to observed molecular effects of SGLT2 inhibition treatment, particularly its antifibrotic and metabolic actions associated with reduced markers of fibrotic pathologic remodeling in treated BPH/2Js during and after pregnancy.

Primary open-angle glaucoma (POAG) is the leading cause of irreversible vision loss. However, its genetic risk factors, such as the vascular hypothesis of POAG, remain unclear. Here, we aimed to explore the genetic associations between mean ocular perfusion pressure (MOPP) and POAG. We performed genome-wide analysis with gene-based analysis from the UK Biobank (N = 459,195), which includes genetic data and ocular phenotypes. Bidirectional two-sample Mendelian randomisation (MR), multivariable MR, and mediation analysis were conducted using summary statistics from a previous meta-analysis of genome-wide association studies (N = 216,257).

CEP85L, GRIA4, GRIN2A, LRFN5, MAGI1, POU6F2, RBFOX1, RBMS1, RBMS3, RBPMS, TRHDE, TUBB3, ZFHX3, and ZMAT4 were significantly correlated with various ocular phenotypes. Furthermore, POAG shared strong genetic associations with corneal resistance factor (CRF), intraocular pressure (IOP), refractive error (RE), and MOPP but none with corneal hysteresis (CH). Univariable MR showed a negative causal effect of CH, CRF, and MOPP and a positive causal effect of IOP on POAG occurrence. In multivariable MR, MOPP exhibited a direct causal effect on POAG, which was supported by the mediation analysis results.

We successfully determined 14 genetic loci related to CH, CRF, IOP, RE, and MOPP. In univariable and multivaribale MR analyses, a causal effect of MOPP on POAG were observed. In addition, the mediation analysis supported that MOPP exerted direct and indirect causal effects on POAG. This finding indicates that MOPP may serve as a potential causal factor in POAG, providing valuable insights into the pathophysiology of POAG as vascular theory.

Beagle dogs are widely used in biomedical research, but their genetic diversity and population structure require further investigation. This study aimed to assess genetic diversity, population structure, and selection signals in a foundational Beagle breeding population using genome-wide SNP genotyping.

A total of 459 Beagle dogs (108 males, 351 females) were genotyped using the Canine 50K SNP chip. After quality control, 456 individuals and 31,198 SNPs were retained. Genetic diversity indices, principal component analysis (PCA), identity-by-state (IBS) distance, a genomic relationship matrix (G-matrix), runs of homozygosity (ROH), and Tajima's D selection scans were analyzed.

The average minor allele frequency was 0.224, observed heterozygosity was 0.303, and expected heterozygosity was 0.305. A total of 2990 ROH segments were detected, with a mean inbreeding coefficient of 0.031. Phylogenetic analysis classified 106 stud dogs into 13 lineages. Selection signal analysis identified TTN (muscle function) and DLA-DRA, DLA-DOA, DLA-DMA (immune regulation) under selection.

The Beagle population exhibits high genetic diversity and low inbreeding. To maintain genetic stability and ensure the long-term conservation of genetic resources, structured breeding strategies should be implemented based on lineage classifications.

Endoplasmic reticulum (ER) stores Ca2+ and plays crucial roles in protein folding, lipid transfer, and it's perturbations trigger an ER stress. In the liver, chronic ER stress is involved in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH). Dysfunction of sarco/endoplasmic reticulum calcium ATPase (SERCA2), a key regulator of Ca2+ transport from the cytosol to ER, is associated with the induction of ER stress and lipid droplet formation. We previously identified NACHT and WD repeat domain-containing protein 1 (Nwd1) localized at the ER and mitochondria. However, the physiological significance of Nwd1 outside the brain remains unclear. In this study, we revealed that Nwd1-/- mice exhibited pathological manifestations comparable to MASH. Nwd1 interacts with SERCA2 near ER membranes. Nwd1-/- livers exhibited reduced SERCA2 ATPase activity and a smaller Ca2+ pool in the ER, leading to an exacerbated state of ER stress. These findings highlight the importance of SERCA2 activity mediated by Nwd1 in the pathogenesis of MASH.

Cerebral ischemia-reperfusion (CIRI) represents a complex disease entity that encompasses multiple pathways. The occurrence of CIRI induces cerebral infarction, accompanied by brain tissue necrosis and focal neuronal impairment. Previous studies have demonstrated that ferroptosis, a specific cell death pathway implicated in CIRI, plays a crucial role in mediating the pathophysiological process of this condition. Puerarin, is known to possess vasodilatory, antioxidant, and neuroprotective properties. However, its precise role in ferroptosis as well as the underlying mechanisms remains elusive. In this study, we delved into the neuroprotective mechanisms of puerarin using both the rat middle cerebral artery occlusion (MCAO) model and the HT22 cell model of oxygen-glucose deprivation/reperfusion (OGD/R). In the MCAO model, puerarin was found to exhibit an inhibitory effect on ACSL4, which was consistent with that of rosiglitazone. Simultaneously, it was capable of counteracting the inhibition of GPX4 by RSL3. These findings suggest that puerarin modulates GPX4 and ACSL4, thereby exerting an inhibitory effect on ferroptosis. The ferroptosis-protective effect of puerarin was further corroborated in the OGD/R through a positive control experiment with ferrostatin-1, a lipid peroxidation inhibitor. Furthermore, we also recognized the importance of other cell death modalities, such as pyroptosis. Consequently, we verified the neuroprotective effect of puerarin by examining the influence of caspase-1 and GSDMD in HT22. Mechanistically, puerarin alleviates CIRI by respectively inhibiting ferroptosis through the SLC7A11/GPX4/ACSL4 axis and pyroptosis through the caspase-1/GSDMD axis. This research provides novel insights into the targeting and therapeutic potential of puerarin for the treatment of CIRI.

Kadsura coccinea is a traditional Chinese medicine whose roots have long been used to treat various ailments, but little is known about the efficacy of its leaves. In this study, the antidiabetic activity of K. coccinea leaf extract (KCLE) was determined, the main components of KCLE were identified using UPLC-TOF-MS, and network pharmacology and molecular docking were integrated to elucidate the antidiabetic mechanism of KCLE. The results showed that KCLE effectively increased the glucose consumption of IR-HepG2 cells through pyruvate kinase (PK) and hexokinase (HK), promoted glycogen synthesis, and inhibited α-glucosidase and α-amylase activities. KCLE also improves diabetes by regulating AKT1, TNF, EGFR, and GSK3β. These targets (especially AKT1 and TNF) have a high binding affinity with the main active ingredients of KCLE (rutin, luteolin, demethylwedelolactone, maritimetin, and polydatin). Pathway enrichment analysis showed that the antidiabetic effect of KCLE was closely related to the PI3K-Akt signaling pathway, MAPK signaling pathway, AGE-RAGE signaling pathway, and FoxO signaling pathway. These findings provide a theoretical basis for promoting the pharmacodynamic development of K. coccinea and its application in treating diabetes.

Multidrug-resistant Escherichia coli poses a significant threat to the healthcare system by causing treatment failure in infected patients. The use of a beta-lactam in combination with a beta-lactamase inhibitor has been shown to be an effective strategy to solve this problem. In vitro antimicrobial susceptibility experiments have demonstrated the antimicrobial activity of aztreonam and clavulanate. In this investigation, we conducted a transcriptomic analysis to reveal the downstream differential gene expression in E. coli ymmD45 (a strain newly isolated and found to carry the New Delhi metallo-β-lactamase gene) following exposure to aztreonam and clavulanate separately, as well as their combination. Differential gene expression, pathway enrichment, and gene network analyses demonstrated the polygenic nature of the response to the combination treatment, which suppressed the expression of pivotal virulence genes, disrupted two-component regulatory systems for bacteria to resist external stress, and interfered with the formation of the cellular membrane. Results from single-step mutant selection combined with deep whole-genome sequencing also revealed the spontaneous origin of the resistance mutations and confirmed action mechanisms during the combination treatment. Our study contributes valuable insights into the impact of antibiotic exposure on gene expression, laying the groundwork for understanding antibiotic resistance development in the treatment of multi-drug resistant infections through in vitro studies.IMPORTANCEMultidrug-resistant Escherichia coli is a major challenge in treating infections effectively. Aztreonam and clavulanate combination is promising in combating these resistant bacteria. By investigating the antimicrobial activity of aztreonam and clavulanate using transcriptomic analysis and mutant selection, this research sheds light on the mechanisms underlying antibiotic resistance and the effectiveness of combination therapies. The findings highlight how this particular antibiotic combination suppresses virulence genes, disrupts bacterial regulatory systems, and interferes with cellular functions critical for resistance. Moreover, the study lays the groundwork for understanding antibiotic resistance development in the treatment of multi-drug resistant infections through in vitro studies, offering insights that could inform future strategies in clinical settings. Ultimately, our findings could guide the development of better treatment strategies for multidrug-resistant infections, improving patient outcomes and helping to manage antibiotic resistance in healthcare.

Enterovirus A71 (EV-A71) is the main pathogen of hand-foot-and-mouth disease and sometimes causes neurological disease complications in severe cases. The most recent large EV-A71 outbreak in Taiwan occurred in 2012. We aimed to investigate the gene expression profile of human neuroblastoma cells infected with mild and severe case EV-A71 isolates. EV-A71-infected SK-N-SH cells were sent for RNA sequencing using Illumina Hiseq. Functional gene analysis, qRT-PCR, and luciferase reporter assay were used to investigate the findings obtained from RNA-seq analysis. Expression profile analysis identified 59 significant differentially expressed genes (DEGs) between mild and severe case EV-A71 infection. Gene ontology analysis showed that most of the genes were involved in the regulation of transcription. KEGG pathway enrichment analysis also showed that the DEGs were mainly enriched in the tumor necrosis factor and nuclear factor kappa B (NF-κB) signaling. We found that EV-A71 may affect neurons to enhance the disease severity by mediating pro-inflammatory cytokines through NF-κB signaling. Additionally, infection with severe case EV-A71 enhances NF-κB activity, increases pro-inflammatory cytokines, and reduces cell survival. These results indicate that possible pathogenic mechanisms that were linked to the neuropathogenesis of EV-A71 infection and the above genes might be potential biomarkers or antiviral targets for the prevention of neuronal complications in severe EV-A71 infections in the future.

Background: Cashmere, valued for its exceptional softness and warmth, is a major focus in goat breeding due to its high economic importance. However, the molecular mechanisms underlying cashmere production remain largely unknown, hindering efforts to optimize yield and quality. Additionally, domestic goats exhibit remarkable adaptability to diverse climates, ranging from arid northern regions to humid southern areas, yet the genetic basis for these adaptations is poorly understood. Exploring the genetic factors driving cashmere production and climatic adaptation could provide crucial insights into trait evolution and support the development of breeding strategies for improved productivity and resilience. Methods: We utilized whole-genome resequencing data from 157 samples representing 14 goat populations to analyze the genetic diversity between cashmere and non-cashmere breeds. Additionally, we conducted the tests of selective sweeps (i.e., pairwise FST, θπ and XP-EHH) for cashmere traits and genome-environment association analysis (i.e., XtX statistic), respectively. Results: We identified strong selective signatures in previous reports (e.g., AKT3, FOXP1, FGF5, TGFBR3) and novel genes (e.g., ZEB1, ZNRF3, MAPK8IP3, MAPK8IP2, AXIN1) associated with cashmere traits. Further gene annotation and KEGG analyses showed that these genes were identified to be the most probable genes accounting for the cashmere traits. Also, we detected some genes such as PDGFRB, PRDM8, SLC26A2, SCAMP1, EPHX1, CDC25A, and POLK that played critical roles in the adaptation of goats to local climate variation. Conclusions: Collectively, our results provide novel insights into the genetic mechanisms underlying the cashmere traits and climatic adaptation, and also identified new genetic markers for genetic improvement in goats.

The objective of this study was to explore the potential genetic link between Crohn's disease and breast cancer, with a focus on identifying druggable genes that may have therapeutic relevance. We assessed the causal relationship between these diseases through Mendelian randomization and investigated gene-drug interactions using computational predictions. This study sought to identify common genetic pathways possibly involved in immune responses and cancer progression, providing a foundation for future targeted treatment research. The dataset comprises single nucleotide polymorphisms used as instrumental variables for Crohn's disease, analyzed to explore their possible impact on breast cancer risk. Gene ontology and pathway enrichment analyses were conducted to identify genes shared between the two conditions, supported by protein-protein interaction networks, colocalization analyses, and deep learning-based predictions of gene-drug interactions. The identified hub genes and predicted gene-drug interactions offer preliminary insights into possible therapeutic targets for breast cancer and immune-related conditions. This dataset may be valuable for researchers studying genetic links between autoimmune diseases and cancer and for those interested in the early identification of potential drug targets.

The proteasome plays a pivotal role in protein degradation, and its impairment is associated with various pathological conditions, including neurodegenerative diseases. It is well understood that Nrf1 coordinates the induction of all proteasome genes in response to proteasome dysfunction. However, the molecular mechanism regulating the basal expression of the proteasome remains unclear. Here we identify the transcription factor THAP1, the causative gene of DYT6 dystonia, as a regulator of proteasome activity through a genome-wide genetic screen. We demonstrated that THAP1 directly regulates the expression of the PSMB5 gene, which encodes the central protease subunit β5. Depletion of THAP1 disrupts proteasome assembly, leading to reduced proteasome activity and the accumulation of ubiquitinated proteins. These findings uncover a regulatory mechanism for the proteasome and suggest a potential role for proteasome dysfunction in the pathogenesis of dystonia.

Evolution in profound darkness often leads to predictable, convergent traits, such as the loss of vision. Yet, the consequences of such repeated evolutionary experiments remain obscure, especially regarding fundamental regulatory behaviors like circadian rhythms. We studied circadian clocks of blind cave spiders and their sighted relatives. In the field, cave spiders exhibit low per expression and maintain constant activity levels. Curiously, their clocks are not permanently lost; exposure to monochromatic blue light restores both circadian gene expression and behavioral rhythms. Conversely, blocking blue light in sighted relatives induces an arrhythmic "cave phenotype." Our RNA interference experiments suggest that clock genes regulate the rhythmicity of the huddle response, establishing a link between circadian gene networks and this behavioral rhythm. We demonstrate that circadian regulation is readily toggled and may play a latent role, even in constant darkness. Overall, our study expands understanding of circadian clock variations and paves the way for future research on the maintenance of silent phenotypes.

How master splicing regulators cross talk with each other and to what extent transcription regulators are differentially spliced remain unclear in the developing brain. Here, cell-type-specific RNA-Seq analyses of the developing neocortex uncover variable expression of the Rbfox1/2/3 genes and enriched alternative splicing events in transcription regulators, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glial progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1 Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1 Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex. (The sex has not been reported to affect cortical neurogenesis in mice, and embryos of both sexes were studied without distinguishing one or the other.).

Ewing sarcomas (ESs) are biologically aggressive tumours of bone and soft tissues caused by chromosomal translocations yielding in-frame fusion proteins driving the neoplastic transformation. The DNA/RNA helicase DHX9 is an important regulator of cellular processes often deregulated in cancer. Using transcriptome profiling, our study reveals cancer-relevant genes whose splicing is modulated by DHX9. Immunodepletion experiments demonstrate that DHX9 impacts on the recruitment of U2 small nuclear RNP (snRNP) onto the pre-mRNA. Analysis of structure and sequence features of DHX9 target exons reveal that DHX9-sensitive exons display shorter flanking introns and contain HNRNPC and TIA1 consensus motifs. A prominent target of DHX9 is exon 11 in the Cortactin (CTTN) gene, which is alternatively spliced to generate isoforms with different activities in cell migration and tumour invasion. Alternative inclusion of the exon 11 in CTTN gene is one of the most recurrent isoform switches in multiple cancer types, thus highlighting the pivotal role of DHX9 in defining the tumour phenotype. Biochemical analyses reveal that DHX9 binding promotes the recruitment of U2snRNP, SF3B1, and SF3A2 to the splice sites flanking exon 11. These findings uncover a new role of DHX9 in the control of co-transcriptional splicing in ES, which may represent a new druggable target to counteract ES malignancy.

The flowers of Pueraria lobate (Puerariae Flos) have served as a traditional Chinese medicinal and food herbage plant for many years. Tectoridin is one of the most active metabolites extracted from flowers of Pueraria lobate and has a variety of beneficial activities, including antioxidative, hypoglycemic, and anti-inflammatory activities. Nevertheless, the functions and potential mechanisms underlying tectoridin in cerebral ischemia/reperfusion injury have not been well interpreted; thus, a network analysis strategy was performed to systematically evaluate its pharmacological mechanisms, which were further validated in rats with cerebral ischemia. Network analysis predicted that tectoridin could attenuate brain damage after stroke by modulating signaling pathways associated with redox, inflammation, and autophagy. The experimental results demonstrated an improvement in neurological function in rats treated with tectoridin, along with a significant reduction in cerebral infarction volume. The neuroprotective benefits of tectoridin stem, in part, from its antioxidant capabilities, which include the upregulation of Nrf2/HO-1 protein expression, reduction of the TLR4/MYD88/NF-κB inflammatory pathway, and inhibition of the PI3K/Akt/mTOR pathway, contributing to its anti-apoptotic effects. This investigation offers a thorough examination of the pathways and targets linked to the therapeutic effects of tectoridin on ischemic stroke, highlighting its anti-inflammatory, antioxidative, and anti-apoptotic mechanisms. These findings serve as a valuable reference for the development and exploration of effective anti-ischemic stroke medications.

To analyze the expression, biological function of branched chain amino-acid transaminase 1 (BCAT1) in oral squamous cell carcinoma (OSCC).

Real-time PCR and immunohistochemistry were used to analyze the expression of BCAT1 protein in OSCC and normal oral tissues. Based on the clinicopathological information of patients, the relationship between the expression of BCAT1 protein and other clinicopathological factors was analyzed. Real-time PCR and western blot assays were used to analyze the expression of BCAT1 gene and protein in normal human oral keratinocytes (HOK) and human OSCC cells, respectively. After BCAT1 overexpression or knockdown, the proliferation, cell cycle, migration, and invasion of human OSCC cells were analyzed by CCK8, flow cytometry, wound healing, and transwell invasion assays, respectively. After adding the BCAT1 inhibitor EGR240 to OSCC cells, the changes in cell proliferation, migration, and invasion ability in OSCC cells were analyzed. Based on the TCGA database, the involved signal pathway in BCAT1-related and BCAT1-binding genes was obtained for Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, verified by western blot assays. After inhibiting PI3K, the effect of BCAT1 on the expression of the downstream phosphorylated protein of the PI3K-Akt signaling pathway was analyzed by western blot assays. The relationship between the expression of BCAT1 and EMT-related protein of OSCC cells was also analyzed.

The expression of BCAT1 gene and protein were upregulated in OSCC tissue, which positively correlated with the pathological grade of patients with OSCC. Compared with normal oral keratinocytes, BCAT1 gene and protein were upregulated in OSCC cells. BCAT1 overexpression promoted the proliferation, migration, and invasion of OSCC cells. BCAT1 knockdown or inhibition could reduce the proliferation, migration, and invasion abilities of OSCC cells. The results of bioinformatics analysis and Western bolt showed that BCAT1 could regulate the activation of PI3K-Akt signaling pathway, and promote epithelial-mesenchymal transition (EMT) of OSCC cells.

BCAT1 could promote the proliferation, migration, and invasion of OSCC cells via PI3K-Akt signaling pathway, which is a potential therapeutic target for OSCC.

Luteolin and quercetin, which are flavonoids, are present in various traditional Chinese medicines. Although they have been shown to improve obesity, the specific mechanisms of action remain unclear. This study aimed to determine pivotal targets and major regulatory pathways involved in their mechanisms of action using network pharmacology and transcriptome sequencing. Data on luteolin/quercetin-related targets were acquired from the PharmMapper platform, and data on known obesity-related targets were collected from the OMIM and GeneCards databases. Differentially expressed genes (DEGs) involved in luteolin and quercetin action that regulate adipogenic differentiation were identified using RNA sequencing (RNA-seq). Bioinformatic analyses were performed to identify potential target genes and pathways regulated by luteolin/quercetin during adipogenesis. Finally, key genes and pathways were validated through quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. Network pharmacology showed that luteolin/quercetin was closely associated with anti-obesity targets. The related pathways were metabolic, PI3K/AKT, and MAPK pathways. RNA-seq revealed 91 common DEGs involved in luteolin/quercetin regulation of adipogenic differentiation. Finally, nine potential target genes (including CIDEC, Mgll, Slc2a4, Pck1, and PNPLA3) were identified, and the AMPK and AKT signaling pathways were verified. The present study provides novel information regarding the molecular mechanism of luteolin and quercetin action in treating obesity and demonstrates their therapeutic effects through multiple targets and pathways.

Heavy metals in our direct environment have profound effects on human health and while some are essential for life, others can be toxic. In vivo studies often focus on clinical features caused by overexposure to, or by deprivation of a heavy metal. However, to understand the cellular impact of heavy metals on health, studies in healthy volunteers before symptom onset are needed. Here, we explored the impact of mercury, lead and selenium in over 800 British female twins on multi-tissue gene expression levels as an intermediate phenotype. Total mercury, lead and selenium concentrations were determined in plasma as a proxy for heavy metal exposure. We identified significant associations between total mercury levels measured in plasma, that fall within normal ranges, and expression of 873 genes within skin tissue, including PUSL1, SAMD10, ERCC1, MRPL17, NDUFB8, SELENOH, SEC31A, and KAT7P1. Functional analysis of genes associated with total mercury levels in plasma show a strong link to the mitochondrial oxidative phosphorylation pathway (p-value = 3.02 × 10-10). Analysis of mitochondrial-specific gene expression supported involvement of genes of oxidative phosphorylation complexes (MT-ND4L, and MT-ND5), which are encoded in mitochondrial DNA. These results suggest that mercury is likely detrimental to the energy metabolism of mitochondria. We also tested for associations between total mercury levels in plasma and gene expression in adipose and whole blood samples, but did not identify significant associations in these tissues, nor with lead or selenium in any tissue. Our results demonstrate that subtoxic mercury exposure leaves a clear molecular signature. It also underscores the necessity of conducting tissue-specific association studies to accurately capture the molecular impact of environmental exposures, as only relevant tissues will manifest a response to environmental exposures.

Insulin resistance is major factor in the development of metabolic syndrome and type 2 diabetes (T2D). We extracted 430 genes from literature associated with both insulin resistance and inflammation. The highly significant pathways were Toll-like receptor signaling, PI3K-Akt signaling, cytokine-cytokine receptor interaction, pathways in cancer, TNF signaling, and NF-kappa B signaling. Among the 297 common genes in all datasets of various T2D patients' tissues including blood, muscle, liver, pancreas, and adipose tissues, 71% and 60% of these genes were differentially expressed in pancreas (GSE25724) and liver (GSE15653), respectively. A total of 169 genes contain highly conserved motifs for various transcription factors involved in immune response, thereby suggesting coordinated expression. Through co-expression analysis, we obtained three modules. The respective modules had 78, 158, and 55 genes, and TRAF2, HMGA1, and RGS5 as hub genes. Further, we used the BioNSi pathways simulation tool and identified the following five KEGG pathways perturbed in four or more tissues, namely Toll-like receptor signaling pathway, RIG-1-like receptor signaling pathway, pathways in cancer, NF-kappa B signaling pathway, and insulin resistance pathway. The genes NFKBIA and IKBKB are common to all these five pathways. In addition, using the NF-κB computational activation model, we identified that the reversal of NF-κB constitutive activation through overexpression of NFKB1 (P50 homodimer), PPARG, PIAS3 could reduce insulin resistance by almost half of its original value. To conclude, co-expression studies, gene expression network simulation, and NF-κB computational modeling substantiate the causal role of NF-κB pathway in insulin resistance. These results taken together with other published evidence suggests that the TNF-TRAF2-IKBKB-NF-κB axis could be explored as a potential target in combination with available metabolic targets in the management of insulin resistance.

The online version contains supplementary material available at 10.1007/s13205-024-04202-4.

Cronobacter sakazakii is a foodborne pathogen linked to severe infections in infants and often associated with contaminated powdered infant formula. The RecA protein, a key player in DNA repair and recombination, also influences bacterial resilience and virulence. This study investigated the impact of recA deletion on the pathogenicity and environmental stress tolerance of C. sakazakii BAA-894. A recA knockout mutant displayed impaired growth, desiccation tolerance, and biofilm formation. In a rat model, the mutant demonstrated significantly reduced virulence evidenced by higher host survival rates and lower bacterial loads in blood and tissues compared to the wild-type strain. Proteomic analysis revealed extensive disruptions in protein expression, particularly downregulation of carbohydrate metabolism and respiration-related proteins, alongside increased protein deamidation and oxidation. Functional assays identified fructose-bisphosphate aldolase as a target of oxidative and deamidative damage, resulting in reduced enzymatic activity and glycolytic disruption. These findings highlight the critical role of RecA in maintaining protein homeostasis, environmental resilience, and pathogenicity in C. sakazakii, providing valuable insights for developing targeted interventions against this pathogen.IMPORTANCECronobacter sakazakii poses significant risks due to its ability to persist in low-moisture environments and cause severe neonatal infections. This study identifies RecA as a key factor in environmental resilience and virulence, making it a promising target for mitigating infections and contamination. Inhibiting RecA function could sensitize C. sakazakii to stress during production and sterilization processes, reducing its persistence in powdered infant formula. Future research on RecA-specific inhibitors may lead to innovative strategies for enhancing food safety and preventing infections caused by this pathogen.

Tourette disorder (TS) is characterized by motor hyperactivity and tics that are believed to originate in the basal ganglia. Postmortem immunocytochemical analyses has revealed decreases in cholinergic (CH), as well as parvalbumin and somatostatin GABA (gamma-aminobutyric acid) interneurons (INs) within the caudate/putamen of individuals with TS.

We obtained transcriptome and open chromatin datasets by single-nucleus RNA sequencing and single-nucleus ATAC sequencing, respectively, from caudate/putamen postmortem specimens of 6 adults with TS and 6 matched normal control subjects. Differential gene expression and differential chromatin accessibility analyses were performed in identified cell types.

The data reproduced the known cellular composition of the human striatum, including a majority of medium spiny neurons (MSNs) and small populations of GABA-INs and CH-INs. INs were decreased by ∼50% in TS brains, with no difference in other cell types. Differential gene expression analysis suggested that mitochondrial oxidative metabolism in MSNs and synaptic adhesion and function in INs were both decreased in subjects with TS, while there was activation of immune response in microglia. Gene expression changes correlated with changes in activity of cis-regulatory elements, suggesting a relationship of transcriptomic and regulatory abnormalities in MSNs, oligodendrocytes, and astrocytes of TS brains.

This initial analysis of the TS basal ganglia transcriptome at the single-cell level confirms the loss and synaptic dysfunction of basal ganglia INs, consistent with in vivo basal ganglia hyperactivity. In parallel, oxidative metabolism was decreased in MSNs and correlated with activation of microglia cells, which is attributable at least in part to dysregulated activity of putative enhancers, implicating altered epigenomic regulation in TS.

This study aims to utilize proteomics, bioinformatics, and machine learning algorithms to identify diagnostic biomarkers in the serum of patients with acute and chronic brucellosis.

Proteomic analysis was conducted on serum samples from patients with acute and chronic brucellosis, as well as from healthy controls. Differential expression analysis was performed to identify proteins with altered expression, while Weighted Gene Co-expression Network Analysis (WGCNA) was applied to detect co-expression modules associated with clinical features of brucellosis. Machine learning algorithms were subsequently used to identify the optimal combination of diagnostic biomarkers. Finally, ELISA was employed to validate the identified proteins.

A total of 1,494 differentially expressed proteins were identified, revealing two co-expression modules significantly associated with the clinical characteristics of brucellosis. The Gaussian Mixture Model (GMM) algorithm identified six proteins that were concurrently present in both the differentially expressed and co-expression modules, demonstrating promising diagnostic potential. After ELISA validation, five proteins were ultimately selected.

These five proteins are implicated in the innate immune processes of brucellosis, potentially associated with its pathogenic mechanisms and chronicity. Furthermore, we highlighted their potential as diagnostic biomarkers for brucellosis. This study further enhances our understanding of brucellosis at the protein level, paving the way for future research endeavors.

Dynamic shuttling of proteins between the nucleus and cytoplasm orchestrates vital functions in eukaryotes. Here, we reveal the multifaceted functions of Arabidopsis Sin3-associated protein 18 kDa (SAP18) in the regulation of development and heat-stress tolerance. Proteomic analysis demonstrated that SAP18 is a core component of the nuclear apoptosis- and splicing-associated protein (ASAP) complex in Arabidopsis, contributing to the precise splicing of genes associated with leaf development. Genetic analysis further confirmed the critical role of SAP18 in different developmental processes as part of the ASAP complex, including leaf morphogenesis and flowering time. Interestingly, upon heat shock, SAP18 translocates from the nucleus to cytoplasmic stress granules and processing bodies. The heat-sensitive phenotype of a SAP18 loss-of-function mutant revealed a novel role for SAP18 in plant thermoprotection. These findings significantly expand our understanding of the relevance of SAP18 for plant growth, linking nuclear splicing with cytoplasmic stress responses and providing new perspectives for future exploration of plant thermotolerance mechanisms.

Jakun, a Proto-Malay subtribe from Peninsular Malaysia, is believed to have inhabited the Malay Archipelago during the period of agricultural expansion approximately 4 thousand years ago (kya). However, their genetic structure and population history remain inconclusive. In this study, we report the genome structure of a Jakun female, based on whole-genome sequencing, which yielded an average coverage of 35.97-fold. We identified approximately 3.6 million single-nucleotide variations (SNVs) and 517,784 small insertions/deletions (indels). Of these, 39,916 SNVs were novel (referencing dbSNP151), and 10,167 were nonsynonymous (nsSNVs), spanning 5674 genes. Principal Component Analysis (PCA) revealed that the Jakun genome sequence closely clustered with the genomes of the Cambodians (CAM) and the Metropolitan Malays from Singapore (SG_MAS). The ADMIXTURE analysis further revealed potential admixture from the EA and North Borneo populations, as corroborated by the results from the F3, F4, and TreeMix analyses. Mitochondrial DNA analysis revealed that the Jakun genome carried the N21a haplogroup (estimated to have occurred ~19 kya), which is commonly found among Malays from Malaysia and Indonesia. From the whole-genome sequence data, we identified 825 damaging and deleterious nonsynonymous single-nucleotide polymorphisms (nsSNVs) affecting 720 genes. Some of these variants are associated with age-related macular degeneration, atrial fibrillation, and HDL cholesterol level. Additionally, we located a total of 3310 variants on 32 core adsorption, distribution, metabolism, and elimination (ADME) genes. Of these, 193 variants are listed in PharmGKB, and 21 are nsSNVs. In summary, the genetic structure identified in the Jakun individual could enhance the mapping of genetic variants for disease-based population studies and further our understanding of the human migration history in Southeast Asia.

Artificial sweeteners (AS) have been widely utilized in the food, beverage, and pharmaceutical industries for decades. While numerous publications have suggested a potential link between AS and diseases, particularly cancer, controversy still surrounds this issue. This study aims to investigate the association between AS consumption and cancer risk.

Targets associated with commonly used AS were screened and validated using databases such as CTD, STITCH, Super-PRED, Swiss Target Prediction, SEA, PharmMapper, and GalaxySagittarius. Cancer-related targets were sourced from GeneCards, OMIM, and TTD databases. AS-cancer targets were identified through the intersection of these datasets. A network visualization ('AS-targets-cancer') was constructed using Cytoscape 3.9.0. Protein-protein interaction analysis was conducted using the STRING database to identify significant AS-cancer targets. GO and KEGG enrichment analyses were performed using the DAVID database. Core targets were identified from significant targets and genes involved in the 'Pathways in cancer' (map05200). Molecular docking and dynamics simulations were employed to verify interactions between AS and target proteins. Pan-cancer and univariate Cox regression analyses of core targets across 33 cancer types were conducted using GEPIA 2 and SangerBox, respectively. Gene chip datasets (GSE53757 for KIRC, GSE21354 for LGG, GSE42568 for BRCA, and GSE46602 for PRAD) were retrieved from the GEO database, while transcriptome and overall survival data were obtained from TCGA. Data normalization and identification of differentially expressed genes (DEGs) were performed on these datasets using R (version 4.3.2). Gene Set Enrichment Analysis (GSEA) was employed to identify critical pathways in the gene expression profiles between normal and cancer groups. A cancer risk prognostic model was constructed for key targets to further elucidate their significance in cancer initiation and progression. Finally, the HPA database was utilized to investigate variations in the expression of key AS-cancer target proteins across KIRC, LGG, BRCA, PRAD, and normal tissues.

Seven commonly used AS (Aspartame, Acesulfame, Sucralose, NHDC, Cyclamate, Neotame, and Saccharin) were selected for study. A total of 368 AS-cancer intersection targets were identified, with 48 notable AS-cancer targets, including TP53, EGFR, SRC, PIK3R1, and EP300, retrieved. GO biological process analysis indicated that these targets are involved in the regulation of apoptosis, gene expression, and cell proliferation. Thirty-five core targets were identified from the intersection of the 48 significant AS-cancer targets and genes in the 'Pathways in cancer' (map05200). KEGG enrichment analysis of these core targets revealed associations with several cancer types and the PI3K-Akt signaling pathway. Molecular docking and dynamics simulations confirmed interactions between AS and these core targets. HSP90AA1 was found to be highly expressed across the 33 cancer types, while EGF showed the opposite trend. Univariate Cox regression analysis demonstrated strong associations of core targets with KIRC, LGG, BRCA, and PRAD. DEGs of AS-cancer core targets across these four cancers were analyzed. GSEA revealed upregulated and downregulated pathways enriched in KIRC, LGG, BRCA, and PRAD. Cancer risk prognostic models were constructed to elucidate the significant roles of key targets in cancer initiation and progression. Finally, the HPA database confirmed the crucial function of these targets in KIRC, LGG, BRCA, and PRAD.

This study integrated data mining, machine learning, network toxicology, molecular docking, molecular dynamics simulations, and clinical sample analysis to demonstrate that AS increases the risk of kidney cancer, low-grade glioma, breast cancer, and prostate cancer through multiple targets and signaling pathways. This paper provides a valuable reference for the safety assessment and cancer risk evaluation of food additives. It urges food safety regulatory agencies to strengthen oversight and encourages the public to reduce consumption of foods and beverages containing artificial sweeteners and other additives.

Post-translational modifications are crucial in regulating biological functions across both prokaryotes and eukaryotes. In Aeromonas hydrophila, CobQ, a recently identified novel deacetylase, plays a significant role in lysine deacetylation, influencing bacterial metabolism and stress responses. The present study utilized quantitative proteomics to investigate the impact of cobQ deletion on the global protein expression profile in A. hydrophila. Through data-independent acquisition mass spectrometry, we identified 233 upregulated and 41 downregulated proteins in the cobQ deletion mutant (ΔahcobQ) strain compared to the wild-type (WT) strain. Key differentially expressed proteins were involved in oxidative phosphorylation, bacterial secretion, and ribosomal function. Additionally, phenotypic assays demonstrated that the ΔahcobQ strain exhibited an increased resistance to oxidative phosphorylation inhibitors, suggesting a pivotal role for AhCobQ in energy metabolism. Outer membrane proteins and efflux pumps also showed altered expression, indicating potential implications for membrane permeability and antibiotic resistance. These results suggested that AhCobQ plays a vital regulatory role in maintaining metabolic homeostasis and responding to environmental stress, highlighting its potential as a target for therapeutic interventions against A. hydrophila infections.