CCL7 suppression alleviates vascular injury by blocking the CCR5/STAT1 signaling pathway in chronic kidney disease.

In this study, we evaluated the in vivo activity of the E1 element within the insulin promoter region. While we successfully obtained mice carrying a deletion exclusively in the E1 element of Ins2 (2E mice), we were unable to obtain mice with a deletion limited to the E1 element of Ins1. To assess the role of the E1 element in Ins1, we compared the mice carrying deletions in the GG2-GG1/A2-C1 elements with or without an additional E1 element deletion (1GC/1GCE mice). 1GCE2E mice developed diabetes. In contrast, 1GCE23 mice (without deletion in the E1 element of Ins2) did not develop diabetes, suggesting that the E1 element of Ins2 is critical for transcriptional regulation. Furthermore, 1GC2E mice (presence of the E1 element of Ins1) developed diabetes. However, the severity of the disease was milder in 1GC2E mice than in 1GCE2E mice, indicating that the E1 element of Ins1 also contributes to transcriptional regulation. These data suggest that the E1 elements in both Ins1/2 promoters are regulated for the in vivo transcription of insulin genes in mice.

Understanding how genetic variation contributes to organism-wide phenotypes is critical for identifying mechanisms of disease. Here, we present a computational approach to analyze whole-organism comorbidities associated with genes underlying non-obstructive azoospermia (NOA), the most severe form of male infertility. We curated 204 mouse genes with experimentally validated spermatogenic failure and mapped their orthologs and phenotype annotations across humans, M. musculus, D. rerio, D. melanogaster, and C. elegans using a unified cross-species phenotype structure. This framework integrates a newly developed reproductive phenotype ontology with standardized whole-body phenotype categories to enable direct cross-species comparisons, using thousands of genotype-phenotype associations stored in model organism databases. Our analysis shows that most NOA genes have conserved orthologs across models, and that perturbation of these genes is frequently associated with non-reproductive phenotypes. In particular, integumentary defects and neoplastic phenotypes recur across species, supporting a shared genetic basis for epidemiological links between male infertility and systemic disease. Gene-level comorbidity patterns are partially predictable from single-cell RNA-seq, whole-body gene expression, and Gene Ontology annotations, suggesting that fundamental biological constraints shape the systemic consequences of reproductive gene dysfunction. Clustering genes by comorbidity profiles further distinguished genes with isolated reproductive effects from those with broad organismal consequences. This work demonstrates the power of ontology-based cross-species analysis for identifying pleiotropic effects of Mendelian disease mutations, and provides a resource, CoMorbidity DataBase Mapper (CoMo DBM), for joint analysis of genotype-phenotype associations in model organism databases.

A genome-wide in vivo CRISPR screen identifies neuroprotective strategies in the mouse and human retina.

Germ cells in zebrafish are specified by a preformation mechanism, unlike in mice. Max (Myc associated factor X) and its associated PRC1.6 (polycomb repressive complex 1.6) act as negative regulators of germ cell- and meiosis-related genes in mice; however, their function in zebrafish remains unknown. Here, we generated max mutants in zebrafish using genome-editing techniques to investigate the role of Max in germ cell development and meiosis. No obvious morphological abnormalities were observed in the mutants up to 4 days post fertilization (dpf), likely due to maternally supplied max mRNAs. However, the mutants failed to form an inflated swim bladder and gradually died after 10 dpf. The number of primordial germ cells (PGCs) did not differ between the max mutant and wild-type larvae up to 12 dpf. In contrast, analysis of protein expression levels of germ cell-related and meiosis-related genes in PGCs at 9 dpf revealed that the levels of Sycp2, Sycp3, and Dmc1 proteins were significantly increased in max mutants, whereas the expression of Ddx4 and Piwil1 remained unchanged. Together, these results suggest that zebrafish Max selectively represses the expression of a subset of meiotic genes in PGCs.

Comparative analysis of key phagocytic genes in humans and mice using machine learning integrated with single-cell RNA sequencing.

Onecut2, negatively regulated by methyltransferase METTL3, inhibits polycystic ovary syndrome by transcriptionally modulating SIRT3 expression.

Clec4a2 deficiency promotes post-fission osteoclast cell death and suppresses acute inflammation-induced bone loss in the mouse.

The prevalence of heart failure is increasing globally, with poor prognosis, highlighting the need for novel therapeutic strategies. PKCα (protein kinase C alpha), encoded by PRKCA, plays a central role in heart failure pathogenesis. Phosphorylation of PKCα at threonine 497 (T497) triggers a series of intramolecular phosphorylation events, leading to its activation. Ablation of T497 phosphorylation leads to reduced stability and activity of PKCα. We generated mice harboring a phospho-resistant PKCα (T497A) mutation in the germline using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9)-mediated homology-directed repair. To assess the clinical feasibility of postnatal genome editing, we used CRISPR-Cas9 adenine base editing delivered by adeno-associated virus 9 to introduce the T497A substitution into the Prkca gene (PrkcaT497A) in wild-type mice. Mice underwent transverse aortic constriction to model heart failure. Cardiac function, hypertrophy, fibrosis, and transcriptional changes were evaluated by echocardiography, wheat germ agglutinin staining, Masson's trichrome staining, and RNA-sequencing. The editing efficiency of PrkcaT497A was assessed using Sanger sequencing and deep amplicon sequencing. To further explore its clinical potential, we introduced the PRKCAT497A mutation into human induced pluripotent stem cells by nucleofection-mediated adenine base editing. Ca2+ homeostasis was analyzed in Fura-2-loaded human induced pluripotent stem cell-derived cardiomyocytes with PRKCAT497A under chronic AngII (angiotensin II) stimulation. The T497A mutation in PKCα prevented its subsequent phosphorylation and led to PKCα protein degradation. Four weeks after transverse aortic constriction surgery, wild-type mice showed impaired cardiac function, cardiac remodeling, and increased lung weight. In contrast, PKCα phospho-resistant mice showed protection against heart failure-related aberrant changes in cardiac hypertrophy, fibrosis, and cardiac gene expression. Mice administered with adeno-associated virus 9 base editors to prevent T497 phosphorylation exhibited similar cardioprotective effects. In vitro, PKCα-edited induced pluripotent stem cell-derived cardiomyocytes were protected from AngII-induced impairments in contractility and Ca2+ transients. The editing of PRKCAT497A through adenine base editing represents a potential therapeutic approach for human cardiac diseases.

Orthodontic bone remodeling relies on the integration of mechanotransduction and osteoimmunological crosstalk. Mitochondria, as central regulators of both mechanical sensing and immune modulation, play increasingly recognized roles in force-induced inflammation. Exosomes are nanoscale extracellular vesicles that facilitate the cell-to-cell transport of substances. Investigating the role of exosomes in mitochondrial component transfer may provide new insights into fibroblast‒macrophage communication in orthodontics. In this study, we found that mechanical compression induced oxidative stress and aberrant release of mitochondrial DNA (mtDNA) in periodontal ligament fibroblasts (PDLFs). Further experiments verified that cytosolic mtDNA in PDLFs was packaged into exosomes and secreted extracellularly. Upon phagocytosis of these mtDNA-enriched exosomes, macrophages initiate NLRP3-dependent pyroptosis, which further amplifies the local inflammatory response and induces alveolar bone remodeling. Knockout of the Casp1/11 or Nlrp3 gene in mice, blockade of exosome secretion via local injection of GW4869, or alleviation of oxidative stress via oral administration of NAC helped attenuate macrophage pyroptosis and suppress orthodontic bone remodeling. This study suggests that exosome-mediated mtDNA transfer plays a role in regulating orthodontic force-related inflammation. Our findings provide novel insights into the communication between mechanosensitive and immune cells and propose a potential therapeutic strategy for modulating the rate of tooth movement and managing oral mechanically associated inflammation.

The global incidence of ulcerative colitis (UC), a chronic inflammatory bowel disease, is rising. Epi-berberine (EPI), an alkaloid from Coptidis Rhizoma, shows potential for UC treatment. This study aimed to assess EPI's effect on UC and explore the mechanism underlying its UC-alleviating effect. The therapeutic effects of EPI on UC were validated in dextran sulfate sodium (DSS)-induced colitis mice and lipopolysaccharide (LPS)-induced Caco-2 inflammatory models and further investigated the underlying mechanism. Invivo, high-dose EPI (200 mg/kg) attenuated weight loss, reduced disease activity index, increased colon length, lowered colon macroscopic/histological scores, restored intestinal mucosal barrier and inhibited colonic inflammation. EPI (25/50 μM) had similar invitro effects. mRNA-seq identified EPI-regulated genes in UC mice, revealing six gene clusters with analogous expression patterns. The largest cluster contained genes upregulated by DSS but downregulated by EPI, potentially involved in the MAPK pathway. Key DEGs were enriched in PI3K-Akt and MAPK pathways, verified invivo and invitro. Literature retrieval and molecular docking predicted glutaminyl-peptide cyclotransferase (QPCT) as EPI's potential UC therapeutic target. EPI inhibited DSS/LPS-induced QPCT upregulation invivo and invitro; QPCT knockdown suppressed inflammation and preserved Caco-2 monolayer barrier function, while QPCT overexpression reversed EPI's therapeutic effects. QPCT mediates PI3K-Akt/MAPK activation, and its overexpression abrogated EPI's inhibitory effects. EPI alleviates murine UC by protecting the intestinal mucosal barrier and inhibiting inflammation, likely via regulating the QPCT-PI3K-Akt/MAPK pathway. It provides a preclinical basis for developing prophylactic strategies for inflammatory bowel disease.

Mutations in the SHANK3B gene have been strongly implicated in the pathogenesis of autism spectrum disorder (ASD). The medial prefrontal cortex (mPFC) is integral to emotional processing and social behavior, and its atypical development is closely associated with ASD pathogenesis. However, the electrophysiological characteristics of pyramidal neurons within the mPFC and the mechanisms of their synaptic transmission remain inadequately characterized. In the present study, we conducted whole-cell patch-clamp recordings on mPFC pyramidal neurons in Shank3bknockout mice. We observed significant alterations in the membrane properties and excitability of mPFC pyramidal neurons in Shank3b knockout mice; these were accompanied by reduced inhibitory postsynaptic currents and deficiencies in γ-aminobutyric acid (GABA) release or GABAA receptor transport. Additionally, RNA sequencing analysis of PFC tissue revealed differentially expressed genes in Shank3b knockout mice compared with WT mice, with these genes enriched in synaptic function and calcium channel signaling pathways. These findings are consistent with our ultrastructural observations of a reduced postsynaptic density at excitatory synapses, which may further contribute to the impaired number and morphology of pyramidal neurons in the mPFC. Our research offers new insights into the disruption of PFC circuitry that is caused by Shank3b deficiency and establishes connections between the pathophysiological mechanisms underlying ASD and synaptic structural anomalies, ion channel dysregulation, and excitatory/inhibitory imbalances. Together, these findings highlight the importance of Shank3b-mediated regulation of GABA signaling and modulation of intrinsic excitability as prospective therapeutic targets for ASD.

Evolutionary shifts in diel activity patterns shape sensory remodeling across mammals, yet the genetic basis remains poorly understood. Tapirs represent a unique natural experiment, having reverted from a cathemeral ancestor to a nocturnal niche characterized by reduced vision but enhanced hearing and olfaction. Here, we investigate the genetic basis of this phenomenon by generating high-quality chromosome-level genomes for Tapirus terrestris and Tapirus indicus. Comparative analyses revealed extensive lineage-specific remodeling of genes and cis-regulatory elements linked to sensory pathways. Notably, functional validation via CRISPR-Cas9 editing of a tapir-specific conserved noncoding element (CNE74) upstream of the FLT1 gene in mice revealed coordinated sensory effects, including retinal degeneration and reduced visual acuity, yet enhanced auditory sensitivity. These findings suggest that regulatory element evolution may induce pleiotropic effects on competing sensory modalities, offering genetic insights into sensory evolution during temporal niche adaptation and potential relevance to human retinal vascular diseases.

BackgroundBisphenol A (BPA), a typical endocrine-disrupting chemical, is implicated in the pathogenesis of Polycystic Ovary Syndrome (PCOS); however, the underlying molecular mechanisms and pathophysiological processes remain unclear. This study aims to decipher molecular interactions between BPA and PCOS-related genetic networks, and to determine the combinatorial impacts of environmental pollutants on PCOS progression.MethodsWe first identified overlapping genes associated with bisphenol A (BPA) exposure and polycystic ovary syndrome (PCOS) using the Comparative Toxicogenomics Database (CTD). Differentially expressed genes (DEGs) were extracted from three Gene Expression Omnibus (GEO) datasets, while oxidative stress- and apoptosis-related genes were retrieved from the GeneCards database. Subsequently, a series of in silico analyses were performed, including protein-protein interaction (PPI) network construction, functional enrichment profiling, Gene Set Enrichment Analysis (GSEA), immune infiltration evaluation, nomogram development, CB-DOCK molecular docking, and single-cell RNA-seq analysis of the mouse ovarian dataset GSE268919 (DHEA-induced PCOS-like model) to provide cell-type-resolved evidence. Finally, in vitro validation was conducted using primary granulosa cells from PCOS patients and healthy controls, as well as KGN cells, to assess hub gene expression. Functional evaluations were carried out via CCK-8 assay, flow cytometry, quantitative polymerase chain reaction (qPCR), and Western blotting.ResultsWe identified 139 hub genes between BPA exposure and PCOS, with enrichment in hormone metabolism, ovarian steroidogenesis, and reproductive signaling pathways—among which the apoptotic pathway was prominently associated with these hub genes, indicating BPA exerts a profound impact on cell survival in PCOS. Five hub genes (PTAFR, RACGAP1, CYP19A1, FSHR, DMD) were pinpointed, and a nomogram integrating these genes showed robust PCOS predictive accuracy. Single-gene GSEA further linked the hub genes to immune modulation, inflammation, and cell apoptosis—validating their functional relevance to apoptotic processes in PCOS. Immune cell infiltration analysis revealed discrepancies between PCOS and control groups, with hub genes correlating with specific immune subsets (e.g., pro-inflammatory cells) that may exacerbate apoptotic signaling in ovarian tissues. Molecular docking demonstrated strong binding affinity between BPA and the protein products of hub genes, suggesting direct BPA-mediated interference with their roles in regulating cell apoptosis. In the mouse ovarian scRNA-seq dataset (GSE268919), we observed cell-type-specific dysregulation of Cyp19a1 and Dmd (mouse gene symbols), with stress/apoptosis signatures enriched in specific ovarian cell populations, thereby providing supportive cell-type localization for the hub-gene–associated phenotypes. In vitro validation confirmed dysregulated expression of hub genes in PCOS primary granulosa cells; BPA treatment dose-dependently regulated hub gene expression, inhibited KGN cell proliferation, and significantly induced granulosa cell apoptosis.ConclusionBPA exposure disrupts granulosa cell survival in PCOS by driving apoptosis-related molecular reprogramming through key gene regulation, thereby elucidating mechanistic links between environmental pollutants and PCOS progression and highlighting potential molecular targets for intervention.

Lipid self-assembling nanoparticles as a novel platform for mRNA-based vaccination.

Increasing lifespans make health problems in the elderly such as opioid misuse a more prominent concern. Understanding the effects that opioids may have on the aged brain can help us address age-related concerns of opioid exposure. This study aimed to assess potential interactions between aging and opioid exposure. Three-month-old (young adult) and 19-month-old (aged) C57BL/6JN mice were assigned to either a morphine (3mg/kg, i.p.) or saline group. A conditioned placed preference (CPP) task was used to assess reward sensitivity, while rotarod and beam walk tests were used to assess sensorimotor coordination. To assess for potential age-dependent effects of morphine on gene expression, we performed RNA sequencing in the prefrontal cortex (PFC). We found that morphine induced CPP in both age groups. Our results indicate impaired motor coordination in aged mice; however, morphine did not significantly affect motor coordination in either age group, although a trend toward an increased number of slips was observed in morphine-treated aged mice. Transcriptomic analysis revealed more robust effects of morphine on gene expression in the aged brain compared to the young brain. Interestingly, we found limited overlap between morphine-regulated genes in young and old mice, suggesting that the molecular effects of morphine are age-dependent. Taken together, while we found no significant interactions between morphine (at the tested dose) and aging in the behavioral assays, morphine caused age-dependent gene expression changes. Our findings suggest that age should be considered when prescribing opioids and that age-specific therapeutics may help address opioid use disorder in the elderly.

SummaryHomeostatic resident tissue macrophages (RTMs) exhibit diversity across tissues but also share common features that are driven by conserved transcriptional programs. While the transcription factor MafB is highly expressed in macrophages, its role in establishing RTM identity and functions remains unclear. Here we show that MafB was required for the development of bone-marrow-derived macrophages (BMDMs) and most RTMs in vivo. MafB deficiency retained RTM in a CD52high immature stage and disrupted global and tissue-specific identities and functions, impairing phagocytosis, splenic iron recycling, and lung, kidney and gut physiology. Epigenetic profiling revealed that MafB directly regulated key RTM genes in mouse and humans, including Csf1r, Mertk, Fcgr1, Cd163 and Zeb2. In silico analyses further demonstrated strong evolutionary conservation of MafB binding sites across vertebrates. Together, these findings establish MafB as a crucial regulator of RTM development and functional identity, linking MafB-dependent transcriptional programs with defining features of RTMs and tissue homeostasis.

Spinal cord injury (SCI) leads to irreversible neurological deficits, with emerging evidence highlighting the pivotal regulatory role of gut microbiota in neural repair through the bidirectional gut-brain axis. This study investigates age-related differences in SCI progression by longitudinally profiling multi-omics signatures in young versus aged mice, integrating spinal cord transcriptomics with gut microbiome analysis. A traumatic SCI model was established at the thoracic level 10 in mice. The gut microbiota was analyzed through 16S rRNA sequencing. Spinal cord gene expression was profiled using transcriptome sequencing. Correlation analysis was performed to evaluate associated between gut microbiota shifts and differential cytokines expression. Aging significantly altered spinal cord gene expression profiles after SCI, KEGG pathway analysis revealed that differentially expressed genes (DEGs) in young and aged SCI mice were highly similar, predominantly involving immune and inflammatory response pathways. The age-dependent upregulation of inflammatory cytokines were observed under both sham and post-SCI conditions. Additionally, aging was associated with distinct shifts in gut microbiota composition across different phases of SCI. The abundance of certain bacterial genera, such as Lactobacillus and Dubosiella, which was significantly reduced in the acute phase, continued to decline in an age-dependent manner during the chronic phase. Correlation analysis indicated that alterations in the abundance of the gut microbiota were closely associated with variations in spinal cord inflammatory cytokine levels. This study delineates host-microbiome interactions in SCI and sheds light on potential mechanisms underlying age-related impairment of neural repair capacity.

Alcohol-associated liver disease (ALD) in its earliest form is evidenced as hepatic steatosis which may progress to liver cirrhosis. The mechanisms behind this are poorly understood and therapeutics limited. Liver is a specialized organ exhibiting heterogeneity along the porto-central axis. Periportal preponderance of lipid droplet accumulation was noted in human ALD livers compared to other causes of hepatic steatosis. Using single cell multiomics, we studied transcriptional mechanisms across the hepatic lobule that could account for zonation of lipid droplets in a murine ALD model. Alcohol led to periportal zonation of lipogenesis-associated genes in mice, including Hsd17b13 and Fasn. Chromatin landscape studies demonstrated zonation of master transcription factors that led to these changes in the transcriptome. We utilized these data to provide novel insight into zone-specific HNF4α and PPARα regulation of HSD17B13. We conclude novel mechanisms underlying ALD leading to spatially distinct establishment of hepatic steatosis and provide insight into disease pathogenesis.

Objective: To characterize the distribution of liver macrophage subsets in metabolic associated steatohepatitis (MASH) mouse models induced by methionine choline-deficient diet (MCD) and a high-fat, high-fructose, and high-cholesterol diet (HFFC), in order to provide a research basis for subsequent macrophage subset studies. Methods: MASH mouse models were induced by feeding an MCD and HFFC diet for four and sixteen weeks, respectively. Real-time fluorescence quantitative reverse transcription PCR (RT qPCR) was used to detect changes in liver inflammation and fat metabolism-related genes in MASH mice. Liver macrophages were isolated by perfusing and digesting mouse livers. Flow cytometry was used to analyze the subpopulations of liver macrophage subsets. Data between different groups was compared using t-test or one-way analysis of variance. Results: The MCD-fed diet led to the inhibition of liver fat synthesis in mice, while the HFFC-fed diet had increased liver fat synthesis in mice. However, both diets led to a decrease in embryonic Kupffer cells (EmKC) that were derived from the livers of mice. The proportion of EmKC in liver macrophages was significantly lower in the HFFC group (73.74%±7.96%) and the MCD group (39.93%±9.03%) than in the normal diet (ND) group (95.14%±1.09%). The proportion of mononuclear macrophages (MDM) in liver macrophages was significantly increased in the HFFC group (19.26%±6.94%) and the MCD group (52.38%±8.38%) compared with the ND group (2.46%±0.53%). The MCD diet led to a greater loss of EmKC and increased recruitment of monocytes. Monocyte-derived Kupffer cells (MoKC) were the main MDM subset in the livers of HFFC diet-fed mice, while lipid-associated macrophages (LAM) and their precursor CCR2+lipid-associated macrophages (C-LAM) were the main MDM subset in MCD diet-fed mice. Conclusion: The recruitment of MDM and the loss of liver EmKC can be induced by both MCD and HFFC diets; however, the composition of MDM subsets varies. The major MDM subset in the HFFC group was MoKC, while the primary MDM subsets in the MCD group were LAM and C-LAM.