Yu-xin Zhang, Hui Wan, Guan-yue Shan, Zhi-cheng Gao, Hai-jun Li
{"title":"Hyperuricemia increases susceptibility to chronic kidney injury exacerbation via autophagic flux blockade-mediated ammonia death pathway","authors":"Yu-xin Zhang, Hui Wan, Guan-yue Shan, Zhi-cheng Gao, Hai-jun Li","doi":"10.1016/j.jare.2025.11.003","DOIUrl":"10.1016/j.jare.2025.11.003","url":null,"abstract":"<div><div><em>Introduction:</em> Ammonia (NH3), a core toxic byproduct of amino acid metabolism in the body, poses a severe threat to cell survival when its homeostasis is disrupted. Maintaining low systemic ammonia concentrations is crucial. Under physiological conditions, the kidneys regulate ammonia metabolism precisely through glutaminase (GLS1)- mediated ammonia production and the urea cycle, ensuring efficient detoxification. Hyperuricemic nephropathy (HN), a common complication of hyperuricemia, impairs patient health significantly. However, whether and how ammonia toxicity triggers cell death under this pathological condition remains unclear.</div><div><em>Objectives:</em> This study aimed to investigate whether ammonia-dependent cell death occurs in HN and to elucidate the underlying molecular mechanisms, focusing on the role of ammonia metabolism disorder and autophagic flux blockade.</div><div><em>Methods:</em> We employed both in vivo and in vivo models of HN. Cellular and tissue damage were assessed by ultrastructural analysis, fluorescent probes for reactive oxygen species and mitochondrial membrane potential, and autophagic flux detection. Causal relationships were verified using ammonia scavengers and gene intervention.</div><div><em>Results:</em> Chronic hyperuricemic stress accelerated renal glutaminolysis to maintain ATP supply, leading to excessive mitochondrial ammonia production. Accumulated ammonia underwent RHCG-dependent transmembrane transport, causing lysosomal alkalinization and dysfunction, which in turn promoted mitochondrial ammonia retention and swelling. This process inhibited autolysosomal disassembly, impaired clearance of damaged mitochondria, and blocked autophagic flux, ultimately driving cell death.</div><div><em>Conclusion:</em> Our findings identified a distinct form of cell death in HN, mechanistically divergent from previously known mechanisms such as apoptosis or pyroptosis. It redefined HN pathogenesis through a metabolic lens, identifying druggable targets to mitigate renal damage in hyperuricemic patients.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 743-757"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145455632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"METTL4 enhances GLI1 translation through m6Am modification to promote tumor progression as a therapeutic target for hepatocellular carcinoma","authors":"Weijie Sun, Weiqi Dai, Chaobo Chen, Qian Qiu, Jianqing Chen, Jiaojiao Chen, Yueyue Li, Yuqi Liu, Dengyu Han, Wenhui Mo, Zishu Wang, Yihang Yuan, Xuanfu Xu","doi":"10.1016/j.jare.2026.01.009","DOIUrl":"10.1016/j.jare.2026.01.009","url":null,"abstract":"<div><h3>Introduction</h3><div>Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality. Epigenetic dysregulation, particularly through methyltransferase METTL4, plays a critical role in HCC progression. METTL4 is known to catalyze m<sup>6</sup>Am methylation of mRNA, yet its pathological significance in liver cancer remains unclear.</div></div><div><h3>Objective</h3><div>This study aims to firstly investigate the role of METTL4 in the pathogenesis of HCC, and then to evaluate the antitumor efficacy of targeting METTL4 in inhibiting HCC growth and metastasis.</div></div><div><h3>Methods</h3><div>In a total of 802 postoperative HCC patients from four independent cohorts, we analyzed METTL4 expression in HCC tissues and its correlation with tumor staging and survival rates. Functional assays assessed the impact of METTL4 knockdown on HCC cell proliferation and metastasis, and patient-derived organoids (PDO) were used to evaluate the therapeutic efficacy of targeting METTL4. m<sup>6</sup>A-seq analyses identified GLI1 as a direct target of METTL4, investigating how METTL4-mediated m<sup>6</sup>Am modification affects GLI1 mRNA translation. Finally, we developed a siMETTL4-carrying nanoparticle and explored their efficacy in treating HCC in orthotopic and spontaneous liver tumor models.</div></div><div><h3>Results</h3><div>METTL4 was significantly upregulated in HCC tissues, correlating with higher tumor staging and poorer survival. Knockdown of METTL4 significantly inhibited HCC cell proliferation, migration, tumor growth, and lung metastasis. Meanwhile, targeting METTL4 effectively inhibited the growth of HCC PDO. METTL4-mediated m<sup>6</sup>Am modification enhanced GLI1 mRNA translation, with recognized target sites confirmed. Finally, siMETTL4-encapsulated nanoparticles effectively inhibited the growth and metastasis of orthotopic and spontaneous liver tumors.</div></div><div><h3>Conclusions</h3><div>Our findings highlight the role of METTL4-mediated m<sup>6</sup>Am modification in promoting HCC progression by enhancing GLI1 translation. Targeting METTL4 with siMETTL4-Nanoparticles represents a novel therapeutic strategy, bridging molecular insights in RNA epitranscriptomics with translational applications for HCC treatment.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 213-228"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dan Liu, YiDan Chen, WenZhao Li, ZhaoLi Li, YuPing Dai, Tong Li, PingYi Li, Hao Cheng, HaiLun He
{"title":"Multi-targeted synergy of Bacillus sp. TC5 fermentation products for transdermal drug delivery and hair regeneration","authors":"Dan Liu, YiDan Chen, WenZhao Li, ZhaoLi Li, YuPing Dai, Tong Li, PingYi Li, Hao Cheng, HaiLun He","doi":"10.1016/j.jare.2026.01.042","DOIUrl":"10.1016/j.jare.2026.01.042","url":null,"abstract":"<div><h3>Introduction</h3><div>The stratum corneum represents a major barrier to transdermal drug delivery, while limited follicular activity contributes to hair loss disorders. <em>Bacillus</em> species, generally recognized as safe microorganisms, have broad applications in biotechnology and industry; however, their application in the cosmetics and pharmaceutical industries still faces certain challenges.</div></div><div><h3>Objective</h3><div><em>Bacillus</em> sp. TC5 is a high-yield keratinase-producing strain. This study evaluated the dermatological potential of <em>Bacillus</em> sp. TC5 fermentation products, focusing on their dual functions in enhancing transdermal drug delivery and promoting hair growth through biochemical and molecular mechanisms.</div></div><div><h3>Methods</h3><div>Non-targeted metabolomics identified bioactive metabolites in TC5 fermentation products. Franz diffusion assays assessed their ability to enhance transdermal permeation of pharmaceuticals (5-fluorouracil, minoxidil, ketoprofen) and cosmetic agents (niacinamide, tripeptides, decapeptides). In vivo efficacy was examined in C57BL/6 mice through hair regrowth observation, follicle morphology (HE staining), and immunofluorescence staining for protein expression.</div></div><div><h3>Results</h3><div>TC5 fermentation products were non-toxic to HDFs, HaCaT cells (200–800 μg/mL), and DPCs (100–500 μg/mL) without inducing ROS. They markedly enhanced skin permeability, shortening lag time and increasing drug permeation. In vivo treatment improved follicle density and diameter, with increased ALP, K5, and Ki67 expression indicating dermal papilla activation. Mechanistically, the products stimulated the Wnt10b/β-catenin and VEGF/IGF-1 pathways, promoting follicular proliferation, angiogenesis, and epithelial renewal, while suppressing TGF-β1 and FGF5 and modulating BMP6 to prolong the anagen phase. Upregulation of keratin 14 and 17 strengthened hair shaft integrity.</div></div><div><h3>Conclusion</h3><div><em>Bacillus</em> sp. TC5 fermentation products effectively promote hair regrowth and enhance transdermal drug absorption. These findings highlight TC5 metabolites as promising, eco-friendly candidates for developing novel skin penetration enhancers and cosmeceuticals for hair restoration and skin repair.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 643-657"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145993340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chunyang Lu, Manish Sridhar Immadi, Yen On Chan, Sameep Dhakal, Dong Xu, Marc Libault, Trupti Joshi
{"title":"scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation","authors":"Chunyang Lu, Manish Sridhar Immadi, Yen On Chan, Sameep Dhakal, Dong Xu, Marc Libault, Trupti Joshi","doi":"10.1016/j.jare.2026.01.035","DOIUrl":"10.1016/j.jare.2026.01.035","url":null,"abstract":"<div><h3>Introduction</h3><div>Accurate cell type annotation remains a major bottleneck in plant single-cell RNA sequencing (scRNA-seq), where existing tools are often adapted from animal studies and perform sub-optimally on plant data. The lack of plant-specific computational frameworks limits the construction of plant cell atlases and downstream biological discovery.</div></div><div><h3>Objectives</h3><div>We develop and evaluate scPlantAnnotate, a Transformer-based reference annotation framework tailored for plant scRNA-seq data, and benchmark it against state-of-the-art deep learning and conventional methods across multiple plant species.</div></div><div><h3>Methods</h3><div>Species-specific scPlantAnnotate models were trained using curated datasets from <em>Arabidopsis thaliana</em>, <em>Zea mays</em>, <em>Oryza sativa</em>, and <em>Glycine</em> max. We compared scPlantAnnotate with leading baselines under both standard random-split evaluation and a more stringent leave-one-dataset-out setting, which tests robustness to completely unseen datasets and tissue types.</div></div><div><h3>Results</h3><div>scPlantAnnotate consistently outperforms existing approaches across all four species under random-split evaluation. In the leave-one-dataset-out setting for <em>A. thaliana</em>, where performance drops markedly for all methods due to strong batch effects and dataset heterogeneity, scPlantAnnotate nonetheless achieves the highest Accuracy, Macro-F1, Balanced Accuracy, and Macro-AUROC on average and ranks first on most held-out datasets. These results demonstrate improved robustness to dataset shifts, a critical yet underexplored challenge in plant scRNA-seq analysis. A freely accessible web server enables users to annotate their own datasets using pretrained models.</div></div><div><h3>Conclusion</h3><div>scPlantAnnotate provides a plant-specific, Transformer-based framework for single-cell annotation that delivers state-of-the-art performance and enhanced robustness to unseen datasets. By addressing limitations of existing tools and enabling scalable reference-based annotation, scPlantAnnotate supports the development of comprehensive plant cell atlases and facilitates broader use of single-cell genomics in plant biology.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 719-730"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145995573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Construction of musculoskeletal quantitative model based on deep learning and study of musculoskeletal relationship in patients with osteoporosis","authors":"Zhenzhen Guan, Yijin Wang, Shiyu Zhang, Yanyang Zhang, Liang Wang, Yixin Chen, Xuhua Lu","doi":"10.1016/j.jare.2026.01.037","DOIUrl":"10.1016/j.jare.2026.01.037","url":null,"abstract":"<div><h3>Introduction</h3><div>Lumbar CT and MRI scans are helpful for osteoporosis (OP) screening. Deep learning enhances the efficiency and accuracy of musculoskeletal quantification for OP screening.</div></div><div><h3>Objectives</h3><div>To develop a deep learning-based model (UNet3D) for musculoskeletal quantification from lumbar CT and MRI in OP patients, and to explore musculoskeletal relationship.</div></div><div><h3>Materials</h3><div>Retrospectively analyzing OP patients’ lumbar CT, MRI and DXA scans between January 2018 and August 2025 from two center, and UNet3D was developed based on U-Net to simultaneously segment L1-S1 vertebrae on CT and paraspinal muscles/intermuscular spaces on MRI. Performance was compared against U-Net, U<sup>2</sup>-Net, Mask-RCNN using pixel accuracy (PA), mean pixel accuracy (mPA), mean intersection over union (mIoU). Following automated HU values calculation within cancellous bone volume of interests (VOIs), we correlated L1-L4 HU values with T-scores and analyzed their relationship with muscle/space volumes across L1-S1, computing corresponding weighting coefficients.</div></div><div><h3>Results</h3><div>The study analyzed 410 OP patients (65 ± 10 years; 240 women) with 76,700 axial CT and 6210 axial T2 slices, including training (266), validation (76), internal test (38) and external test (30) sets. On the internal test set, UNet3D’s accuracy in CT (PA/mPA/mIoU, 0.984/0.849/0.760) and MRI (PA/mPA/mIoU, 0.973/0.849/0.724), outperformed U-Net/U<sup>2</sup>-Net/Mask R-CNN. On the external test set, UNet3D attained PA, mPA, and mIoU values of 0.971, 0.852, 0.741 in CT, and of 0.969, 0.834, 0.713 in MRI. HU values varied across vertebral VOIs, ranging from 80.33 HU (L2) to 195.14 HU (S1), and correlations existed between L1-L4 HU values and T-scores (<em>r</em> ≥ 0.85, <em>P</em> < 0.05). Volumetric measurements across L1-S1 identified the psoas major as the largest muscle (173,317.68 mm<sup>3</sup>) and the quadratus lumborum as the smallest (65,167.78 mm<sup>3</sup>); among spaces, the psoas-vertebral was largest (124,301.86 mm<sup>3</sup>) and the quadratus lumborum-iliocostalis was smallest (29,676.63 mm<sup>3</sup>). Vertebral HU values correlated positively with muscle volumes (ω > 0) and negatively with space volumes and fatty infiltration (ω < 0).</div></div><div><h3>Conclusion</h3><div>UNet3D outperformed U-Net/U<sup>2</sup>-Net/Mask R-CNN on CT/MRI segmentation, enabling accurate musculoskeletal volume quantification in OP patients. Musculoskeletal correlations differed across spinal segments.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 899-909"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145995510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dandan Wang, Mei Li, Jun Ma, Guocheng Du, Jingwen Zhou, Jian Chen, Xin Guan
{"title":"Mitocytosis, mitophagy, and apoptosis coordinately drive mitochondrial clearance to regulate myogenic differentiation","authors":"Dandan Wang, Mei Li, Jun Ma, Guocheng Du, Jingwen Zhou, Jian Chen, Xin Guan","doi":"10.1016/j.jare.2026.01.065","DOIUrl":"10.1016/j.jare.2026.01.065","url":null,"abstract":"<div><h3>Introduction</h3><div>Skeletal muscle is a high-energy-consuming tissue whose development and function critically depend on mitochondrial homeostasis. Mitochondrial quality control involves multiple clearance mechanisms, including mitocytosis, mitophagy, and apoptosis. However, how these pathways are coordinated during myogenic differentiation remains systematically unexplained.</div></div><div><h3>Objectives</h3><div>This study aimed to investigate the sequential activation and coordination of mitocytosis, mitophagy, and apoptosis in<!--> <!-->response to gradient mitochondrial damage, and to explore their impact on myogenesis.</div></div><div><h3>Methods</h3><div>We established a gradient mitochondrial damage model in myoblasts using different concentrations of CCCP. Through fluorescence imaging, western blotting, genetic interventions, and small-molecule inhibitors, we investigated the activation sequence and crosstalk among different clearance pathways, and explored their effects on myotube formation and function.</div></div><div><h3>Results</h3><div>Escalating mitochondrial damage triggered a sequential activation of clearance mechanisms: KIF5B-mediated mitocytosis was first induced, followed by PINK1-dependent mitophagy, and ultimately Caspase 3-mediated apoptosis. When mitocytosis was inhibited, mitophagy dominated mitochondrial clearance, whereas enhanced mitocytosis suppressed both mitophagy and apoptosis. When mitophagy was impaired, cellular homeostasis could be maintained by upregulating mitocytosis under mild mitochondrial damage, but this led to premature apoptosis under severe mitochondrial damage. Myogenesis was significantly suppressed when either mitocytosis or mitophagy was impaired, whether through small-molecule inhibitors or the genetic knockdown of KIF5B or PINK1. Notably, low-dose CCCP treatment promoted myotube formation and mitochondrial function, and also attenuated the myogenic deficits resulting from KIF5B or PINK1 deficiency. Furthermore, KIF5B overexpression enhanced glycolytic metabolism and accelerated myoblast proliferation, highlighting its role beyond mitochondrial clearance.</div></div><div><h3>Conclusion</h3><div>These findings provide new insights into the coordinated regulatory network among mitochondrial clearance mechanisms and their roles in myogenic differentiation. These insights advance the understanding of muscle biology and offer potential strategies for enhancing muscle regeneration in biomedical and cellular agriculture applications.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 519-537"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Targeted delivery of senolytic drugs using macrophage membrane-camouflaged magnetic nanoparticles inhibits endplate sclerosis","authors":"Weiping Su, Chenhao Shi, Yixiao Pan, Boyan Ma, Yueke Sun, Mingzhe Fan, Lantian Zhao, Yuanyang Zhu, Xianglong Zhuo, Shiqing Feng, Shuangfei Ni","doi":"10.1016/j.jare.2026.01.054","DOIUrl":"10.1016/j.jare.2026.01.054","url":null,"abstract":"<div><h3>Introduction</h3><div>Low back pain (LBP) is a prevalent cause of disability worldwide. A crucial mechanism underlying LBP is that senescent-like macrophages induce endplate sclerosis by coupling angiogenesis-osteogenesis through IL-10. Then, the osteoclasts attract sensory innervation to perceive pain during endplate sclerosis. Therefore, targeted clearance of senescent-like macrophages is expected to be a new direction for LBP treatment.</div></div><div><h3>Objectives</h3><div>In light of the side effects of systemic application of senolytic drugs, we propose to construct a targeted drug delivery system to accurately remove senescent-like macrophages in degenerating endplates.</div></div><div><h3>Methods</h3><div>In this study, iron oxide nanoparticles (Fe<sub>3</sub>O<sub>4</sub> NPs) and the senolytic drug ABT-263 were co-encapsulated in PLGA to form magnetic nanospheres (MS@ABT), then coated with macrophage membranes (MM@MS@ABT), thus a drug-loaded delivery system with improved dual targeting ability of magnetism and inflammatory microenvironments was generated. <em>In vivo</em> and ex vivo imaging studies demonstrated that MM@MS@ABT aggregated at the designated mouse lumbar spine instability (LSI) modeling site.</div></div><div><h3>Results</h3><div><em>In vivo</em> and <em>in vitro</em> findings showed that senescent-like macrophages were effectively eliminated by MM@MS@ABT, thereby inhibiting the expression and secretion of IL-10 from senescent-like macrophages. This reduced CD31<sup>+</sup>Emcn<sup>+</sup> angiogenesis, and ultimately alleviated endplate sclerosis.</div></div><div><h3>Conclusion</h3><div>Together, MM@MS@ABT exhibits a dual-targeting ability to aggregate near degenerated endplates and release senolytic drugs precisely to eliminate senescent-like macrophages in the endplates of LSI mice. It represents a potentially effective strategy for the treatment of LBP.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"88 ","pages":"Pages 453-468"},"PeriodicalIF":17.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}