Phenomics (Cham, Switzerland)最新文献

{"title":"Cohort Profile: The Chinese Ovarian Aging Cohort (COACH).","authors":"Changjing Wang, Tingting Meng, Wei Luo, Jiangtao Zhang, Yongzhi Cao, Cheng Li, Jing Zhang, Xuan Gao, Peihao Liu, Chenxi Li, Dongshan Zhu, Tao Zhang, Junling Liu, Jingmei Hu, Kuona Hu, Linlin Cui, Gang Liu, Shiling Chen, Songying Zhang, Zi-Jiang Chen, Yingying Qin, Xue Jiao","doi":"10.1007/s43657-025-00290-1","DOIUrl":"https://doi.org/10.1007/s43657-025-00290-1","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 3","pages":"321-331"},"PeriodicalIF":6.2,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13578176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep Learning Models for Automatic Diagnosis and Efficacy Assessment of Scars: A Case Study.","authors":"Yixin Li, Lai Zhang, Wenbo Bu, Chaofei Han, Wu Zhu, Xiaoyu He, Kai Sun, Renliang He, Shuang Zhao","doi":"10.1007/s43657-025-00251-8","DOIUrl":"https://doi.org/10.1007/s43657-025-00251-8","url":null,"abstract":"<p><p>Scars affect millions of patients each year. High recurrence makes it difficult to treat. There are a variety of treatments for different subtypes of scars; however, there are significant interindividual differences in the efficacy of these treatments. Thus, an accurate and objective tool to assist physicians in evaluating scars is necessary. This study aimed to demonstrate the effectiveness and application value of intelligent systems in scar clinical diagnosis and efficacy assessment. An intelligent system can be designed to assist physicians in providing personalized treatment plans for scarring patients and monitoring the effectiveness of treatment. In this study, deep learning models were trained using standardized imaging of 3000 normal skin images, 2142 scar images and 1431 other skin diseases images. All scar images were matched to Vancouver Scar Scale (VSS) scores, as determined by three experienced dermatologists, to train efficacy assessment models. We evaluated the performance of various models and compared the best-performing model with five dermatologists. The results showed that Swin Transformer achieved the highest Area Under the Curve (AUC) of 0.9696 in scar subtype classification, the precision and recall were 0.9027 and 0.8876, respectively. For scar efficacy assessment, Swin Transformer also showed the best consistency with the lowest average Mean Absolute Error (MAE, 0.5137) for VSS item scores. Compared with human performance, Swin Transformer showed better objectivity and coherence (average MAE of 0.4369) but the evaluation was based on a very small sample. The study demonstrated that the deep learning system enabled more accurate scar subtype diagnosis and more objective and consistent efficacy assessment, demonstrating the potential to assist physicians in personalizing scar management.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s43657-025-00251-8.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 3","pages":"296-306"},"PeriodicalIF":6.2,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13578144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma MicroRNA and Protein Signature Associated with Obesity in the Chinese Han Population Using MicroRNA Omics and Proteomics Analysis of 1026 Subjects.","authors":"Yun-Xia Xie, Jian-Ge Qiu, Zhao-Hui Yang, Chen Ding, Le-Ming Shi, Si-Jia Wang, Li Jin, Bing-Hua Jiang","doi":"10.1007/s43657-025-00259-0","DOIUrl":"https://doi.org/10.1007/s43657-025-00259-0","url":null,"abstract":"<p><p>Overweight and obesity have become major health risks around the world. The risk factors and mechanisms for overweight and obesity are not fullyunderstood. It is critical to establish reliable factors associated with overweight and obesity. For future predictions, we examined the microRNA (miRNA) and protein expression levels of the Chinese population. Between 2017 and 2021, we conducted a community-based prospective cohort study of 1026 Chinese Han healthy adults in Zhengzhou, China. In this study, we analyzed the differentially expressed miRNA and protein profiles generated from 1026 subjects using RNA sequencing and proteomic analysis to investigate the potential association of levels of differential miRNAs and proteins with overweight and/or obesity in the Chinese Han adults. In our study, we identified 21 differential expression levels as a miRNA signature (10 up-regulated: hsa-miR-199b-5p, hsa-miR-548av-5p|hsa-miR-548 k, hsa-miR-362-5p, hsa-miR-181c-3p, hsa-miR-664b-5p, hsa-miR-148a-5p, hsa-miR-885-5p, hsa-miR-18a-3p, hsa-miR-590-3p and hsa-miR-450b-5p; 11 down-regulated: hsa-miR-26b-3p, hsa-miR-143-3p, hsa-miR-145-5p, hsa-miR-760, hsa-miR-205-5p, hsa-miR-654-5p, hsa-miR-1306-3p, hsa-miR-5010-5p, hsa-miR-655-3p, hsa-miR-196b-5p and hsa-miR-141-3p) associated with overweight or obese subjects. We then identified these potential miRNA direct target proteins and the associated miRNA-protein regulatory network with the Chinese obese phenotype. Furthermore, we found that these miRNA signatures and protein panels are associated with the onset and progression of obesity-related illnesses. These miRNA signatures and target protein panels may be used to predict obesity, identify potential new pathways, and serve as new biomarkers to predict overweight- and obesity-related diseases in the future.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00259-0.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 1","pages":"1-14"},"PeriodicalIF":6.2,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13226744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148159291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Tryptophan Metabolite Indole-3-ethanol of <i>Cutibacterium acnes</i> Promotes Skin Barrier Repair via AHR.","authors":"Ruomei Han, Yuxiao Chen, Junhao Xu, Thomas Worzfeld, Jiucun Wang, Jingjing Xia","doi":"10.1007/s43657-025-00306-w","DOIUrl":"https://doi.org/10.1007/s43657-025-00306-w","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 2","pages":"205-209"},"PeriodicalIF":6.2,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Self-adapting Polygenic Risk Score Model Improves Risk Prediction of Venous Thromboembolism in Han Chinese Cohorts.","authors":"Yan Che","doi":"10.1007/s43657-025-00238-5","DOIUrl":"https://doi.org/10.1007/s43657-025-00238-5","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 2","pages":"210-211"},"PeriodicalIF":6.2,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma Proteomic Insights into the Digestive System Disorders Unveil Causal Associations and Drug Repurposing Targets.","authors":"Shixuan Zhang, Zhenqiu Liu, Dayan Sun, Fei Wu, Yang Wei, Li Jin, Shen Yang, Jinshi Huang, Jiucun Wang","doi":"10.1007/s43657-025-00231-y","DOIUrl":"https://doi.org/10.1007/s43657-025-00231-y","url":null,"abstract":"<p><p>Digestive system disorders (DSDs) are prevalent and burdensome conditions worldwide. The human proteome serves as a primary source for designing disease treatment targets and holds great potential for drug repurposing. We applied Mendelian randomization analyses to examine the genetic associations between 2321 plasma proteins and 47 DSDs using data from the FinnGen project, identifying 12 causal proteins and validating four (Tripartite Motif Containing 40, Sulfotransferase Family 2A Member 1, Peptidase Inhibitor 16, MHC Class I Polypeptide-Related Sequence B) of them in the UK Biobank. Mediation analysis showed that SULT2A1 may increase the risk of cholelithiasis by reducing 25-hydroxyvitamin D levels. Molecular interaction simulations indicated that the interaction between SULT2A1 and 25-hydroxyvitamin D is comparable to that with the defined substrate 24-OHChol-24-sulfate. We found that elevated levels of SULT2A1 may increase metabolism of approved drugs for cholelithiasis (i.e., ursodeoxycholic acid and chenodeoxycholic acid) by binding deoxycholic acid, thus reducing drug efficacy. We applied the AlphaFold3 strategy to simulate interactions between SULT2A1 and 10,052 small molecules, identifying 5 molecules that may competitively bind to SULT2A1, potentially enhancing the treatment efficacy of deoxycholic acid for cholelithiasis. Overall, our study reveals several causal associations between plasma proteins and DSDs and identifies SULT2A1 as a promising drug repurposing target for cholelithiasis.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00231-y.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 2","pages":"168-180"},"PeriodicalIF":6.2,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome Analysis of <i>Angiostrongylus</i> spp. of Veterinary and Clinical Importance and Exploratory Remarks on Potential New Drugs in <i>Angiostrongylus costaricensis</i>.","authors":"José Arturo Molina-Mora, Javier Mora, Alicia Rojas","doi":"10.1007/s43657-025-00301-1","DOIUrl":"https://doi.org/10.1007/s43657-025-00301-1","url":null,"abstract":"<p><p>The genus <i>Angiostrongylus</i> includes parasitic nematodes infecting diverse mammalian hosts and characterized by complex life cycles involving gastropod intermediate hosts. Among them, <i>A. costaricensis, A. cantonensis,</i> and <i>A. vasorum</i> cause severe inflammatory diseases affecting mesenteric, cerebral, and cardiopulmonary systems. Notably, <i>A. costaricensis</i> is the etiological agent of abdominal angiostrongyliasis, a condition lacking effective antiparasitic treatment. To better understand host specificity, pathogenicity, and identify potential therapeutic targets, we performed a comparative pan-genomic analysis integrating genomic and transcriptomic data from these three species. A total of 51,955 genes from four genomes were analyzed, with 89.4% assigned to 11,331 orthogroups and ~51.5% comprising the core genome shared across species. This conserved fraction likely reflects similarities in life cycle and pathogenic mechanisms, while accessory and species-specific genes suggest adaptive divergence. In <i>A. costaricensis</i>, 226 preliminary species-specific genes were identified, of which 179 were supported by transcriptomic data. However, most of these encode uncharacterized proteins, highlighting important annotation gaps. Functional and interactome analyses with species-specific genes identified candidate proteins related to enzymatic activity, cytoskeletal structure, and other domains. Drug-target analysis revealed 11 proteins with potential interactions with known compounds, including actin-related proteins predicted to interact with agents such as artenimol and copper. Additional targets included apoptotic protease-activating factor 1, receptor of activated protein C kinase 1, and an uncharacterized species-specific protein (ACOC_0000228101) with no orthologs in other <i>Angiostrongylus</i>. Despite limitations in available data and annotations, this study provides new insights into <i>Angiostrongylus</i> genomics and identifies candidate targets for drug development against abdominal angiostrongyliasis.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00301-1.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 2","pages":"200-204"},"PeriodicalIF":6.2,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human Cardiac Organoids Reveal Anti-Fibrotic Therapeutic Potential of JAK1/2 Inhibition Following Cryogenic Injury.","authors":"Bo Yang, Yiyun Liang, Yulu Chen, Xinhua Lin, Qinghang Meng","doi":"10.1007/s43657-026-00320-6","DOIUrl":"https://doi.org/10.1007/s43657-026-00320-6","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 1","pages":"96-99"},"PeriodicalIF":6.2,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13226758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148159338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-Intensity Sports Participation Induces Itch-Associated Sensitive Skin.","authors":"Yanqing Liu, Fushuo Li, Xinyuan Zhang, Chungan Liao, Ritsuko Yamazaki, Ichiki Fukuda, Jing Liu, Weilin Pu, Yiyu Wang, Wei Liu, Jiucun Wang, Yanyun Ma","doi":"10.1007/s43657-025-00255-4","DOIUrl":"10.1007/s43657-025-00255-4","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 1","pages":"82-85"},"PeriodicalIF":6.2,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13226766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148159323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteostasis Collapse Drives Effector Memory T Cells Re-expressing CD45RA (TEMRA) Generation in the Tumor Microenvironment.","authors":"Linlin Li, Shuo Kan, Qiang Huang, Shiwen Wang, Yuchen Han, Liang Chen, Jun Jin","doi":"10.1007/s43657-025-00309-7","DOIUrl":"https://doi.org/10.1007/s43657-025-00309-7","url":null,"abstract":"<p><p>T cell senescence causes T cell dysfunction in tumors, but its drivers are unclear. Here we found that protein overload in the tumor microenvironment (TME) induces T cell differentiation into effector memory T cells re-expressing CD45RA (TEMRA). TEMRA cells exhibit senescent-like features, including reduced proliferative capacity and expression of senescence-associated markers. Both CD4⁺ and CD8⁺ T cells activated under high protein-to-amino-acid-ratio conditions <i>in vitro</i> or within TME niches underwent enhanced TEMRA differentiation. Single-cell transcriptomics showed that protein overload co-activates terminal effector and senescence programs. Mechanistically, it disrupts proteostasis by inhibiting lysosomal and proteasomal degradation, triggering a maladaptive unfolded protein response (UPR) that drives TEMRA commitment. Exogenous amino acid supplementation prevented UPR activation and TEMRA differentiation. In humanized tumors, intra-tumoral amino-acid administration reduced TEMRA accumulation, boosted T cell proliferation, and improved tumor control. Our work reveals managing proteostatic stress as a strategy to counter TEMRA generation and restore anti-tumor immunity.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00309-7.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"6 2","pages":"150-167"},"PeriodicalIF":6.2,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}