Phenomics (Cham, Switzerland)最新文献

{"title":"The Protective Mechanism of ApoE3 R136S in Alzheimer's Disease: A New Hope for Neurodegeneration.","authors":"Rongcan Luo, Kun Guo","doi":"10.1007/s43657-025-00253-6","DOIUrl":"10.1007/s43657-025-00253-6","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"466-467"},"PeriodicalIF":6.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152253","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":"Characteristic 'Pattern of Autofluorescence' of the Fingernails and Certain Skin's Positions is a Novel Diagnostic Biomarker for Acute Ischemic Stroke: A Preliminary Study.","authors":"Danhong Wu, Mingchao Zhang, Yue Tao, Yujia Li, Haibo Yu, Shufan Zhang, Yufan Luo, Tianqing Chu, Xin Chen, Weihai Ying","doi":"10.1007/s43657-024-00209-2","DOIUrl":"https://doi.org/10.1007/s43657-024-00209-2","url":null,"abstract":"<p><p>Early and economical diagnosis of acute ischemic stroke (AIS) is pivotal for therapeutic efficacy, particularly for the settings where medical imaging resource is deficient. We have obtained evidence supporting our hypothesis that collective properties of the green autofluorescence (AF) of the fingernails and certain skin's positions may be a novel diagnostic biomarker for AIS: both the green AF intensity and AF asymmetry of the AIS patients in their Index Fingernails and most examined skin' s positions were significantly higher than that of the healthy subjects and the Non-AIS subjects. Receiver operating characteristic (ROC) analyses and machine learning-based analyses on the AF properties showed that area under curve (AUC) was 0.93 and 0.87, respectively, for differentiating the AIS patients from the healthy subjects and for differentiating the AIS patients from the Non-AIS subjects. The AIS patients had significantly higher AF intensity and AF asymmetry at several examined positions, compared to those of the patients of Parkinson's disease, pulmonary infection and transient ischemic attack. The AUC was 0.79-0.88 for differentiating AIS patients from each of these diseases. Our study has also obtained evidence implicating that the AF originates from keratins. Collectively, our study has obtained preliminary evidence suggesting that the characteristic AIS's 'Pattern of AF' is a novel diagnostic biomarker for the disease. The 'Pattern of AF Technology' holds potential to become a new non-invasive, label-free and economical diagnostic approach for AIS, which is particularly valuable when Magnetic Resonance Imaging (MRI) or Computed Tomography (CT) imaging resource is deficient.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00209-2.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 6","pages":"681-696"},"PeriodicalIF":6.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12886686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146168470","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":"Association Between Healthy Lifestyles and Adverse Health Outcomes, and the Mediating Role of Inflammation.","authors":"Jingyi Wu, Yaqi Huang, Shuishan Zhang, Meng Hao, Hui Zhang, Xiangnan Li, Zixin Hu, Jingdong Tang, Li Han, Li Jin, Shuai Jiang, Yi Li","doi":"10.1007/s43657-025-00265-2","DOIUrl":"10.1007/s43657-025-00265-2","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"461-465"},"PeriodicalIF":6.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152303","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":"SIMPLE: A One-Pot RPA-Cas12b Method for Single Nucleotide Variations Identification with an Expanded Scope and Clinical Applications.","authors":"Kaiming Guo, Yongkang Lai, Yiru Han, Linlin Bai, Ting Wang, Shengzhou Wang, Ziqin Zhang, Dianwei Liu, Yanju Chen, Jiulong Zhao, Yanan Pang, Feng Qian, Yanni Mo, Yongming Wang, Rui Wang","doi":"10.1007/s43657-025-00240-x","DOIUrl":"10.1007/s43657-025-00240-x","url":null,"abstract":"<p><p>Rapid and reliable nucleic acid detection methods are essential in clinical diagnostics and biotechnology. The clustered regularly interspaced short palindromic repeats (CRISPR) system is emerging as a next-generation nucleic acid detection technology, offering versatility, convenience and rapid detection. However, CRISPR methods are significantly limited by the protospacer adjacent motif (PAM) sequence, and achieving a one-pot reaction for detecting single nucleotide variations (SNVs) within a short time still remains challenging. Here, we developed a comprehensive method for screening PAM sequences, which significantly expands the CRISPR detection scope. Additionally, we also proposed a one-pot CRISPR method, termed \"SIMPLE\", capable of identifying SNVs within 30 min. We applied the SIMPLE method to the clinical diagnostics of drug-resistant bacteria and the screening of cancer hotspot mutations. The SIMPLE method successfully detected drug-resistant bacteria mediated by canonical PAM TTN sequence with a sensitivity of 10 copies per reaction and achieved 100% consistency with next-generation sequencing results. Furthermore, the SIMPLE method proved effective in detecting hotspot mutations in cancer, even at a low mutation rate of 1% in the presence of high background interference mediated by non-canonical PAM ATN sequence. Therefore, the SIMPLE method not only expands the CRISPR detection scope but also offers a one-pot reaction with high specificity for SNVs identification, making it a promising tool for next-generation molecular diagnostics.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00240-x.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"418-434"},"PeriodicalIF":6.2,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152240","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":"Cohort Profile: Precision Environmental Health Cohort of Healthy Undergraduates.","authors":"Yanbing Li, Yayuan Mei, Jiaxin Zhao, Quan Zhou, Kai Li, Ming Yang, Liu Liu, Huicai Guo, Qun Xu, Ang Li","doi":"10.1007/s43657-024-00215-4","DOIUrl":"10.1007/s43657-024-00215-4","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 3","pages":"301-310"},"PeriodicalIF":6.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981706","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":"Metabolomics for the Identification of Biomarkers in Rheumatoid Arthritis.","authors":"Swarnima Pandey","doi":"10.1007/s43657-025-00242-9","DOIUrl":"10.1007/s43657-025-00242-9","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 3","pages":"343-345"},"PeriodicalIF":6.2,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12390890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981737","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":"Links Between Psychiatric Disorders and Cardiovascular Diseases.","authors":"Minhan Dai, Qiang Wang","doi":"10.1007/s43657-024-00217-2","DOIUrl":"10.1007/s43657-024-00217-2","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 3","pages":"330-332"},"PeriodicalIF":6.2,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12390889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981696","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":"Breast Cancer Bone Metastasis: Novel Prognostic Biomarkers Identified.","authors":"Meiling Chu, Yan Zhang, Jie Chen, Hui Cong, Yulian Yin, Hongfeng Chen","doi":"10.1007/s43657-025-00221-0","DOIUrl":"10.1007/s43657-025-00221-0","url":null,"abstract":"<p><p>The impact of lipid metabolism on the development and prognosis of bone metastasis from breast cancer (BRCA) is currently unknown. Sequencing data of BRCA samples in this study were obtained from the University of California, Santa Cruz (UCSC) Xena database. The differentially expressed genes (DEGs1) between the BRCA group and the control group, the differentially expressed genes (DEGs2) between the bone metastasis group and the non-bone metastasis group, and the lipid metabolism score-related genes (LMSRGs) were intersected to obtain LMSRGs (DE-LMSRGs). Biomarkers were obtained using univariate logistic regression analysis, support vector machine recursive feature elimination (SVM-RFE) and multivariate logistic regression analysis for Correlation Analysis, Gene Set Enrichment Analysis, Immunohistochemistry, Co-creation of Networks, and Drug Prediction, and then analyses were performed using Immunohistochemistry, Western blot analyses to validate the samples. We identified two biomarkers (<i>Regulator of G-protein Signaling 9 Binding Protein</i> (<i>RGS9BP</i>) and <i>suppressor of cytokine signaling 3</i> (<i>SOCS3</i>)). There were nine immune cells that were markedly differential between bone metastasis and non-bone metastasis groups, such as activated dendritic cell, neutrophil, plasmacytoid dendritic cell, etc. Then, the lncRNA-miRNA-mRNA network was created, including the regulated relationship pairs <i>HLX-AS1-hsa-mir-541-SOCS3</i>, <i>ZNF337-AS1-hsa-mir-541-SOCS3</i>. Molecular docking analyses have demonstrated that the complexes formed by <i>SOCS3</i> alongside folic acid, estradiol, and S-Adenosylmethionine exhibit heightened stability. Similarly, the pairing of <i>RGS9BP</i> with benzopyrene showcases a notable degree of stability. Finally, the biomarkers were associated with angiogenesis scores and most angiogenesis related genes (ARGs). Our study identified two potential biomarkers (<i>RGS9BP</i> and <i>SOCS3</i>) for prognostic evaluation of bone metastasis patients with BRCA. These findings provided a scientific reference for further research on bone metastasis in BRCA patients.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-025-00221-0.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 4","pages":"404-417"},"PeriodicalIF":6.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152235","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":"Reduced Usage of <i>GLS</i> Intronic Polyadenylation Promotes Cellular Senescence.","authors":"Xueping Li, Yuxin Li, Dong Ding, Baiyun Xie, Jun Yao, Yu Chen, Zhaozhao Zhao, Peng Yu, Shengwei Zhang, Fu Yang, Ting Ni, Gang Wei","doi":"10.1007/s43657-024-00198-2","DOIUrl":"10.1007/s43657-024-00198-2","url":null,"abstract":"<p><p>Alternative polyadenylation (APA) of mRNA is a widespread transcriptomic mechanism which fine-tunes gene expression and plays important roles in diverse biological processes. Of the different APA types, intronic polyadenylation is a prevalent but not well understood one. Although the upstream regulation of intronic polyadenylation is extensively investigated, the understanding of its biological function largely lags behind. Here, we discovered that intronic polyadenylation of glutaminase-encoding gene <i>Glutaminase</i> (<i>GLS</i>) generated an isoform termed <i>Glutaminase C</i> (<i>GAC</i>, encoding glutaminase C), which played regulatory roles in cellular senescence, the basis of individual aging and also an important anti-cancer mechanism. Reduced usage of <i>GLS</i> intronic polyadenylation (pA) site was consistent in both human and mouse senescence models. GAC protein mainly located in mitochondria, and downregulation of <i>GAC</i> induced cellular senescence in both human and mouse cells. Increased reactive oxygen species (ROS) level and decreased ATP synthesis explained the senescence-associated phenotypes in GAC deficient cells. Polyadenylation factor CPSF6 bound to the last exon of <i>GAC</i> to regulate its expression. Rescue experiment confirmed that <i>CPSF6-GAC</i> signal axis did play important roles in regulating cellular senescence. Together, the present study demonstrated for the first time that intronic polyadenylation could regulate cellular senescence, largely extending our understanding of the biological roles of intronic polyadenylation.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00198-2.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 5","pages":"487-501"},"PeriodicalIF":6.2,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12881237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146144903","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":"Metabolomics Reveals Reasons for the Efficacy of Acupuncture in Migraine Patients: The Role of Anaerobic Glycolysis and Mitochondrial Citrate in Migraine Relief.","authors":"Zishan Gao, Xianzhong Yan, Rui Wang-Sattler, Marcela Covic, Guang Yu, Feifei Ge, Jia Lin, Qin Chen, Juan Liu, Sapna Sharma, Sophie Molnos, Brigitte Kuehnel, Rory Wilson, Jonathan Adam, Stefan Brandmaier, Shuguang Yu, Fanrong Liang, Christian Gieger","doi":"10.1007/s43657-024-00205-6","DOIUrl":"10.1007/s43657-024-00205-6","url":null,"abstract":"<p><p>Acupuncture is used worldwide to treat migraine, but its scientific mechanism remains unclear. Here, we report a ¹H NMR metabolomics study involving 40 migraine patients and 10 healthy individuals randomly receiving acupuncture or sham acupuncture, followed by machine learning techniques and functional analysis. We found that acupuncture at acupoints particularly enhanced anaerobic glycolysis and modified mitochondrial function by adjusting the levels of plasma pyruvic acid (<i>p</i> = 0.012), lactic acid (<i>p</i> = 0.031) and citrate (<i>p</i> = 0.00079) at a Bonferroni-corrected level of significance compared to the pre-treatment level of these three metabolites in migraine patients. Therefore, acupuncture supplies energy to migraine patients and relieves migraine attacks. In contrast, we observed that sham acupuncture may partially supply energy to migraine patients through lipid metabolism by changing the levels of plasma lipid (<i>p</i> = 0.0012), glycerine (<i>p</i> = 0.021), and pyruvic acid (<i>p</i> = 0.047) at a Bonferroni-corrected level of significance. The functional network analysis further indicates this different way of supplying energy contributes to the different effects of acupuncture and sham acupuncture. Our findings reveal novel metabolic evidence for the specific effect of acupuncture in relation to sham acupuncture. This metabolic evidence could enlighten a brand new direction into acupuncture analgesia mechanism, which in turn would pose fresh challenges for future acupuncture research.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-024-00205-6.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"5 6","pages":"707-728"},"PeriodicalIF":6.2,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12886611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146168484","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}