Molecular omics最新文献_第2页

Gene expression analysis of carbohydrate catabolism in Leucoagaricus gongylophorus LEU18496. 弓形白松菇LEU18496碳水化合物分解代谢基因表达分析。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag007

Freddy Castillo-Alfonso, Gabriela Cejas-Añón, Cecilio Valadez-Cano, Juan Carlos Sigala-Alanis, Gabriel Vigueras-Ramírez, Roberto Olivares-Hernández

{"title":"Gene expression analysis of carbohydrate catabolism in Leucoagaricus gongylophorus LEU18496.","authors":"Freddy Castillo-Alfonso, Gabriela Cejas-Añón, Cecilio Valadez-Cano, Juan Carlos Sigala-Alanis, Gabriel Vigueras-Ramírez, Roberto Olivares-Hernández","doi":"10.1093/molecular-omics/aaiag007","DOIUrl":"10.1093/molecular-omics/aaiag007","url":null,"abstract":"The fungal symbiont of leaf-cutter ant Atta mexicana, Leucoagaricus gongylophorus LEU18496 has the capability to produce enzymes such as cellulases, hemicellulases, and ligninases for plant biomass degradation. In this study, the fungus has been cultivated in submerged culture conditions using glucose and cellulose as carbon sources to explore gene expression level and unravel the molecular mechanisms responsible of enzyme production and carbohydrate catabolism. The transcriptomic analysis of L. gongylophorus LEU18496 using RNA-seq data, allowed the examination of the gene expression profiles across different carbon sources and growth phases. During the exponential growth phase on glucose there is a constitutive expression of several CAZymes, including β-glucosidase, pectinase, and endo-β-1,3-glucanase. The transcriptome data showed high expression of the creA repressor gene in the presence of glucose, underscoring its regulatory role in carbohydrate degradation and suggesting a regulatory mechanism governing CAZyme production and secretion when glucose is used as a carbon source. This study offers detailed insights into the pathways of cellulose and glucose catabolism, emphasizing the expression of key components involved in carbohydrate metabolism unravelling the metabolic strategies of L. gongylophorus providing information of the CAZymes and FOLymes production as high-value product suitable for biotechnological applications.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146195172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring infection biology with mass spectrometry-based proteomics. 以质谱为基础的蛋白质组学探索感染生物学。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag009

Grisna I Prensa, Andrea García Navarro, David Parker, Andrea Fossati

{"title":"Exploring infection biology with mass spectrometry-based proteomics.","authors":"Grisna I Prensa, Andrea García Navarro, David Parker, Andrea Fossati","doi":"10.1093/molecular-omics/aaiag009","DOIUrl":"10.1093/molecular-omics/aaiag009","url":null,"abstract":"Investigating host-pathogen interactions at the molecular level is critical for understanding infection mechanisms and identifying potential therapeutic targets. Mass spectrometry (MS)-based proteomics has rapidly become one of the most employed techniques for the study of almost every aspect of the proteome, hence offering strong potential to study protein dynamics during viral infections. This review presents an overview of key MS-based approaches used in host-virus research to study changes in protein expression, cell signalling, and protein-protein interactions. For each method, we outline its underlying principles, practical and analytical expertise required and key strengths and limitations, with a particular focus on how each can be applied to study specific aspects of the dynamic interplay between host and virus. By comparing these approaches side by side, the review aims to give researchers a conceptual and practical guide on how to select the adequate MS technique for their specific biological questions in infectious biology. Ultimately, this resource is intended to support informed experimental design in host-pathogen research, helping to harness the full potential of MS-based proteomics in uncovering the complexity of infection biology.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Green synthesis of silver nanoparticles using Padina tetrastromatica against malaria and deciphering the mechanism through machine learning-driven metabolomics and network pharmacology. 绿色合成抗疟疾银纳米颗粒，并通过机器学习驱动的代谢组学和网络药理学解读其机制。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag011

Nikhila Yaladanda, Yashwanth Kumar Budige, Dileepkumar Veeragoni, Jhansi Venkata Nagamani Josyula, Ramesh Rodda, Vineeta Singh, Prabhakar Sripadi, Srinivasa Rao Mutheneni

{"title":"Green synthesis of silver nanoparticles using Padina tetrastromatica against malaria and deciphering the mechanism through machine learning-driven metabolomics and network pharmacology.","authors":"Nikhila Yaladanda, Yashwanth Kumar Budige, Dileepkumar Veeragoni, Jhansi Venkata Nagamani Josyula, Ramesh Rodda, Vineeta Singh, Prabhakar Sripadi, Srinivasa Rao Mutheneni","doi":"10.1093/molecular-omics/aaiag011","DOIUrl":"10.1093/molecular-omics/aaiag011","url":null,"abstract":"Malaria remains a major public health challenge due to drug and insecticide resistance, underscoring the need for novel therapies with distinct mechanisms of action. In this study, silver nanoparticles were green-synthesized using the brown marine algae Padina tetrastromatica (Ag-PT) and evaluated through integrated in vitro, in vivo, metabolomics, network pharmacology, and in silico approaches. Ag-PT showed potent antiplasmodial activity, with significantly lower IC50 values and superior parasite suppression compared to chemically synthesized silver nanoparticles. Untargeted metabolomics revealed that Ag-PT treatment specifically restored malaria-induced disruptions in fatty acid, arginine, and arachidonic acid metabolism. This included elevating precursors of specialized pro-resolving mediators such as DHA, 14-HDHA, and 18-HEPE, and replenishing l-arginine to improve nitric oxide synthesis and vascular function. Integration with network pharmacology identified COX-2 (PTGS2) as a key hub gene. Molecular docking and dynamics confirmed strong binding of the Ag-PT phytochemical eriodictyol to COX-2, suggesting inhibition that shifts arachidonic acid metabolism toward anti-inflammatory specialized pro-resolving mediator production. Collectively, these findings reveal that Ag-PT offers a multifaceted therapeutic strategy by simultaneously targeting the parasite while modulating host inflammatory and metabolic pathways. This integrated therapeutic strategy highlights the potential of eco-friendly, plant-based nanomedicines as a next-generation intervention for malaria management.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147369813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-omics integration in genome-scale metabolic models: a review of constraint-based approaches. 基因组尺度代谢模型中的多组学整合：基于约束的方法综述。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag005

Nabia Shahreen, Abraham Osinuga, Sunayana Malla, Tahereh Razmpour, Masoud Tabibian, Rajib Saha

{"title":"Multi-omics integration in genome-scale metabolic models: a review of constraint-based approaches.","authors":"Nabia Shahreen, Abraham Osinuga, Sunayana Malla, Tahereh Razmpour, Masoud Tabibian, Rajib Saha","doi":"10.1093/molecular-omics/aaiag005","DOIUrl":"10.1093/molecular-omics/aaiag005","url":null,"abstract":"Genome-scale metabolic models (GEMs) have progressed from stoichiometric reconstructions to predictive, constraint-aware platforms. In this review, we organize strategies for multi-omics integration not by data type, but by the constraint logic they impose on model solution spaces. Biomass functions enforce composition and maintenance demands, while transcriptomic switches prune network feasibility. Enzyme and expression valves cap flux capacity, proteome budgeting enforces allocation trade-offs, and thermodynamics and fluxomics provide physical and experimental calibration. Machine learning (ML) bridges to infer missing priors while retaining mechanistic structure. These categories translate into practical workflows, spanning enzyme-constrained modelling, thermodynamic embedding, and fluxomics-guided calibration, together with minimal reporting standards to ensure transparency and reproducibility. Emerging directions include the integration of single-cell and spatial data, physics-informed and graph-based ML, and translational pipelines that couple computational predictions with experimental validation. By framing omics integration through constraint architectures, this review provides a coherent agenda for making GEMs reproducible, portable, and biologically meaningful across biotechnology, medicine, agriculture, and environmental applications.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A practical guide to experimental design and power analysis for metaproteomics studies. b宏蛋白质组学研究的实验设计和功率分析实用指南。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag014

Luman Wang, Qianyi Zhou, Yutong Li, Feng Sun, Xin Zhou, Leyuan Li

{"title":"A practical guide to experimental design and power analysis for metaproteomics studies.","authors":"Luman Wang, Qianyi Zhou, Yutong Li, Feng Sun, Xin Zhou, Leyuan Li","doi":"10.1093/molecular-omics/aaiag014","DOIUrl":"10.1093/molecular-omics/aaiag014","url":null,"abstract":"Metaproteomics is an effective tool for characterizing the functional profiles of microbial communities by directly identifying and quantifying abundances. However, prospective power analysis and sample-size estimation are often overlooked at the study design stage in metaproteomics, which can result in underpowered experiments and reduced ability to detect biologically meaningful effects. In this study, we present a practical, end-to-end workflow for conducting power analysis prior to data collection. We focus on three common experimental designs: between-group comparisons, parallelized perturbation experiments, and beta diversity analyses. To tailored these experimental designs, we consider three major statistical approaches for power estimation: parametric tests (e.g. t-test, ANOVA), non-parametric tests (e.g. Wilcoxon rank-sum test, Kruskal-Wallis test), and distance-based multivariate methods (e.g. PERMANOVA using Bray-Curtis). By presenting detailed case studies, we provide practical guidance on how to calculate effect sizes, generate simulated datasets, and estimate statistical power across varying sample sizes. We also supply corresponding visualizations for each scenario to support sample-size determination and power assessment. This framework is intended to help researchers optimize sample size, improve experimental efficiency, and reduce costs, thereby enabling more reliable and interpretable biological insights from metaproteomic studies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147504345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

You are what you degrade: tracking the cellular fates of the proteasomal degradome. 你就是你所降解的：跟踪蛋白酶体降解的细胞命运。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/momics/aaiaf002

Duno S Dantis, Darci J Trader

{"title":"You are what you degrade: tracking the cellular fates of the proteasomal degradome.","authors":"Duno S Dantis, Darci J Trader","doi":"10.1093/momics/aaiaf002","DOIUrl":"https://doi.org/10.1093/momics/aaiaf002","url":null,"abstract":"The ubiquitin-proteasome system (UPS) is the primary protein degradation machinery in eukaryotic cells, composed of multiple proteasome isoforms. It plays critical roles in cellular proliferation, metabolism, immune regulation, oxidative stress, and aging, making it a long-standing focus of biological and therapeutic research. Recently, the UPS has been harnessed for the targeted degradation of disease-relevant proteins using proximity-inducing agents such as proteolysis-targeting chimeras and molecular glue degraders, which have transformed our understanding of druggability. Despite these advances, major gaps remain, particularly in understanding the proteasome's functional heterogeneity across biological contexts. Traditional research emphasizes proteasome structure, subunit function, and substrate features to guide chemical tool and therapeutic development. However, an often-overlooked aspect is the proteasomal degradome, the repertoire of peptide fragments generated during protein degradation. These peptides can exhibit biological activities distinct from their parent proteins, and pathogens, including viruses, have evolved mechanisms to block their production to evade immune detection. Thus, degradome characterization is essential to fully appreciate the proteasome's role in shaping cellular phenotypes in both healthy and diseased states. This review highlights recent studies exploring the degradome, with particular attention to -omic technologies applied to profile and interrogate these peptide products. By focusing on degradation outcomes rather than only the machinery, we aim to underscore the importance of tracing proteasome-derived peptides and their biological consequences. Ultimately, this perspective will broaden our understanding of the UPS while suggesting new avenues for therapeutic exploitation beyond current strategies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation. 放大到重排基因组：应用细胞学，基因组学和转录组学方法的管道结构变异解释。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/molecular-omics/aaiag006

Maria Gridina, Timofey Lagunov, Polina Belokopytova, Nikita Torgunakov, Artem Nurislamov, Darya A Yurchenko, Zhanna G Markova, Tatiana V Markova, Yana Stepanchuk, Galina Koksharova, Pavel Orlov, Anna Subbotovskaia, Oxana Ryzhkova, Nadezhda V Shilova, Veniamin Fishman

{"title":"Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation.","authors":"Maria Gridina, Timofey Lagunov, Polina Belokopytova, Nikita Torgunakov, Artem Nurislamov, Darya A Yurchenko, Zhanna G Markova, Tatiana V Markova, Yana Stepanchuk, Galina Koksharova, Pavel Orlov, Anna Subbotovskaia, Oxana Ryzhkova, Nadezhda V Shilova, Veniamin Fishman","doi":"10.1093/molecular-omics/aaiag006","DOIUrl":"10.1093/molecular-omics/aaiag006","url":null,"abstract":"Recent advances in genomic technologies have greatly enhanced our understanding of genotype-phenotype relationships and improved the diagnosis of genetic diseases. However, the dissection of complex structural variants (SVs) remains challenging due to the limitations of current methods in resolving their breakpoints and interpreting phenotypes involving multiple disrupted genes. In this study, we demonstrate how an integrative approach-combining molecular cytogenetic, genomic, and transcriptomic methods-enables the detection and structural and functional characterization of complex SVs affecting the MBD5, USP34, and XPO1 genes. Our findings underscore the utility of the Exo-C, a modified chromosome conformation capture technique in resolving complex rearrangements. We also report, for the first time, a composite neurodevelopmental phenotype resulting from the combined effects of MBD5-associated intellectual disability and 2p15p16.1 microdeletion syndromes.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A mass spectrometry-based approach identifies a putative plasma protein biomarker signature for early diabetic kidney disease diagnosis. 一种基于质谱的方法确定了早期糖尿病肾病诊断的推定血浆蛋白生物标志物。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/molecular-omics/aaiag003

Sumaiya Nazli, Kip Zimmerman, Zeeshan Hamid, Arisbeth Camarillo Reyes, Katharyn Wallis, Avinash Jadhav, Abhijit Mallick, Tiffany Chambers, Heather A Newman, Lei Cao, Shaymaa M Abousaad, Christine Adhiambo, Elimelda M Ongeri, Robert H Newman, Michael Olivier

{"title":"A mass spectrometry-based approach identifies a putative plasma protein biomarker signature for early diabetic kidney disease diagnosis.","authors":"Sumaiya Nazli, Kip Zimmerman, Zeeshan Hamid, Arisbeth Camarillo Reyes, Katharyn Wallis, Avinash Jadhav, Abhijit Mallick, Tiffany Chambers, Heather A Newman, Lei Cao, Shaymaa M Abousaad, Christine Adhiambo, Elimelda M Ongeri, Robert H Newman, Michael Olivier","doi":"10.1093/molecular-omics/aaiag003","DOIUrl":"10.1093/molecular-omics/aaiag003","url":null,"abstract":"Diabetic kidney disease (DKD) is the leading cause of kidney failure among diabetic patients. At the time of clinical diagnosis, kidney function has already significantly deteriorated, limiting treatment options. We developed a novel approach using tandem mass tags (TMT) labelling to identify kidney proteins in plasma samples and putative protein biomarker signatures that distinguish patients with DKD or reduced kidney function from control individuals. Plasma samples from 28 patients from the NC A&T Men's Minority Health Initiative Cohort included 7 healthy controls, 7 patients with diabetes and microalbuminuria (DM), and 2 patients with DKD. In addition, our sample set included 12 individuals with DM but no detectable microalbuminuria. Plasma samples were depleted, and analysed using TMT labelling with kidney lysate as a reference sample to identify potentially kidney-derived proteins in plasma that could indicate early kidney cell damage and protein leakage. A total of 424 proteins were identified in the plasma samples. Of these, the Human Protein Atlas labels 375 as proteins expressed in the kidney and 4 proteins as kidney-enriched. We identified 13 proteins whose abundance levels were different between patients with kidney injury and controls (P < .05). Using sparse partial least squares discriminant analysis, we identified a biomarker signature of four plasma proteins that confidently distinguish samples from individuals with kidney injury and control individuals. Interestingly, samples from DM patients without any detectable kidney dysfunction align between the controls and individuals with kidney damage, suggesting that some of these individuals are more similar in their biomarker signature to DKD patients and may be progressing to microalbuminuria.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Paxillin mediates endothelial cell migration and angiogenesis following spinal cord injury: a transcriptomic and functional analysis. 帕罗西林介导脊髓损伤后内皮细胞迁移和血管生成：转录组学和功能分析。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/momics/aaiaf001

Manjeet Chopra, Jaidev Sharma, Aditya A Singh, Zarna Pathak, Priyanka Patel Vats, Vibhor Kumar, Amit Mandoli, Hemant Kumar

{"title":"Paxillin mediates endothelial cell migration and angiogenesis following spinal cord injury: a transcriptomic and functional analysis.","authors":"Manjeet Chopra, Jaidev Sharma, Aditya A Singh, Zarna Pathak, Priyanka Patel Vats, Vibhor Kumar, Amit Mandoli, Hemant Kumar","doi":"10.1093/momics/aaiaf001","DOIUrl":"https://doi.org/10.1093/momics/aaiaf001","url":null,"abstract":"Spinal cord injury (SCI) is a destructive neurological condition that leads to significant functional deficits in the affected individual. To map the altered pathways within the lesion epicentre and the surrounding rostrocaudal segments, we performed RNA-sequencing on injured spinal cord tissue. Samples were collected from three regions-rostral, epicentre, and caudal-at Days 1, 14, and 28 post-injury to systematically profile the transcriptomic changes and identify pathways associated with angiogenesis following SCI. Gene set enrichment analysis revealed enriched pathways, including hepatocyte growth factor (HGF) receptor and alpha 6 beta 4 integrin signalling, indicating an active angiogenic response. The involvement of HGF receptor signalling was further validated by quantitative polymerase chain reaction (qPCR), confirming its role in pathological remodelling after SCI. Subsequently, we identified paxillin (Pxn) as a candidate gene that promotes endothelial cell migration via HGF receptor signalling. Immunohistochemistry demonstrated the role of Pxn in mediating endothelial cell migration and proliferation post-SCI. In summary, our findings indicate that Pxn is a key mediator of endothelial cell proliferation and migration in response to angiogenic factors, such as HGF, following SCI. However, further mechanistic studies are required to fully establish the role of Pxn in endothelial cell migration and proliferation after SCI.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of metabolomic signatures of diabetic kidney disease in urine and plasma using untargeted gas chromatography-mass spectrometry. 使用非靶向气相色谱-质谱法鉴定尿和血浆中糖尿病肾病的代谢组学特征。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-16 DOI: 10.1093/molecular-omics/aaiag001

Benlian Wang, Emilia Marin Quintero, Margaret Sojka, Katharyn Wallis, Danu Perumalla, Arisbeth Camarillo Reyes, Elimelda M Ongeri, Robert H Newman, Kip Zimmerman, Michael Olivier

{"title":"Identification of metabolomic signatures of diabetic kidney disease in urine and plasma using untargeted gas chromatography-mass spectrometry.","authors":"Benlian Wang, Emilia Marin Quintero, Margaret Sojka, Katharyn Wallis, Danu Perumalla, Arisbeth Camarillo Reyes, Elimelda M Ongeri, Robert H Newman, Kip Zimmerman, Michael Olivier","doi":"10.1093/molecular-omics/aaiag001","DOIUrl":"https://doi.org/10.1093/molecular-omics/aaiag001","url":null,"abstract":"Diabetic kidney disease (DKD) is a complication of diabetes and the leading cause of kidney failure among diabetic patients. Unfortunately, it is typically diagnosed after normal kidney function is already significantly impaired. We used gas chromatography-mass spectrometry (GC-MS) of urine and plasma to explore whether metabolites can serve as potential biomarkers for the early diagnosis of DKD. Urine and plasma samples were obtained from 41 individuals [11 healthy controls, 20 patients with diabetes (diabetes mellitus or DM) and microalbuminuria, 10 patients with DKD]. A total of 342 metabolites were identified in urine samples and 252 metabolites were identified in plasma samples, with 182 metabolites overlapping between the two sample types. Among these, 58 metabolites from urine and 22 metabolites from plasma showed suggestive evidence (P-value < .05) of differences between samples from patients with DKD and samples from healthy control individuals. Sparse partial least squares discriminant analysis (sPLS-DA) was applied to identify metabolomics profiles (in urine, plasma, or both) that maximize separation between DKD patients and controls. A set of four metabolites in plasma, including tyrosine and threo-hydroxyaspartic acid, shows promise as an early-stage biomarker signature that will need to be validated in a larger study. Using this set of metabolites, we estimated the probability of DKD for each of the DM patients, based on their metabolomic profiles, and found a significant correlation with DM designation (low, medium, and high) and estimated glomerular filtration rate. Further validation in larger cohorts is needed to confirm their clinical utility and the ability to predict individuals at risk for DKD.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146202278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0