{"title":"Characterizing metabolic dysregulation in early-stage chronic kidney disease for diagnostic insights†","authors":"Upasna Gupta, Amrita Sahu, Dharmendra Singh Bhadauria, Bikash Baishya and Neeraj Sinha","doi":"10.1039/D5MO00018A","DOIUrl":"10.1039/D5MO00018A","url":null,"abstract":"<p >The progressive illness known as chronic kidney disease (CKD) can often be challenging to diagnose in its early stages with conventional diagnostic approaches such as serum creatinine and albumin assessment. Early-stage CKD (stages G1–G3) is defined by a GFR of ≥30 mL min<small><sup>−1</sup></small>/1.73 m<small><sup>2</sup></small>, which indicates normal to moderately reduced kidney function with or without symptoms of impaired kidney function. Identifying possible biomarkers for early detection and personalised treatment, as well as physiological changes linked to early CKD—an area that has not been fully investigated before—is the goal of the study to address this gap. We performed a metabolomic analysis using <small><sup>1</sup></small>H NMR on 115 human serum samples (24 healthy controls and 91 patients with early-stage CKD). MetaboAnalyst 6.0 was used for data pre-processing and statistical analyses (PCA, PLS-DA, OPLS-DA, ANOVA, and Wilcoxon Mann–Whitney test). Strong differentiation between CKD stages was achieved by random forest modelling. The KEGG database was used to perform pathway enrichment, and ROC analysis was used to evaluate the diagnostic value of important metabolites. Across CKD stages, significant changes were observed in ten different metabolites: myo-Inositol, glycerol, pyruvate, carnitine, phenylalanine, tyrosine, histidine, TMAO, 2-hydroxyisobutyrate, and 3-hydroxyisobutyrate (<em>p</em> < 0.05, VIP > 1). AUC values > 0.7 from ROC curves demonstrated its potential for diagnosis. Pathway analysis revealed significant dysregulation in the metabolism of inositol phosphate, tyrosine, histidine, and pyruvate, and biosynthesis of phenylalanine, tryptophan and tyrosine. This comprehensive metabolomics investigation identified potential early-stage CKD biomarkers in addition to significant metabolic abnormalities. These findings could help provide individualized care for early CKD management.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 6","pages":" 607-620"},"PeriodicalIF":2.4,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173984","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}
Fan Da, Shuanghu Cai, Liangliang Xu, Shixi Chen, Bin Li and Min Tao
{"title":"Transcriptome and proteome analyses reveal the virulence of the Vibrio alginolyticus effector gene vopR†","authors":"Fan Da, Shuanghu Cai, Liangliang Xu, Shixi Chen, Bin Li and Min Tao","doi":"10.1039/D5MO00010F","DOIUrl":"10.1039/D5MO00010F","url":null,"abstract":"<p > <em>Vibrio alginolyticus</em> is an opportunistic infectious pathogen, and its pathogenicity is related to various virulence factors, with the type III secretion system (T3SS) being one of the important systems for secreting virulence factors. <em>vopR</em> is one of the effector genes of <em>V. alginolyticus</em> T3SS1. To investigate its pathogenicity, this study constructed an overexpression vector to express <em>vopR</em> in host cells, using the empty plasmid as a control, and analyzed its impact on the mRNA and protein expression levels of host cells. Transcriptomic analysis revealed that overexpression of <em>vopR</em> led to the upregulation of 410 genes and the downregulation of 207 genes. Proteomic analysis showed that 126 proteins were upregulated, and 518 proteins were downregulated. GO enrichment analysis indicated that the differential genes were significantly enriched in various biological processes such as cellular processes, metabolic processes, and biological regulation, as well as in cellular components like cell parts and membranes, and molecular functions such as binding and catalytic activity. KEGG enrichment analysis demonstrated that the differential genes were mainly enriched in metabolic pathways, cancer-related pathways, and the MAPK signaling pathway. The combined analysis of the transcriptome and proteome screened out 144 overlapping differentially expressed genes, with 60 being upregulated and 54 being downregulated. These results suggest that <em>vopR</em> has a significant impact on the cytoskeleton, metabolism, and immune regulation of host cells during the pathogenic process of <em>V. alginolyticus.</em> This study provides a theoretical basis for a deeper understanding of the pathogenic mechanism of <em>V. alginolyticus</em>.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 5","pages":" 446-455"},"PeriodicalIF":2.4,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258524","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}
Fengting Liu, Fan Yang, Hailin Xiong, Jingnan Huang, Zhenhui Huang, Jingying Song, Xinyi Liu, Hongchao Zhou, Jing Xu, Jimin Yuan, Lin Jia and Lingyun Dai
{"title":"Proteomic and metabolomic dissection of the BRAF V600E mutation-induced cellular state transition in lung epithelial cells†","authors":"Fengting Liu, Fan Yang, Hailin Xiong, Jingnan Huang, Zhenhui Huang, Jingying Song, Xinyi Liu, Hongchao Zhou, Jing Xu, Jimin Yuan, Lin Jia and Lingyun Dai","doi":"10.1039/D4MO00249K","DOIUrl":"10.1039/D4MO00249K","url":null,"abstract":"<p >Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer, and 4% of NSCLC patients are reported to harbor mutations in <em>BRAF</em>, which encodes a serine/threonine kinase capable of activating the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway. However, the role and effects of <em>BRAF</em> mutation in NSCLC or lung lineage cells are not fully understood. To mimic the naturally occurring <em>BRAF</em> V600E mutation in lung cancer, a <em>BRAF</em> V600E knock-in BEAS-2B cell model was established using CRISPR/Cas9. Although the <em>BRAF</em> V600E mutation alone was not sufficient to drive lung carcinogenesis, it induced remarkable changes in cellular migration capacity and tumorigenic potential. Proteomics analysis revealed significant changes in the proteins involved in the biological processes including epithelial–mesenchymal transition (EMT), extracellular matrix (ECM)–receptor interaction, cell adhesion, focal adhesion, and cell metabolism upon the <em>BRAF</em> V600E mutation. Untargeted metabolomics experiments revealed that amino acid metabolism, especially glycine, serine and threonine metabolism, was significantly modulated in <em>BRAF</em> V600E knock-in cells. In summary, this study provides a new isogenic cell model that allows us to systematically dissect the underlying molecular events involved in the transition of cellular states upon the introduction of the <em>BRAF</em> V600E mutation.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 5","pages":" 422-432"},"PeriodicalIF":2.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174001","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}
Gobichettipalayam Balasubramaniam Maadurshni, Balamurali Mahalakshmi, Manikandan Nagarajan and Jeganathan Manivannan
{"title":"Human circulatory proteome interaction, oxidative stress-associated signalling and cardiovascular implications during titanium dioxide nanoparticle (TiO2-NP) exposure†","authors":"Gobichettipalayam Balasubramaniam Maadurshni, Balamurali Mahalakshmi, Manikandan Nagarajan and Jeganathan Manivannan","doi":"10.1039/D4MO00205A","DOIUrl":"10.1039/D4MO00205A","url":null,"abstract":"<p >The increasing exposure to nanoparticles raises a concern over their toxicity. Incidentally, reactive oxygen species (ROS) are produced as a result of the nanoparticle's physicochemical characteristics and interactions with intracellular elements, primarily enzymes, leading to oxidative stress. In this context, the extent of oxidative stress resulting from the toxicity of titanium dioxide nanoparticles (TiO<small><sub>2</sub></small>-NPs) on the cardiovascular system has not yet been thoroughly investigated. Initially, the gel/label-free proteomics (nLC-HRMS/MS) method was used to examine human serum protein interaction and corona composition. Furthermore, different oxidative stress assays (superoxide, total ROS, mitochondrial ROS, and lipid peroxidation) and cell stress assays (apoptosis, ER stress, mitochondrial dysfunction, autophagy, and hypertrophy) were performed in conjunction with endothelial (rat aortic cells) and cardiomyoblast (H9c2) cell cultures. In addition, expression studies (RT-qPCR and immunofluorescence), kinase signalling, and siRNA-mediated gene knockout (NOX2 and XO) studies were conducted. Alongside, in ovo effects on the heart's antioxidant enzymes (SOD and CAT) and metabolomic pathways (1H NMR) confirmed the involvement of oxidative stress in cardiotoxicity. The present results demonstrate a dose-dependent increase in cytotoxicity <em>via</em> the activation of caspase 3 and 9. The dose-dependent increase and its synergistic relationship with cardiovascular stress signalling (ET-1 and Ang-II) highlight the significant role of oxidative stress in nanoparticle toxicity. In summary, this study expands our understanding of the precise health risks associated with human exposure by establishing a connection between the role of the redox system and molecular stress pathways in TiO<small><sub>2</sub></small>-NPs-induced cardiotoxicity.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 282-302"},"PeriodicalIF":2.4,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811898","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}
{"title":"Transcriptome profiling of serum exosomes by RNA-Seq reveals lipid metabolic changes as a potential biomarker for evaluation of roxadustat treatment of chronic kidney diseases","authors":"Ru Zhou, YaXuan Zhen, Hualin Ma, Zhen Wang, LiXia Liu, Xinzhou Zhang and Baochun Guo","doi":"10.1039/D4MO00025K","DOIUrl":"10.1039/D4MO00025K","url":null,"abstract":"<p >The incidence of chronic kidney disease (CKD) is increasing globally; however, effective preventive and therapeutic strategies are currently limited. Roxadustat is being clinically used to treat renal anemia in CKD patients to reduce anemia-related complications and improve patients' life quality. Exosomes are small vesicles carrying important information that contribute to cell-to-cell communication and are present in various body fluids. However, little is known about the role of serum exosomes and their association with CKD after roxadustat treatment. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential as sensitive nucleic acid biomarkers in various human diseases. In this study, we aimed to identify the changed mRNAs–lncRNAs after roxadustat treatment as novel biomarkers for assessing the efficiency of the treatment. Through our study using RNA-seq data, we identified 957 mRNAs (626 upregulated and 331 downregulated after roxadustat treatment) and 914 lncRNAs (444 upregulated and 470 downregulated) derived from exosomes that were significantly changed, which was highly correlated to lipid metabolism. Our analysis through whole transcriptome profiling of exosome RNAs encompasses an identified differentially expressed mRNA–lncRNA regulatory axis in a larger patient cohort for the validation of suitable biomarkers for assessing CKD after roxadustat treatment.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 3","pages":" 240-249"},"PeriodicalIF":2.4,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/mo/d4mo00025k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Melanie T. Odenkirk, Haley C. Jostes, Kevin R. Francis and Erin S. Baker
{"title":"Lipidomics reveals cell specific changes during pluripotent differentiation to neural and mesodermal lineages†","authors":"Melanie T. Odenkirk, Haley C. Jostes, Kevin R. Francis and Erin S. Baker","doi":"10.1039/D4MO00261J","DOIUrl":"10.1039/D4MO00261J","url":null,"abstract":"<p >Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipidomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins, and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 259-269"},"PeriodicalIF":2.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11904469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143616477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dinesh Sharma, Danish Aslam, Kopal Sharma, Aditya Mittal and B. Jayaram
{"title":"Exon–intron boundary detection made easy by physicochemical properties of DNA†","authors":"Dinesh Sharma, Danish Aslam, Kopal Sharma, Aditya Mittal and B. Jayaram","doi":"10.1039/D4MO00241E","DOIUrl":"10.1039/D4MO00241E","url":null,"abstract":"<p >Genome architecture in eukaryotes exhibits a high degree of complexity. Amidst the numerous intricacies, the existence of genes as non-continuous stretches composed of exons and introns has garnered significant attention and curiosity among researchers. Accurate identification of exon–intron (EI) boundaries is crucial to decipher the molecular biology governing gene expression and regulation. This includes understanding both normal and aberrant splicing, with aberrant splicing referring to the abnormal processing of pre-mRNA that leads to improper inclusion or exclusion of exons or introns. Such splicing events can result in dysfunctional or non-functional proteins, which are often associated with various diseases. The currently employed frameworks for genomic signals, which aim to identify exons and introns within a genomic segment, need to be revised primarily due to the lack of a robust consensus sequence and the limitations posed by the training on available experimental datasets. To tackle these challenges and capitalize on the understanding that DNA exhibits function-dependent local physicochemical variations, we present ChemEXIN, an innovative novel method for predicting EI boundaries. The method utilizes a deep-learning (DL) architecture alongside tri- and tetra-nucleotide-based structural and energy features. ChemEXIN outperforms existing methods with notable accuracy and precision. It achieves an accuracy of 92.5% for humans, 79.9% for mice, and 92.0% for worms, along with precision values of 92.0%, 79.6%, and 91.8% for the same organisms, respectively. These results represent a significant advancement in EI boundary annotations, with potential implications for understanding gene expression, regulation, and cellular functions.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 3","pages":" 226-239"},"PeriodicalIF":2.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143649866","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}
Mariana Sa, Mayara da Silva, Brianna Ball and Jennifer Geddes-McAlister
{"title":"Revealing the dynamics of fungal disease with proteomics","authors":"Mariana Sa, Mayara da Silva, Brianna Ball and Jennifer Geddes-McAlister","doi":"10.1039/D4MO00222A","DOIUrl":"10.1039/D4MO00222A","url":null,"abstract":"<p >The occurrence and distribution of new and re-emerging fungal pathogens, along with rates of antifungal resistance, are rising across the globe, and correspondingly, so are our awareness and call for action to address this public health concern. To effectively detect, monitor, and treat fungal infections, biological insights into the mechanisms that regulate pathogenesis, influence survival, and promote resistance are urgently needed. Mass spectrometry-based proteomics is a high-resolution technique that enables the identification and quantification of proteins across diverse biological systems to better understand the biology driving phenotypes. In this review, we highlight dynamic and innovative applications of proteomics to characterize three critical fungal pathogens (<em>i.e.</em>, <em>Candida</em> spp., <em>Cryptococcus</em> spp., and <em>Aspergillus</em> spp.) causing disease in humans. We present strategies to investigate the host–pathogen interface, virulence factor production, and protein-level drivers of antifungal resistance. Through these studies, new opportunities for biomarker development, drug target discovery, and immune system remodeling are discussed, supporting the use of proteomics to combat a plethora of fungal diseases threatening global health.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 3","pages":" 173-184"},"PeriodicalIF":2.4,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/mo/d4mo00222a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Inês Nobre, Inês M. S. Guerra, Marisa Pinho, Ana D. Martins, Laura Goracci, Stefano Bonciarelli, Tânia Melo, Pedro Domingues, Artur Paiva, Pedro F. Oliveira and M. Rosário Domingues
{"title":"Unmasking the lipid landscape: carbamazepine induces alterations in Leydig cell lipidome†","authors":"Inês Nobre, Inês M. S. Guerra, Marisa Pinho, Ana D. Martins, Laura Goracci, Stefano Bonciarelli, Tânia Melo, Pedro Domingues, Artur Paiva, Pedro F. Oliveira and M. Rosário Domingues","doi":"10.1039/D4MO00221K","DOIUrl":"10.1039/D4MO00221K","url":null,"abstract":"<p >Leydig cells rely on lipids and fatty acids (FA) for essential functions like maintaining structural integrity, energy metabolism, and steroid hormone synthesis, including testosterone production. Carbamazepine (CBZ), a common anticonvulsant medication, can influence lipid metabolism and profiles, potentially impacting Leydig cell function and testosterone levels. Understanding this interplay is crucial to optimize treatment strategies for individuals requiring CBZ therapy while mitigating any adverse effects on male reproductive health. This study focuses on evaluating the effects of selected CBZ concentrations on the lipid homeostasis of BLTK-1 murine Leydig cells. By employing liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS), we aimed to uncover the specific changes in lipid profiles induced by CBZ exposure (25 and 200 μM). FA analysis demonstrated a significant decrease in FA 22:6 <em>n</em>-3 with increasing CBZ concentration and an increase in the <em>n</em>-6/<em>n</em>-3 ratio. Furthermore, changes in the lipidome, particularly in lipid species belonging to phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and sphingomyelin (SM) classes were observed. PE and PC lipid species were significantly elevated in Leydig cells exposed to 200 μM CBZ, whereas PG and SM species were downregulated. CBZ treatment significantly altered the Leydig cell phospholipidome, suggesting specific phospholipids such as PG 40:4, PG 34:1, PC O-32:1, PC 32:2, and PE P-38:6, which exhibited the lowest <em>p</em>-values, as potential biomarkers for clinical assessment of CBZ's impact on Leydig cells. These findings underscore the intricate relationship between CBZ exposure and alterations in lipid profiles, offering potential insights for monitoring and mitigating the drug's effects on male reproductive health.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 3","pages":" 202-214"},"PeriodicalIF":2.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/mo/d4mo00221k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}