Molecular omics最新文献_第3页

Integration of focal adhesion morphogenesis and polarity by DOCK5 promotes YAP/TAZ-driven drug resistance in TNBC† DOCK5整合局灶黏附形态和极性，促进了YAP/ taz驱动的TNBC耐药。

IF 2.4 4区生物学

Molecular omics Pub Date : 2025-05-12 DOI: 10.1039/D4MO00154K

Patricia Pascual-Vargas, Mar Arias-Garcia, Theodoros I. Roumeliotis, Jyoti S. Choudhary and Chris Bakal

{"title":"Integration of focal adhesion morphogenesis and polarity by DOCK5 promotes YAP/TAZ-driven drug resistance in TNBC†","authors":"Patricia Pascual-Vargas, Mar Arias-Garcia, Theodoros I. Roumeliotis, Jyoti S. Choudhary and Chris Bakal","doi":"10.1039/D4MO00154K","DOIUrl":"10.1039/D4MO00154K","url":null,"abstract":"YAP and TAZ are transcriptional co-activators that are inhibited by sequestration in the cytoplasm. Cellular signalling pathways integrate soluble, mechanical (cytoskeleton, adhesion), and geometric (cell size, morphology) cues to regulate the translocation of YAP/TAZ to the nucleus. In triple-negative breast cancer (TNBC) cells, both signalling and morphogenesis are frequently rewired, leading to increased YAP/TAZ translocation, which drives proliferation, invasion, and drug resistance. However, whether this increased YAP/TAZ translocation is due to alterations in upstream signalling events or changes in cell morphology remains unclear. To gain insight into YAP/TAZ regulation in TNBC cells, we performed multiplexed quantitative genetic screens for YAP/TAZ localisation and cell shape, enabling us to determine whether changes in YAP/TAZ localisation following gene knockdown could be explained by alterations in cell morphology. These screens revealed that the focal adhesion (FA)-associated RhoGEF DOCK5 is essential for YAP/TAZ nuclear localisation in TNBC cells. DOCK5-defective cells exhibit defects in FA morphogenesis and fail to generate a stable, polarised leading edge, which we propose contributes to impaired YAP/TAZ translocation. Mechanistically, we implicate DOCK5's ability to act as a RacGEF and as a scaffold for NCK/AKT as key to its role in FA morphogenesis. Importantly, DOCK5 is essential for promoting the resistance of LM2 cells to the clinically used MEK inhibitor Binimetinib. Taken together, our findings suggest that DOCK5's role in TNBC cell shape determination drives YAP/TAZ upregulation and drug resistance.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 5","pages":" 390-421"},"PeriodicalIF":2.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004111","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}

引用次数: 0

A multi-omics machine learning classifier for outgrowth of cow's milk allergy in children† 儿童牛奶过敏生长的多组学机器学习分类器。

IF 3 4区生物学

Molecular omics Pub Date : 2025-05-09 DOI: 10.1039/D4MO00245H

Diana M. Hendrickx, Mariyana V. Savova, Pingping Zhu, Ran An, Sjef Boeren, Kelly Klomp, Sumanth K. Mutte, PRESTO study team, Harm Wopereis, Renate G. van der Molen, Amy C. Harms and Clara Belzer

{"title":"A multi-omics machine learning classifier for outgrowth of cow's milk allergy in children†","authors":"Diana M. Hendrickx, Mariyana V. Savova, Pingping Zhu, Ran An, Sjef Boeren, Kelly Klomp, Sumanth K. Mutte, PRESTO study team, Harm Wopereis, Renate G. van der Molen, Amy C. Harms and Clara Belzer","doi":"10.1039/D4MO00245H","DOIUrl":"10.1039/D4MO00245H","url":null,"abstract":"Cow's milk protein allergy (CMA) is one of the most common food allergies in children worldwide. However, it is still not well understood why certain children outgrow their CMA and others do not. While there is increasing evidence for a link of CMA with the gut microbiome, it is still unclear how the gut microbiome and metabolome interact with the immune system. Integrating data from different omics platforms and clinical data can help to unravel these interactions. In this study, we integrate clinical, microbial, (meta)proteomics, immune and metabolomics data into machine learning (ML) classification, using multi-view learning by late integration. The aim is to group infants into those that outgrew their CMA and those that did not. The results show that integration of microbiome data with clinical, immune, (meta)proteomics and metabolomics data could considerably improve classification of infants on outgrowth of CMA, compared to only considering one type of data. Moreover, pathways previously linked to development of CMA could also be related to outgrowth of this allergy.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 343-352"},"PeriodicalIF":3.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128344","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}

引用次数: 0

Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer† 用轨道阱上升三重质谱分析亲和纯化蛋白复合物的FAIMS。

IF 3 4区生物学

Molecular omics Pub Date : 2025-05-07 DOI: 10.1039/D5MO00038F

Pratik Goswami, Joseph Cesare, Michaella J. Rekowski, Zachary Clark, Janet Thornton and Michael P. Washburn

{"title":"Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer†","authors":"Pratik Goswami, Joseph Cesare, Michaella J. Rekowski, Zachary Clark, Janet Thornton and Michael P. Washburn","doi":"10.1039/D5MO00038F","DOIUrl":"10.1039/D5MO00038F","url":null,"abstract":"In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend tribrid mass spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Lastly, we searched the datasets for multiple post-translational modifications important in chromatin remodeling and found several arginine methylation sites on the bait protein SAP25. Our findings highlight the potential of FAIMS with Orbitrap Ascend tribrid mass spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifier MSV000096548.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 303-314"},"PeriodicalIF":3.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111457","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

PPI network identifies interacting pathogenic signaling pathways in Candida albicans† PPI网络识别白色念珠菌相互作用的致病信号通路。

IF 3 4区生物学

Molecular omics Pub Date : 2025-05-01 DOI: 10.1039/D5MO00042D

Deepanjan Chattopadhyay, Sanjib Das, Paromita Saha Mondal, Tanushree Mondal, Subhasree Samanta, Amalesh Mondal, Achintya Mohan Goswami and Tanima Saha

{"title":"PPI network identifies interacting pathogenic signaling pathways in Candida albicans†","authors":"Deepanjan Chattopadhyay, Sanjib Das, Paromita Saha Mondal, Tanushree Mondal, Subhasree Samanta, Amalesh Mondal, Achintya Mohan Goswami and Tanima Saha","doi":"10.1039/D5MO00042D","DOIUrl":"10.1039/D5MO00042D","url":null,"abstract":" Candida albicans, an opportunistic and systemic infection causing fungus, causes skin, nail, and mucosal layer lesions in healthy individuals and hospital borne catheter-related and nosocomial infections. This particular fungus exists in two distinct stages in its life cycle: yeast and hyphae. In this study, 20 signaling pathways associated with 177 proteins from C. albicans were identified to construct a PPI network. The core part of the network consisted of 165 proteins. Network topology analyses revealed that the formed PPI network is biologically robust and scale-free, with significant interactions between proteins through 19 252 shortest pathways. In this network, the top 10 hub proteins (RAS1, CDC42, HOG1, CPH1, STE11, EFG1, CEK1, HSP90, TEC1 and CST20) were identified using network analysis, which seem to be the most important proteins involved in different pathways for the development of pathogenesis and virulence. Modular analysis of the network resulted in top six sub-networks, three of which shared eight hub proteins. Ontology and functional enrichment analyses revealed that the majority of the proteins were associated with regulation of transcription by RNA polymerase II, plasma membrane and nucleic acid binding in biological processes, and cellular components and molecular functions, respectively. Enrichment analysis indicated that the proteins were mostly involved in oxidative phosphorylation and purine metabolism signaling pathways. We determined the complex web of signaling pathway involving proteins via PPI network analysis to unravel and decipher protein interactions within C. albicans to understand the complex pathogenesis processes for targeted therapeutic interferences using novel bioinformatics strategies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 315-333"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111459","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

Transcriptome and proteome analyses reveal the virulence of the Vibrio alginolyticus effector gene vopR† 转录组和蛋白质组分析揭示了溶藻弧菌效应基因vopR的毒力。

IF 2.4 4区生物学

Molecular omics Pub Date : 2025-04-25 DOI: 10.1039/D5MO00010F

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":" Vibrio alginolyticus 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. vopR is one of the effector genes of V. alginolyticus T3SS1. To investigate its pathogenicity, this study constructed an overexpression vector to express vopR 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 vopR 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 vopR has a significant impact on the cytoskeleton, metabolism, and immune regulation of host cells during the pathogenic process of V. alginolyticus. This study provides a theoretical basis for a deeper understanding of the pathogenic mechanism of V. alginolyticus.","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}

引用次数: 0

Proteomic and metabolomic dissection of the BRAF V600E mutation-induced cellular state transition in lung epithelial cells† BRAF V600E突变诱导肺上皮细胞细胞状态转变的蛋白质组学和代谢组学解剖

IF 2.4 4区生物学

Molecular omics Pub Date : 2025-04-23 DOI: 10.1039/D4MO00249K

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":"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 BRAF, 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 BRAF mutation in NSCLC or lung lineage cells are not fully understood. To mimic the naturally occurring BRAF V600E mutation in lung cancer, a BRAF V600E knock-in BEAS-2B cell model was established using CRISPR/Cas9. Although the BRAF 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 BRAF V600E mutation. Untargeted metabolomics experiments revealed that amino acid metabolism, especially glycine, serine and threonine metabolism, was significantly modulated in BRAF 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 BRAF V600E mutation.","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}

引用次数: 0

Retraction: Tetracycline-controllable artificial microRNA-HOTAIR + EZH2 suppressed the progression of bladder cancer cells 撤回：四环素可控人工微rna - hotair + EZH2抑制膀胱癌细胞的进展

IF 3 4区生物学

Molecular omics Pub Date : 2025-04-22 DOI: 10.1039/D5MO90007G

Yincong Chen, Haibiao Xie, Yifan Zou, Xiulan Lai, Lian Ma, Yuchen Liu and Jianfa Li

引用次数: 0

Human circulatory proteome interaction, oxidative stress-associated signalling and cardiovascular implications during titanium dioxide nanoparticle (TiO2-NP) exposure† 二氧化钛纳米颗粒（TiO2-NP）暴露过程中人体循环蛋白质组相互作用、氧化应激相关信号传导和心血管影响

IF 3 4区生物学

Molecular omics Pub Date : 2025-04-09 DOI: 10.1039/D4MO00205A

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":"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 (TiO2-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 via 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 TiO2-NPs-induced cardiotoxicity.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 282-302"},"PeriodicalIF":3.0,"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}

引用次数: 0

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 通过RNA-Seq对血清外泌体进行转录组分析，发现脂质代谢变化是评估罗沙司他治疗慢性肾病的潜在生物标记物。

IF 3 4区生物学

Molecular omics Pub Date : 2025-03-17 DOI: 10.1039/D4MO00025K

Ru Zhou, YaXuan Zhen, Hualin Ma, Zhen Wang, LiXia Liu, Xinzhou Zhang and Baochun Guo

{"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":"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.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 3","pages":" 240-249"},"PeriodicalIF":3.0,"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}

引用次数: 0

Lipidomics reveals cell specific changes during pluripotent differentiation to neural and mesodermal lineages† 脂质组学揭示了神经和中胚层谱系多能分化过程中细胞的特异性变化。

IF 3 4区生物学

Molecular omics Pub Date : 2025-03-13 DOI: 10.1039/D4MO00261J

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":"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.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 259-269"},"PeriodicalIF":3.0,"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}

引用次数: 0