Molecular omics最新文献

{"title":"Enhanced anti-inflammatory and anti-fibrotic effects of nanoparticles loaded with a combination of <i>Aloe vera</i>-<i>Moringa oleifera</i> extracts.","authors":"Gabriela I Carballo-López, Jhordan Ojeda-González, Kevin D Martínez-García, Karla E Cervantes-Luevano, Aldo Moreno-Ulloa, Ana B Castro-Ceseña","doi":"10.1039/d4mo00195h","DOIUrl":"https://doi.org/10.1039/d4mo00195h","url":null,"abstract":"<p><p>Metabolic associated steatohepatitis characterized by lipid accumulation, inflammation and fibrosis, is a growing global health issue, contributing to severe liver-related mortality. With limited effective treatments available, there is an urgent need for novel therapeutic strategies. <i>Moringa oleifera</i>, rich in antioxidants, offers potential for combating steatohepatitis, but its cytotoxicity presents challenges. <i>Aloe vera</i>, renowned for its cytocompatibility and anti-inflammatory effects, shows promise in mitigating these risks. Using infrared spectrometry and mass spectrometry, we identified 1586 metabolites from both plants across 84 chemical classes. By encapsulating these phytochemicals in nanoparticles, we achieved increased solubility, cytocompatibility, and gene modulation to hepatic stellate cells affected by steatohepatitis. Chemoinformatic analysis revealed bioactive metabolites, including hesperetin analogs, known to inhibit TGF-β. Our results demonstrate that these nanoparticles not only improved gene expression modulation related to metabolic associated steatohepatitis, particularly TGF-β and COL1A1, but also outperformed free compounds, highlighting their potential as a novel therapeutic approach.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058155","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":"Unraveling the phenotypic and metabolic responses induced by urea-encapsulated hydrogel beads on <i>Brassica juncea</i> (L.) Czern & Coss.","authors":"Muthumari Balakrishnan, Vignesh Kumar Balasubramanian, Kavitha Murugan, John Praveen Kumar John Kennedy, Subashri Dhanasekaran, Shih-Feng Fu, Shang-Tse Ho, Jothi Basu Muthuramalingam, Jui-Yu Chou","doi":"10.1039/d4mo00192c","DOIUrl":"https://doi.org/10.1039/d4mo00192c","url":null,"abstract":"<p><p>Hydrogels, three-dimensional polymeric networks capable of absorbing and retaining significant amounts of aqueous solution, offer a promising platform for controlled release of desired compounds. In this study, we explored the effects of urea delivery through galactoxyloglucan-sodium alginate hydrogels on the phenotypic and metabolic responses of <i>Brassica juncea</i>, a vital oilseed and vegetable crop. The experiments were conducted with four treatments: control (without hydrogel beads and urea), direct urea supplementation (U), hydrogel beads with urea (HBWU), and hydrogel beads without urea (HBWOU). Our findings revealed that HBWU-treated plants exhibited commendable plant growth with significantly higher chlorophyll content (11.06 mg/0.1 g) compared to the control (3.67 mg/0.1 g) and U-treated group (6.41 mg/0.1 g). Metabolic analysis identified 17 major intra-cellular metabolites involved in nitrogen metabolism. HBWU treatment significantly boosted nitrogen assimilation in plants, as evidenced by the upregulation of 9 metabolites. Furthermore, a proposed schematic diagram illustrates the HBWU induced-metabolic pathways and nitrogen metabolism in <i>B. juncea</i>. These findings demonstrate the potential of hydrogel-based controlled-release systems to enhance plant growth and nitrogen assimilation.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053026","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":"The investigation of early metabolic level perturbation of northern quahog (<i>Mercenaria mercenaria</i>) in response to brevetoxin.","authors":"Bo Wang, Nicole McKenna, Julie Pollak, Moses Mayonu, Lin Jiang","doi":"10.1039/d4mo00207e","DOIUrl":"https://doi.org/10.1039/d4mo00207e","url":null,"abstract":"<p><p>Brevetoxins are a type of neurotoxin produced in red tide blooms. Northern quahogs (<i>M. mercenaria</i>) are extensively used in commercial aquaculture farming, and early-stage metabolomics studies can provide early warnings of brevetoxins for farmers. In this study, NMR-based metabolomics was performed to investigate the response of clam gills and digestive glands under a series of sublethal doses of brevetoxins. Our study showed that the brevetoxin PbTx-2 had minimal influence on the physical activities of <i>M. mercenaria</i> for a short exposure time (24 hours). However, major metabolic level perturbations were observed in the clam gill extracts from the 1 ppb treatment. In addition, in the low concentration (0.1 ppb) study, clam gills showed combinational metabolite perturbations, as observed by an OPLS-DA study. The highly disturbed metabolites in the gill samples were the upregulated serine, glucose, hypotaurine, and glycine and the downregulated lactate, leucine, isoleucine, threonine, biotin, taurine, and valine. The results indicated that the brevetoxin PbTx-2 potentially affects glycolysis, glycine, serine, and threonine metabolism, taurine and hypotaurine metabolism, and biotin metabolism. While the digestive gland had less significantly changed metabolites, the potential combinational metabolite changes from PCA were observed from the 5-ppb treatment. Glucose and glycine are the primary metabolites that showed high contributions to the OPLS-DA model, which indicates the potential influence of digestive activities. The study indicated that metabolomic analysis of the gills and digestive glands of <i>M. mercenaria</i> is a feasible method to monitor the toxicity of brevetoxins, especially under sublethal doses in marine water.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914843","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":"Proteomic analysis reveals anticancer mechanisms of Bhallataka taila in inhibiting lung cancer progression and metastasis.","authors":"Suchitha G P, Akhila B Rai, Ravishankar Pervaje, Chinmaya Narayana Kotimoole, Prashant Kumar Modi, T S Keshava Prasad, Shobha Dagamajalu","doi":"10.1039/d4mo00156g","DOIUrl":"https://doi.org/10.1039/d4mo00156g","url":null,"abstract":"<p><p>Lung cancer remains the leading cause of cancer-related deaths worldwide due to its poor prognosis. Despite significant advancements in the understanding of cancer development, improvements in diagnostic methods, and multimodal therapeutic regimens, the prognosis of lung cancer has still not improved. Therefore, it is reasonable to look for newer and alternative medicines for treatment. Bhallataka nut extract, derived from the seeds of <i>Semecarpus anacardium</i>, is known for its anti-inflammatory and antioxidant properties, suggesting potential as a treatment for cancer. In this study, we investigated the molecular networks associated with the Bhallataka taila-mediated inhibition of lung adenocarcinoma. Treating lung cancer cell lines with Bhallataka taila resulted in decreased colony formation, proliferation, and migration, and increased apoptosis. Using a tandem mass tag (TMT)-based temporal quantitative proteomic analysis, we identified 173 overexpressed and 249 downregulated proteins among a total of 2879 proteins. Significantly altered proteins are associated with lung cancer progression, metastasis, invasion, migration, and epithelial-mesenchymal transition (EMT). The analysis of these altered proteins revealed molecular networks underlying the anticancer mechanisms of Bhallataka taila. Validation of these proteins and pathways affected by Bhallataka taila confirmed its utility in cancer treatment.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914814","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":"Differential modulation of the hepatocellular metabolome, cytoprotective and inflammatory responses due to endotoxemia and lipotoxicity.","authors":"Jyoti Sharma, Priyankar Dey","doi":"10.1039/d4mo00140k","DOIUrl":"https://doi.org/10.1039/d4mo00140k","url":null,"abstract":"<p><p>The present work aimed to examine the primary mechanisms of liver damage, namely the impact of gut-derived endotoxins along the gut-liver axis and adipose-derived free fatty acids along the adipose-liver axis. These processes are known to play a significant role in the development of hepatic inflammation and steatosis. Although possible overlapping in the pathogenesis was expected, these processes have unique pathophysiological consequences. Therefore, we used HepG2 cells as a model system to investigate the impact of lipopolysaccharides (LPS) and free fatty acid (FFA; albumin conjugated palmitic acid) on the intracellular metabolome. Although both LPS and FFA triggered the expression of nuclear factor κB (NFκB)-dependent inflammation, only LPS treatment was able to trigger a Toll-like receptor 4 (TLR4) dependent response. The intracellular cytoprotective enzymatic levels (catalase, peroxidase, glutathione) were increased due to FFA but lowered due to LPS. The free-radical neutralizing efficacies of cell-free metabolites of FFA-treated cells were better than those of the LPS-treated ones. The use of untargeted metabolomics allowed for the identification of distinct metabolic pathway enrichments, providing further insights into the differential effects of LPS and FFA on the metabolism of hepatocytes. Collectively, the current study highlights the distinct impacts of endotoxemia and lipotoxicity on the metabolome of hepatocytes, hence offering valuable insights into hepatocellular function.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914876","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":"Selective labeling of tyrosine residues in proteins: insights from PTAD labeling and tandem mass spectrometry analysis.","authors":"Adway O Zacharias, Sharel Cornelius, Saiful M Chowdhury","doi":"10.1039/d4mo00186a","DOIUrl":"https://doi.org/10.1039/d4mo00186a","url":null,"abstract":"<p><p>Designing reagents for protein labeling is crucial for investigating cellular events and developing new therapeutics. Historically, much effort has been focused on labeling lysine and arginine residues due to their abundance on the protein periphery. The chemo-selectivity of these reagents is a challenging yet crucial parameter for deciphering properties specifically associated with the targeted amino acid. Consequently, there is a growing demand for new conjugation reagents and workflows that facilitate selective binding to amino acids other than lysine, cysteine, and arginine. Tyrosine, an aromatic amino acid, occurs moderately on the protein periphery, with its phenolic ring often buried within the tertiary protein structure. This presents a challenging environment for tyrosine-specific protein bioconjugation efforts. The hydrophobic aromatic side chain of tyrosine is known to engage in π-stacking interactions, while the hydroxyl group of the phenyl ring can participate in hydrogen bonding and form tyrosyl radicals involved in electron transfer. 4-Phenyl-3<i>H</i>-1,2,4-triazole-3,5(4<i>H</i>)-dione (PTAD) has been previously investigated for its ability to bind to tyrosine. This work presents an extensive structural proteomics investigation of tyrosine labeling across samples of varying complexity, ranging from peptides and proteins to entire cell lysates. Mass spectrometry is utilized to study the behavior of tyrosine-labeled samples through tandem mass spectrometry experiments. We believe these studies will offer valuable insights into tyrosine bioconjugation with PTAD and demonstrate its potential as a covalent labeling reagent for chemical proteomics research.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882327","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":"Integrating OMICS-based platforms and analytical tools for diagnosis and management of pancreatic cancer: a review.","authors":"Patrícia Sousa, Laurentina Silva, José S Câmara, Paula Guedes de Pinho, Rosa Perestrelo","doi":"10.1039/d4mo00187g","DOIUrl":"https://doi.org/10.1039/d4mo00187g","url":null,"abstract":"<p><p>Cancer remains the second leading cause of death worldwide, surpassed only by cardiovascular disease. From the different types of cancer, pancreatic cancer (PaC) has one of the lowest survival rates, with a survival rate of about 20% after the first year of diagnosis and about 8% after 5 years. The lack of highly sensitive and specific biomarkers, together with the absence of symptoms in the early stages, determines a late diagnosis, which is associated with a decrease in the effectiveness of medical intervention, regardless of its nature - surgery and/or chemotherapy. This review provides an updated overview of recent studies combining multi-OMICs approaches (<i>e.g.</i>, proteomics, metabolomics) with analytical tools, highlighting the synergy between high-throughput molecular data generation and precise analytical tools such as LC-MS, GC-MS and MALDI-TOF MS. This combination significantly improves the detection, quantification and identification of biomolecules in complex biological systems and represents the latest advances in understanding PaC management and the search for effective diagnostic tools. Large-scale data analysis coupled with bioinformatics tools enables the identification of specific genetic mutations, gene expression patterns, pathways, networks, protein modifications and metabolic signatures associated with PaC pathogenesis, progression and treatment response through the integration of multi-OMICs data.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877478","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":"Phosphoproteomics guides low dose drug combination of cisplatin and silmitasertib against concurrent chemoradiation resistant cervical cancer†","authors":"Irene A. George, Janani Sambath, R. E. Dhawale, Manisha Singh, Vinita Trivedi, R. Venkataramanan, Richa Chauhan and Prashant Kumar","doi":"10.1039/D4MO00147H","DOIUrl":"10.1039/D4MO00147H","url":null,"abstract":"<p >Cisplatin-based concurrent chemoradiotherapy (CCRT) is the standard treatment for cervical patients with locally advanced disease. Despite the improved survival rates and prognosis observed in patients undergoing CCRT, over 30–40% do not achieve complete response and are at risk of locoregional recurrence. Targeting crucial molecules that confer resistance may improve the clinical outcomes of the treatment resistant patient cohort. Herein, we employed a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based phosphoproteomic approach to identify the altered phosphophorylation events, activated kinases and dysregulated pathways involved in treatment resistance. We quantified 2531 unique phosphopeptides mapping to 1099 proteins of which 74 proteins were differentially phosphorylated between the cohorts. Pathway analysis revealed dysregulation of the DNA repair pathway and the proteins involved in DNA repair in the non-responder cohort. Additionally, we identified kinase signature associated with CCRT resistance. Kinases such as CSNK2A1, PRKDC, PLK-1, NEK2, ATM and CDK1 are predicted to be activated in non-responders. In particular, we showed that CSNK2A1 is involved in oncogenesis of cervical cancer and pharmacological inhibition led to reduced cell proliferation, migration and colony formation. Moreover, the combination of the CSNK2A1 inhibitor, silmitasertib with cisplatin demonstrated synergism (combination index &lt; 1) and yielded a beneficial reduction in dosage. The dose reduced combination potentially reduced the proliferative, migratory and colony formation ability <em>in vitro</em>. Our findings highlight the potential of phosphoproteomics to identify clinically significant targets and pathways implicated in CCRT resistance. Our study also indicates that combination therapy could serve as an effective treatment strategy to improve the efficacy of patients undergoing CCRT.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 87-100"},"PeriodicalIF":3.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/mo/d4mo00147h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813713","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}

{"title":"Competing technologies: determining the geographical origin of strawberries (Fragaria × ananassa) using laboratory based near-infrared spectroscopy compared to a simple portable device†","authors":"Johannes Brockelt, Felix Schmauder, Kim Brettschneider, Marina Creydt, Stephan Seifert and Markus Fischer","doi":"10.1039/D4MO00161C","DOIUrl":"10.1039/D4MO00161C","url":null,"abstract":"<p >The application and development of fast and simple screening methods for the authentication of foods has increased continuously in recent years. A widely used analytical technique is Fourier transform near-infrared spectroscopy (FT-NIR). Despite the simple application of FT-NIR analysis, the analyses are usually carried out on benchtop devices in the laboratory. However small, inexpensive and mobile NIR devices could be used on-site. Despite the simple use of FT-NIR analysis, the examinations are usually carried out on a stationary benchtop device in a laboratory. However, in order to be able to perform the application directly on site, the application of small, cost-effective and mobile NIR devices for food analysis is crucial. In this study, both, a benchtop NIR instrument and a handheld NIR device with a lower resolution and analyzed wavenumber range were applied for the differentiation of strawberries from different geographical origins. Distinguishing German and non-German strawberries using linear discriminant analysis (LDA) yielded an accuracy of 91.9% and 84.0% using the benchtop and the handheld devices, respectively. Relevant variables could be assigned to lipids, carbohydrates and proteins. Overall, our study demonstrated for the first time that analyzing the geographical origin of strawberries using NIR spectroscopy is also possible by means of a handheld device.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 7-18"},"PeriodicalIF":3.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/mo/d4mo00161c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142786193","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}

{"title":"Investigating the mechanism of Qifu Yin in ameliorating memory disorders through pseudo-targeted lipidomics†","authors":"Fuxia Zhao, Jing Wang, Minjun Wu, Jiaqi Fan, Shiqi Liu, Fanying Deng, Shihui Wang, Yangang Cheng and Yan Wang","doi":"10.1039/D4MO00141A","DOIUrl":"10.1039/D4MO00141A","url":null,"abstract":"<p >Memory disorder (MD) is a neurodegenerative disease with an increasing incidence rate that adversely affects the quality of life of patients. Qifu Yin (QFY), a classic traditional Chinese medicine formula used for treating dementia, is known for its neuroprotective properties, although its mechanism of action requires further exploration. In this study, <small>D</small>-galactose combined with aluminum chloride was used to establish an MD rat model, and behavior, histopathology, and related indicators were used to evaluate the pharmacodynamics of the formula in the rats. Furthermore, brain tissues were examined using pseudo-targeted lipidomics analysis, and candidate ion pairs were screened through mass spectrometry using UPLC-Q/Orbitrap HRMS. An sMRM detection method for candidate ion pairs was developed using UHPLC-Q-TRAP-MS/MS and validated. This approach was applied to the lipidomics study of QFY in improving MD. Differential metabolites screened through pseudo-targeted lipidomics were analyzed by employing network pharmacology, and the pathway was verified to explore their mechanism of action. Results demonstrated that QFY could improve memory impairment. A total of 1052 ion pairs were constructed in the pseudo-targeted lipidomics analysis, identifying 33 differential metabolites and 5 metabolic pathways. Furthermore, 31 differential metabolites in MD rats treated with QFY were significantly reversed. Immunohistochemical analysis showed that QFY could inhibit the expression of inflammatory factors. Network pharmacological analysis showed that the calcium signaling pathway was the main signaling pathway, and QFY could significantly reverse the expression levels of mRNA and protein. Thus, QFY can improve memory impairment in rats, which may be related to the regulation of oxidative stress, lipid metabolism disorder and the calcium signaling pathway.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 69-86"},"PeriodicalIF":3.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750615","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}