Molecular omics最新文献

{"title":"Cancer evaluation in dogs using cerumen as a source for volatile biomarker prospection†","authors":"João Marcos G. Barbosa, Engy Shokry, Lurian Caetano David, Naiara Z. Pereira, Adriana R. da Silva, Vilma F. de Oliveira, Maria Clorinda S. Fioravanti, Paulo H. Jorge da Cunha, Anselmo E. de Oliveira and Nelson Roberto Antoniosi Filho","doi":"10.1039/D3MO00147D","DOIUrl":"10.1039/D3MO00147D","url":null,"abstract":"<p >Cancer is one of the deadliest diseases in humans and dogs. Nevertheless, most tumor types spread faster in canines, and early cancer detection methods are necessary to enhance animal survival. Here, cerumen (earwax) was tested as a source of potential biomarkers for cancer evaluation in dogs. Earwax samples from dogs were collected from tumor-bearing and clinically healthy dogs, followed by Headspace/Gas Chromatography-Mass Spectrometry (HS/GC-MS) analyses and multivariate statistical workflow. An evolutionary-based multivariate algorithm selected 18 out of 128 volatile metabolites as a potential cancer biomarker panel in dogs. The candidate biomarkers showed a full discrimination pattern between tumor-bearing dogs and cancer-free canines with high accuracy in the test dataset: an accuracy of 95.0% (75.1–99.9), and sensitivity and specificity of 100.0% and 92.9%, respectively. In summary, this work raises a new perspective on cancer diagnosis in dogs, being carried out painlessly and non-invasive, facilitating sample collection and periodic application in a veterinary routine.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 27-36"},"PeriodicalIF":2.9,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41105027","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 role of intra-cellular metabolites in the lactic acid production by novel Bacillus amyloliquefaciens using sugarcane molasses as a substratum†","authors":"Balasubramanian Vignesh Kumar, Balakrishnan Muthumari, Murugan Kavitha, John Kennedy John Praveen Kumar and Muthuramalingam Jothi Basu","doi":"10.1039/D3MO00141E","DOIUrl":"10.1039/D3MO00141E","url":null,"abstract":"<p >Lactic acid is a versatile, multi-functional organic monomer in various industries, creating worldwide demand. High titer lactic acid production was achieved by novel <em>Bacillus amyloliquefaciens</em> J2V2AA through sugarcane molasses fermentation up to 178 mg mL<small>⁻¹</small>. A metabolomics approach such as combined GC-MS and LC-MS was applied to elucidate the involvement of key metabolites in lactic acid production. The results revealed the participation of 58 known intra-cellular metabolites at various pathways in lactic acid production. Twenty-eight highly up-regulated and down-regulated metabolites were analyzed, and a schematic diagram of a possible lactic acid production pathway was proposed. The produced lactic acid was analyzed through FTIR, UV-Spectrum, and HPLC analysis.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 19-26"},"PeriodicalIF":2.9,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10205429","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":"Characterization of methionine dependence in melanoma cells†","authors":"Sarita Garg, Lauren C. Morehead, Jordan T. Bird, Stefan Graw, Allen Gies, Aaron J. Storey, Alan J. Tackett, Rick D. Edmondson, Samuel G. Mackintosh, Stephanie D. Byrum and Isabelle R. Miousse","doi":"10.1039/D3MO00087G","DOIUrl":"10.1039/D3MO00087G","url":null,"abstract":"<p >Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood. We do know that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with its precursor homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent and methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generalized rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of <em>S</em>-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but triggers different outcomes in methionine dependent <em>versus</em> independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and immune functions in the cellular response to methionine stress in melanoma.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 37-47"},"PeriodicalIF":2.9,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41128976","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":"Advancing science through data sharing: a new data policy for Molecular Omics","authors":"","doi":"10.1039/D3MO90028B","DOIUrl":"https://doi.org/10.1039/D3MO90028B","url":null,"abstract":"<p >A graphical abstract is available for this content</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 606-606"},"PeriodicalIF":2.9,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49994739","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":"Single cell proteomics analysis of drug response shows its potential as a drug discovery platform†","authors":"Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek and Bogdan Budnik","doi":"10.1039/D3MO00124E","DOIUrl":"10.1039/D3MO00124E","url":null,"abstract":"<p >Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling, nanoscale super-resolution microscopy, advances in single cell RNAseq and proteomics technologies, provide more detailed information about biological processes which were not evident with the analysis of bulk material. This new era of single-cell biology provides a better understanding of such complex biological systems as cancer, inflammation, immunity mechanism and aging processes, and opens the door into the field of drug response heterogeneity. The latest discoveries of cellular heterogeneity gives us a unique understanding of complex biological processes, such as disease mechanism, and will lead to new strategies for better and personalized treatment strategies. Recently, single-cell proteomics techniques that allow quantification of thousands of proteins from single mammalian cells have been introduced. Here we present an improved single-cell mass spectrometry-based proteomics platform called SCREEN (<strong>S</strong>ingle <strong>C</strong>ell p<strong>R</strong>ot<strong>E</strong>om<strong>E</strong> a<strong>N</strong>alysis) for deep and high-throughput single-cell proteome coverage with high efficiency, less turnaround time and with an improved ability for protein quantitation across more cells than previously achieved. We applied this new platform to analyze the single-cell proteomic landscape under different drug treatment over time to uncover heterogeneity in cancer cell response, which for the first time, to our knowledge, has been achieved by mass spectrometry based analytical methods. We discuss challenges in single-cell proteomics, future improvements and general trends with the goal to encourage forthcoming technical developments.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 6-18"},"PeriodicalIF":2.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10185642","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":"Integrated proteomic and metabolomic analysis of plasma reveals regulatory pathways and key elements in thyroid cancer†","authors":"Zijian Sun, Dongdong Feng, Liehao Jiang, Jingkui Tian, Jiafeng Wang and Wei Zhu","doi":"10.1039/D3MO00142C","DOIUrl":"10.1039/D3MO00142C","url":null,"abstract":"<p >Thyroid cancer (TC) is the most common endocrine malignancy with increasing incidence in recent years. Fine-needle aspiration biopsy (FNAB), as a gold standard for the initial evaluation of thyroid nodules, fails to cover all the cytopathologic conditions resulting in overdiagnosis. There is an urgent need for a better classification of thyroid cancer from benign thyroid nodules (BTNs). Here, data independent acquisition (DIA)-based proteomics and untargeted metabolomics in plasma samples of 10 patients with TC and 15 patients with BTNs were performed. Key proteins and metabolites were identified specific to TC, and an independent cohort was used to validate the potential biomarkers using enzyme-linked immunosorbent assay (ELISA). In total, 1429 proteins and 1172 metabolites were identified. Principal component analysis showed a strong overlap at the proteomic level and a significant discrimination at the metabolomic level between the two groups, indicating a more drastic disturbance in the metabolome of thyroid cancer. Integrated analysis of proteomics and metabolomics shows glycerophospholipid metabolism and arachidonic acid metabolism as key regulatory pathways. Furthermore, a multi-omics biomarker panel was developed consisting of LCAT, GPX3 and leukotriene B4. Based on the AUC value for the discovery set, the classification performance was 0.960. The AUC value of the external validation set was 0.930. Altogether, our results will contribute to the clinical application of potential biomarkers in the diagnosis of thyroid cancer.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 800-809"},"PeriodicalIF":2.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10111449","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":"Association of lipid metabolism-related metabolites with overweight/obesity based on the FTO rs1421085†","authors":"Sabiha Farooq, Sobia Rana, Amna Jabbar Siddiqui, Ayesha Iqbal, Adil Anwar Bhatti and Syed Ghulam Musharraf","doi":"10.1039/D3MO00112A","DOIUrl":"10.1039/D3MO00112A","url":null,"abstract":"<p >Globally, obesity is a severe health issue. A more precise and practical approach is required to enhance clinical care and drug development. The FTO (fat mass and obesity-associated) gene variant rs1421085 is strongly associated with an increased susceptibility to obesity in numerous populations; however, the precise mechanism behind this association concerning metabolomics is still not understood. This study aims to examine the association between metabolites and obesity-related anthropometric traits based on the variant FTO rs1421085. This study was based on a case-control design involving a total of 542 participants including overweight/obese cases and healthy controls. The blood samples were collected from all the participants. The isolated serum samples were subjected to untargeted metabolomics using GC-MS. The isolated DNA samples were genotyped for the FTO rs1421085 variant. Initially, a total of 42 metabolites were identified on GC-MS, which were subjected to further association analyses. The study observed a significant association of two metabolites, glycerol and 2,3-dihydroxypropyl stearate with FTO gene variant rs1421085 and obesity-related anthropometric traits including % BF, WHtR, WC, and HC. The CT genotype of FTO rs1421085 may greatly increase the risk of overweight/obesity by changing the lipid metabolism-related metabolites. Therefore, this study highlights the significance of biochemical networks in the progression of obesity in carriers of the FTO rs1421085 risk genotype.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 697-705"},"PeriodicalIF":2.9,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9989111","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":"Metabolomic analysis reveals stress tolerance mechanisms in common bean (Phaseolus vulgaris L.) related to treatment with a biostimulant obtained from Corynebacterium glutamicum†","authors":"Stephanie Nemesio da Silva, Luis Fernando de Oliveira, Rodrigo Alberto Repke, Alana Kelyene Pereira, Luidy Darlan Barbosa, Rafael Leiria Nunes, Alessandra Sussulini, Fabio Pinheiro and Taicia Pacheco Fill","doi":"10.1039/D3MO00110E","DOIUrl":"10.1039/D3MO00110E","url":null,"abstract":"<p >Microbial biostimulants have emerged as a sustainable alternative to increase the productivity and quality of important crops. Despite this, the effects of the treatment on plant metabolism are poorly understood. Thus, this study investigated the metabolic response of common bean (<em>Phaseolus vulgaris</em>) related to the treatment with a biostimulant obtained from the extract of <em>Corynebacterium glutamicum</em> that showed positive effects on the development, growth, and yield of crops previously. By untargeted metabolomic analysis using UHPLC-MS/MS, plants and seeds were subjected to treatment with the biostimulant. Under ideal growth conditions, the plants treated exhibited higher concentration levels of glutamic acid, nicotiflorin and glycosylated lipids derived from linolenic acid. The foliar application of the biostimulant under water stress conditions increased the chlorophyll content by 17% and induced the accumulation of flavonols, mainly quercetin derivatives. Also, germination seed assays exhibited longer radicle lengths for seeds treated compared to the untreated control even in the absence of light (13–18% increase, <em>p</em>-value &lt;0.05). Metabolomic analysis of the seeds indicated changes in concentration levels of amino acids (tryptophan, phenylalanine, tyrosine, glutamine, and arginine) and their derivatives. The results point out the enhancement of abiotic stress tolerance and the metabolic processes triggered in this crop associated with the treatment with the biostimulant, giving the first insights into stress tolerance mechanisms in <em>P. vulgaris</em>.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 743-755"},"PeriodicalIF":2.9,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9997848","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":"Untargeted metabolomics and phenotype data indicate the therapeutic and prophylactic potential of Lysimachia candida Lindl. towards high-fat high-fructose-induced metabolic syndrome in rats†","authors":"Md Jahangir Alam, Parul Kamboj, Soumalya Sarkar, Sonu Kumar Gupta, Siva Swapna Kasarla, Sneh Bajpai, Deepika Kumari, Neema Bisht, Sagar Ramrao Barge, Bhaswati Kashyap, Barsha Deka, Simanta Bharadwaj, Seydur Rahman, Partha Pratim Dutta, Jagat C. Borah, Narayan Chandra Talukdar, Yashwant Kumar and Sanjay K Banerjee","doi":"10.1039/D3MO00104K","DOIUrl":"10.1039/D3MO00104K","url":null,"abstract":"<p >The present study evaluated the therapeutic potential of the medicinal plant <em>Lysimachia candida</em> Lindl. against metabolic syndrome in male SD rats fed with a high-fat high-fructose (HFHF) diet. Methanolic extract of <em>Lysimachia candida</em> Lindl. (250 mg kg<small>⁻¹</small> body weight p.o.) was administrated to the HFHF-fed rats daily for 20 weeks. Blood samples were collected, and blood glucose levels and relevant biochemical parameters were analysed and used for the assessment of metabolic disease phenotypes. In this study, <em>Lysimachia candida</em> decreased HFHF diet-induced phenotypes of metabolic syndrome, <em>i.e.</em>, obesity, blood glucose level, hepatic triglycerides, free fatty acids, and insulin resistance. Liquid chromatography-mass spectrometry-based metabolomics was done to study the dynamics of metabolic changes in the serum during disease progression in the presence and absence of the treatment. Furthermore, multivariate data analysis approaches have been employed to identify metabolites responsible for disease progression. <em>Lysimachia candida</em> Lindl. plant extract restored the metabolites that are involved in the biosynthesis and degradation of amino acids, fatty acid metabolism and vitamin metabolism. Interestingly, the results depicted that the treatment with the plant extract restored the levels of acetylated amino acids and their derivatives, which are involved in the regulation of beta cell function, glucose homeostasis, insulin secretion, and metabolic syndrome phenotypes. Furthermore, we observed restoration in the levels of indole derivatives and <em>N</em>-acetylgalactosamine with the treatment, which indicates a cross-talk between the gut microbiome and the metabolic syndrome. Therefore, the present study revealed the potential mechanism of <em>Lysimachia candida</em> Lindl. extract to prevent metabolic syndrome in rats.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 787-799"},"PeriodicalIF":2.9,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10284190","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":"Anti-inflammatory effects of myristic acid mediated by the NF-κB pathway in lipopolysaccharide-induced BV-2 microglial cells†","authors":"Qiong Huang, Chunyan Chen, Zhongxiao Zhang and Qun Xue","doi":"10.1039/D3MO00063J","DOIUrl":"10.1039/D3MO00063J","url":null,"abstract":"<p >Parkinson's disease (PD) is a serious neurodegenerative disorder wherein changes in metabolites related to lipids, glutathione, and energy metabolism occur. Currently, metabolite changes in PD have been reported, yet their role in the prognosis of disease remains poorly understood. Functional metabolites can be used to diagnose diseases, especially PD, and can exert neuroprotective effects. This study used a PD animal model and a lipopolysaccharide (LPS)—mediated inflammatory response model (using the BV-2 mouse microglial cell line) to identify functional metabolites that can identify important metabolic disorders during PD, and comprehensively evaluated their profiles using a metabolomics-based approach. Our results showed that co-treatment with myristic acid and heptadecanoic acid downregulated the expression of interleukin (IL)-1β, IL-6, and tumor necrosis factor-α in BV-2 cells. Additionally, myristic acid and 10 μM heptadecanoic acid significantly inhibited the LPS-induced inflammatory response through the nuclear factor-κB pathway in BV-2 microglial cells, which provides a potential approach for PD treatment. Myristic acid and heptadecanoic acid were the active metabolites found by active metabolomics technology, but at present, there is no research report about their function for PD treatment, and our findings offer a novel research strategy for PD diagnosis and treatment.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 726-734"},"PeriodicalIF":2.9,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9834757","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}