Molecular omics最新文献

{"title":"Size exclusion chromatography based proteomic and degradomic profiling of inflammasome-activated, murine bone marrow-derived dendritic cells highlights complex retention and release of cleavage products†","authors":"Daniel Vogele, Svenja Wöhrle, Benedikt S. Saller, Klemens Fröhlich, Bálint András Barta, Miguel Cosenza-Contreras, Olaf Groß and Oliver Schilling","doi":"10.1039/D4MO00163J","DOIUrl":"10.1039/D4MO00163J","url":null,"abstract":"<p >Coupling size exclusion chromatography (SEC) with mass spectrometry-based proteomics enables investigating protein complexes, with degradomic profiling providing deeper insights into complex-associated proteolytic processing and retaining of cleavage products. This study aims to map protein complex formation upon inflammasome activation in bone marrow-derived dendritic cells (BMDCs) from gasdermin D-deficient mice, focusing on proteolytic enzymes and truncated proteins in higher molecular weight complexes. Cultured BMDCs were primed with LPS and subsequently treated with nigericin or Val-boroPro (VbP). SEC-fractionated proteins were TMT-labelled and analyzed <em>via</em> liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified 6862 proteins and 70 802 peptides, including 14 714 semi-tryptic peptides indicating elevated endogenous proteolytic processing. The sequence motif of numerous cleavage sites maps to caspase-like activity. Inflammasome activation was corroborated by elevated levels of apoptosis-associated speck-like protein containing a CARD (ASC) in higher molecular weight (MW) fractions and increased IL-1β levels in low MW fractions upon nigericin or VbP treatment. The majority of truncated cleavage products remained within their corresponding, higher MW protein complexes while caspase-specific cleavage products of Rho-associated protein kinase 1, gelsolin, and AP-2 complex subunit alpha-2 dissociated to lower MW fractions. SEC profiles identified 174 proteases, with cell surface proteases forming high MW complexes, including ADAMs and DPP4 but not MMP14. VbP treatment led to the accumulation of ISG15 in low MW fractions while RNA polymerase II coactivator p15 shifted to higher MW fractions. This study demonstrates that SEC-coupled proteomics and degradomic profiling offer unique insights into protein complex dynamics and proteolytic processes upon inflammasome activation.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 595-610"},"PeriodicalIF":3.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392001","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":"Comprehensive untargeted lipidomic profiling of third generation lentiviral vectors and packaging cells†","authors":"Joshua A. Roberts, Elena Godbout, Jocelyn A. Menard, Christopher N. Boddy, Jean-Simon Diallo and Jeffrey C. Smith","doi":"10.1039/D4MO00052H","DOIUrl":"10.1039/D4MO00052H","url":null,"abstract":"<p >Lentiviral vectors (LV) are emerging tools for genetic therapies and novel cancer treatments. While effective, LV-based therapies have extremely large costs associated with their manufacturing and delivery. LV technology descends from human immunodeficiency virus (HIV), whose lipid envelope has been previously measured and shown to have a direct impact on its transduction efficiency. We developed a rapid, robust, and sensitive untargeted lipidomics pipeline to analyze novel LV biotherapeutic products and demonstrate its utility on HEK 293T packaging cells and concentrated culture media containing LV. The impact of 48 hours of LV production on the lipidome of HEK 293T cells was measured and compared to the expression of vesicular stomatitis virus G protein (VSV G) over the same timeframe. 151 lipids were identified in HEK 293T packaging cells, 84 of which had fold changes with FDR-corrected <em>P</em> &lt; 0.05 compared to HEK 293T treated with media. It was found that fold changes with FDR-adjusted <em>P &lt;</em> 0.05 after VSV G expression and LV production were highly correlated (<em>R</em><small>²</small> = 0.89). Concentrating LV in culture media led to the identification of 102 lipids, half of which were determined to be unique LV virion lipids after subtracting the media lipidome. Our approach can be readily used to study the lipid dynamics of large-scale LV production and be rapidly translated into targeted methods to quantify individual lipid components or applied to other viral vector platforms.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 642-653"},"PeriodicalIF":3.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392000","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":"Systemic analysis of lipid metabolism from individuals to multi-organism systems†","authors":"Samuel Furse, Carlos Martel, David F. Willer, Daniel Stabler, Denise S. Fernandez-Twinn, Jennifer Scott, Ryan Patterson-Cross, Adam J. Watkins, Samuel Virtue, Thomas A. K. Prescott, Ellen Baker, Jennifer Chennells, Antonio Vidal-Puig, Susan E. Ozanne, Geoffrey C. Kite, Milada Vítová, Davide Chiarugi, John Moncur, Albert Koulman, Geraldine A. Wright, Stuart G. Snowden and Philip C. Stevenson","doi":"10.1039/D4MO00083H","DOIUrl":"10.1039/D4MO00083H","url":null,"abstract":"<p >Lipid metabolism is recognised as being central to growth, disease and health. Lipids, therefore, have an important place in current research on globally significant topics such as food security and biodiversity loss. However, answering questions in these important fields of research requires not only identification and measurement of lipids in a wider variety of sample types than ever before, but also hypothesis-driven analysis of the resulting ‘big data’. We present a novel pipeline that can collect data from a wide range of biological sample types, taking 1 000 000 lipid measurements per 384 well plate, and analyse the data systemically. We provide evidence of the power of the tool through proof-of-principle studies using edible fish (mackerel, bream, seabass) and colonies of <em>Bombus terrestris</em>. Bee colonies were found to be more like mini-ecosystems and there was evidence for considerable changes in lipid metabolism in bees through key developmental stages. This is the first report of either high throughput LCMS lipidomics or systemic analysis in individuals, colonies and ecosystems. This novel approach provides new opportunities to analyse metabolic systems at different scales at a level of detail not previously feasible, to answer research questions about societally important topics.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 570-583"},"PeriodicalIF":3.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154634","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":"Outstanding Reviewers for Molecular Omics in 2023","authors":"","doi":"10.1039/D4MO90019G","DOIUrl":"10.1039/D4MO90019G","url":null,"abstract":"<p >We would like to take this opportunity to thank all of <em>Molecular Omics’</em> reviewers for helping to preserve quality and integrity in chemical science literature. We would also particularly like to highlight the Outstanding Reviewers for <em>Molecular Omics</em> in 2023.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 504-504"},"PeriodicalIF":3.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133293","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":"Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G†","authors":"Philip J. Shaw, Parichat Prommana, Chawanee Thongpanchang, Sumalee Kamchonwongpaisan, Darin Kongkasuriyachai, Yan Wang, Zhihua Zhou and Yiqing Zhou","doi":"10.1039/D4MO00088A","DOIUrl":"10.1039/D4MO00088A","url":null,"abstract":"<p >The natural product 9-methoxystrobilurin G (9MG) from <em>Favolaschia</em> spp basidiomycetes is a potent and selective antimalarial. The mechanism of action of 9MG is unknown. We induced 9MG resistance in <em>Plasmodium falciparum</em> 3D7 and Dd2 strains and identified mutations associated with resistance by genome sequencing. All 9MG-resistant clones possessed missense mutations in the cytochrome b (CYTB) gene, a key component of mitochondrial complex III. The mutations map to the quinol oxidation site of CYTB, which is also the target of antimalarials such as atovaquone. In a complementary approach to identify protein targets of 9MG, a photoactivatable derivative of 9MG was synthesized and applied in chemoproteomic-based target profiling. Three components of mitochondrial complex III (QCR7, QCR9, and COX15) were specifically enriched consistent with 9MG targeting CYTB and complex III function in <em>P. falciparum</em>. Inhibition of complex III activity by 9MG was confirmed by ubiquinone cytochrome <em>c</em> reductase assay using <em>P. falciparum</em> extract. The findings from this study may be useful for developing novel antimalarials targeting CYTB.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 584-594"},"PeriodicalIF":3.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183150","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":"Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 – insights into a yet unknown micro-ecosystem†","authors":"Mayurakshi Nag, Janardhan Pallavi, Sandipan Chakraborty, Trina Roychoudhury, Sangita Mondal, Abhrajyoti Ghosh, Chinmay Saha, Manidipa Banerjee and Anindita Seal","doi":"10.1039/D3MO00273J","DOIUrl":"10.1039/D3MO00273J","url":null,"abstract":"<p > <em>Rhodotorula mucilaginosa</em> JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely <em>Stutzerimonas</em> (<em>Pseudomonas</em>) <em>stutzeri</em> and <em>Bradyrhizobium</em> sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form <em>viz. Bacillus velezensis</em> and <em>Staphylococcus</em> sp. under nitrogen-replete conditions and <em>Lysinibacillus telephonicus.</em>, <em>Brevibacillus</em> sp., and <em>Niallia circulans</em> under nitrogen-depleted conditions. <em>S. stutzeri</em> and <em>Bradyrhizobium</em> sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts <em>Staphylococcus</em> sp. and <em>Bacillus velezensis</em> appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of <em>S. stutzeri</em> and <em>B. velezensis</em> increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 630-641"},"PeriodicalIF":3.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183151","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 of peripheral blood mononuclear cells from OSCC patients reveals potential immune checkpoints to enable personalized treatment†","authors":"Anjana Aravind, Rohan Thomas Mathew, Lepakshi Kuruba, Manavalan Vijayakumar and Thottethodi Subrahmanya Keshava Prasad","doi":"10.1039/D4MO00112E","DOIUrl":"10.1039/D4MO00112E","url":null,"abstract":"<p >Oral squamous cell carcinoma (OSCC) is one of the most prevalent cancers worldwide, with high mortality and prevalence rates. OSCC is defined as an immunogenic tumor with the potential to be recognized and targeted by the immune system. It is characterized by the extensive infiltration of immune cells and plays a vital role in tumorigenesis. Peripheral blood mononuclear cells (PBMC) are a functional subset of immune cells readily accessible through minimally invasive procedures. The molecular characterization of immune cells aids in understanding their functional roles in various pathophysiological conditions. Proteomic analysis of PBMCs from cancer patients provides insight into the mechanism of immunoregulation and the role of immune cells in impeding tumor development and progression. Therefore, the present study investigated the immune cell proteome of a cancer control cohort within OSCC, leveraging data-independent acquisition analysis by mass spectrometry (DIA-MS). Among the differentially abundant proteins in OSCC, we identified promising molecular targets, including LMNB1, CTSB, CD14, CD177, and SPI1. Further exploration of the signaling pathways related to the candidate molecules demonstrated their involvement in cancer immunomodulation. Therefore, this study can serve as a platform for identifying new candidate proteins to further investigate their potential as immunotherapeutic targets and prognostic markers.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 532-545"},"PeriodicalIF":3.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036374","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":"Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species†","authors":"Freddy Castillo-Alfonso, Cecilio Valadez-Cano, Gabriela Cejas-Añón, José Utrilla, Juan-Carlos Sigala Alanis, Sylvie Le Borgne, Alfonso Mauricio Sales-Cruz, Gabriel Vigueras-Ramírez and Roberto Olivares-Hernández","doi":"10.1039/D4MO00108G","DOIUrl":"10.1039/D4MO00108G","url":null,"abstract":"<p >The basidiomycete fungus <em>Leucoagaricus gongylophorus</em> is able to grow in the fungus garden of leaf-cutter ants. This mutualistic interaction has driven the evolutionary adaptation of <em>L. gongylophorus</em>, shaping its metabolism to produce enzymes adept at lignocellulosic biomass degradation. In this study, we undertook the comprehensive sequencing, assembly, and functional annotation of the genome of <em>L. gongylophorus</em> strain LEU18496, mutualistic fungus of the <em>Atta mexicana</em>. Our genomic analyses revealed a distinctive bimodal nature to the genome: a predominant region characterized by AT enrichment and low genetic density, alongside a smaller region exhibiting higher GC content and higher genetic density. The presence of transposable elements (TEs) within the AT-enriched region suggests genomic compartmentalization, facilitating differential evolutionary rates. With a gene count of 6748, the assembled genome of <em>L. gongylophorus</em> LEU18496 surpasses previous reports for this fungal species. Inspection of genes associated with central metabolism unveiled a remarkable abundance of carbohydrate-active enzymes (CAZymes) and fungal oxidative lignin enzymes (FOLymes), underscoring their pivotal roles in the life cycle of this fungus.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 524-531"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004865","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":"YAP activation is robust to dilution†","authors":"Ian Jones, Mar Arias-Garcia, Patricia Pascual-Vargas, Melina Beykou, Lucas Dent, Tara Pal Chaudhuri, Theodoros Roumeliotis, Jyoti Choudhary, Julia Sero and Chris Bakal","doi":"10.1039/D4MO00100A","DOIUrl":"10.1039/D4MO00100A","url":null,"abstract":"<p >The concentration of many transcription factors exhibits high cell-to-cell variability due to differences in synthesis, degradation, and cell size. Whether the functions of these factors are robust to fluctuations in concentration, and how this may be achieved, is poorly understood. Across two independent panels of breast cancer cells, we show that the average whole cell concentration of YAP decreases as a function of cell area. However, the nuclear concentration distribution remains constant across cells grouped by size, across a 4–8 fold size range, implying unperturbed nuclear translocation despite the falling cell wide concentration. Both the whole cell and nuclear concentration was higher in cells with more DNA and CycA/PCNA expression suggesting periodic synthesis of YAP across the cell cycle offsets dilution due to cell growth and/or cell spreading. The cell area – YAP scaling relationship extended to melanoma and RPE cells. Integrative analysis of imaging and phospho-proteomic data showed the average nuclear YAP concentration across cell lines was predicted by differences in RAS/MAPK signalling, focal adhesion maturation, and nuclear transport processes. Validating the idea that RAS/MAPK and cell cycle regulate YAP translocation, chemical inhibition of MEK or CDK4/6 increased the average nuclear YAP concentration. Together, this study provides an example case, where cytoplasmic dilution of a protein, for example through cell growth, does not limit a cognate cellular function. Here, that same proteins translocation into the nucleus.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 554-569"},"PeriodicalIF":3.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/mo/d4mo00100a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183152","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":"Extraction and untargeted analysis of metabolome from undemineralised cortical bone matrix†","authors":"Andrea Bonicelli, George Taylor and Noemi Procopio","doi":"10.1039/D4MO00015C","DOIUrl":"10.1039/D4MO00015C","url":null,"abstract":"<p >Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) untargeted metabolomics has become the gold standard for the profiling of low-molecular-weight compounds. Recently, this discipline has raised great interest in forensic sciences, especially in the field of toxicology and for <em>post-mortem</em> interval estimation. The current study aims at evaluating three extraction protocols and two LC-MS/MS assays run in both positive and negative modes, to identify the most suitable method to conduct <em>post-mortem</em> metabolomic profiling of bone tissue. A fragment of the anterior tibia of a 82 years-old male sampled from a human taphonomy facility was powdered <em>via</em> freeze-milling. The powdered sub-samples were extracted in five replicates per protocol. Methods tested were (I) a biphasic chloroform–methanol–water protocol, (II) a single phase methanol–water protocol, and (III) a single phase methanol–acetonitrile–water protocol. LC-MS/MS analyses were carried out <em>via</em> high performance liquid chromatography, either on hydrophilic interaction (HILIC) or on reversed-phase (C18) columns in both positive and negative ionisation modes, coupled with a Q-TOF mass spectrometer. Results suggest that the highest consistency between replicates and quality control samples was obtained with the single phase extractions (<em>i.e.</em>, methanol–acetonitrile–water), whilst the ideal combination of instrumental set up HILIC chromatography in positive ionisation mode and of C18 chromatography in negative ionisation mode. For the purpose of forensic investigations, a combination of a single phase extraction and the two aforementioned chromatographic and mass spectrometry modes could represent an ideal set up for obtaining bone metabolomic profiles from taphonomically altered bones.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 517-523"},"PeriodicalIF":3.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/mo/d4mo00015c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141737538","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}