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Carlo MJ, Nanney ALM, Patrick AL. Energy-Resolved In-Source Collison-Induced Dissociation for Isomer Discrimination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39016059 DOI: 10.1021/jasms.4c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
While mass spectrometry remains a gold-standard tool for analyte detection, characterization, and quantitation, isomer differentiation is often a challenge. Tandem mass spectrometry is a common approach to increase the selectivity of mass spectrometry and energy-resolved measurements can provide further improvements. However, not all mass spectrometers, especially those that are very compact and affordable, are amenable to such experiments. For instance, single-stage mass spectrometers with soft ionization provide no dissociation information and quadrupole ion trap instruments with resonant excitation do not necessarily provide as informative of energy-resolved curves, for instance when extensive sequential dissociation is responsible for much of the "fingerprint". In-source collision-induced dissociation (IS-CID) is one approach to overcoming these barriers to exploit the analytical selectivity of energy-resolved CID without the need for additional instrumentation; this approach could broaden the reach of these selectivity gains to additional user bases (e.g., educational settings, field portable devices). Here, we specifically investigate energy-resolved IS-CID with the goal of (1) comparing between energy-resolved appearance curves measured with true tandem mass spectrometry on a quadrupole time-of-flight instrument and those obtained using IS-CID, (2) evaluating the approach as a means of differentiating isomers/isobar sets, especially those with similar dissociation patterns, and (3) exploring additional analytical considerations relevant to method development and implementation. This proof-of-concept work establishes the analytical potential of this approach, opening doors for future method development for specific applications.
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Affiliation(s)
- Matthew J Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Andie L M Nanney
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Amanda L Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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Li F, Zhang J, Li K, Peng Y, Zhang H, Xu Y, Yu Y, Zhang Y, Liu Z, Wang Y, Huang L, Zhou F. GANSamples-ac4C: Enhancing ac4C site prediction via generative adversarial networks and transfer learning. Anal Biochem 2024; 689:115495. [PMID: 38431142 DOI: 10.1016/j.ab.2024.115495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model. This study introduces GANSamples-ac4C, a novel framework that synergizes transfer learning and generative adversarial network (GAN) to generate synthetic RNA sequences to train a better ac4C modification site prediction model. Comparative analysis reveals that GANSamples-ac4C outperforms existing state-of-the-art methods in identifying ac4C sites. Moreover, our result underscores the potential of synthetic data in mitigating the issue of data scarcity for biological sequence prediction tasks. Another major advantage of GANSamples-ac4C is its interpretable decision logic. Multi-faceted interpretability analyses detect key regions in the ac4C sequences influencing the discriminating decision between positive and negative samples, a pronounced enrichment of G in this region, and ac4C-associated motifs. These findings may offer novel insights for ac4C research. The GANSamples-ac4C framework and its source code are publicly accessible at http://www.healthinformaticslab.org/supp/.
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Affiliation(s)
- Fei Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Jiale Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Kewei Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China.
| | - Yu Peng
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Haotian Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yiping Xu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Yue Yu
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yuteng Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Zewen Liu
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Ying Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, China.
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Yang J, Chen R, Wang C, Li C, Ye W, Zhang Z, Wang S. A widely targeted metabolite modificomics strategy for modified metabolites identification in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:810-823. [PMID: 38375781 DOI: 10.1111/jipb.13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
The structural and functional diversity of plant metabolites is largely created via chemical modification of a basic backbone. However, metabolite modifications in plants have still not been thoroughly investigated by metabolomics approaches. In this study, a widely targeted metabolite modificomics (WTMM) strategy was developed based on ultra-high performance liquid chromatography-quadrupole-linear ion trap (UHPLC-Q-Trap) and UHPLC-Q-Exactive-Orbitrap (UHPLC-QE-Orbitrap), which greatly improved the detection sensitivity and the efficiency of identification of modified metabolites. A metabolite modificomics study was carried out using tomato as a model, and over 34,000 signals with MS2 information were obtained from approximately 232 neutral loss transitions. Unbiased metabolite profiling was also performed by utilizing high-resolution mass spectrometry data to annotate a total of 2,118 metabolites with 125 modification types; of these, 165 modified metabolites were identified in this study. Next, the WTMM database was used to assess diseased tomato tissues and 29 biomarkers were analyzed. In summary, the WTMM strategy is not only capable of large-scale detection and quantitative analysis of plant-modified metabolites in plants, but also can be used for plant biomarker development.
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Affiliation(s)
- Jun Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Ridong Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Chao Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Chun Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Weizhen Ye
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Zhonghui Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Shouchuang Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
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Zhang H, Lu R, Huang J, Li L, Cao Y, Huang C, Chen R, Wang Y, Huang J, Zhao X, Yu J. N4-acetylcytidine modifies primary microRNAs for processing in cancer cells. Cell Mol Life Sci 2024; 81:73. [PMID: 38308713 PMCID: PMC10838262 DOI: 10.1007/s00018-023-05107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
N4 acetylcytidine (ac4C) modification mainly occurs on tRNA, rRNA, and mRNA, playing an important role in the expression of genetic information. However, it is still unclear whether microRNAs have undergone ac4C modification and their potential physiological and pathological functions. In this study, we identified that NAT10/THUMPD1 acetylates primary microRNAs (pri-miRNAs) with ac4C modification. Knockdown of NAT10 suppresses and augments the expression levels of mature miRNAs and pri-miRNAs, respectively. Molecular mechanism studies found that pri-miRNA ac4C promotes the processing of pri-miRNA into precursor miRNA (pre-miRNA) by enhancing the interaction of pri-miRNA and DGCR8, thereby increasing the biogenesis of mature miRNA. Knockdown of NAT10 attenuates the oncogenic characters of lung cancer cells by regulating miRNA production in cancers. Moreover, NAT10 is highly expressed in various clinical cancers and negatively correlated with poor prognosis. Thus, our results reveal that NAT10 plays a crucial role in cancer initiation and progression by modulating pri-miRNA ac4C to affect miRNA production, which would provide an attractive therapeutic strategy for cancers.
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Affiliation(s)
- Hailong Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Runhui Lu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiayi Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lian Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingting Cao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Caihu Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ran Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanli Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Sijko-Szpańska M, Kozłowska L. Analysis of Relationships between Metabolic Changes and Selected Nutrient Intake in Women Environmentally Exposed to Arsenic. Metabolites 2024; 14:75. [PMID: 38276310 PMCID: PMC10820439 DOI: 10.3390/metabo14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/17/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
Nutrients involved in the metabolism of inorganic arsenic (iAs) may play a crucial role in mitigating the adverse health effects associated with such exposure. Consequently, the objective of this study was to analyze the association between the intake levels of nutrients involved in iAs metabolism and alterations in the metabolic profile during arsenic exposure. The study cohort comprised environmentally exposed women: WL (lower total urinary arsenic (As), n = 73) and WH (higher As, n = 73). The analysis included urinary untargeted metabolomics (conducted via liquid chromatography-mass spectrometry) and the assessment of nutrient intake involved in iAs metabolism, specifically methionine, vitamins B2, B6, and B12, folate, and zinc (based on 3-day dietary records of food and beverages). In the WL group, the intake of all analyzed nutrients exhibited a negative correlation with 5 metabolites (argininosuccinic acid, 5-hydroxy-L-tryptophan, 11-trans-LTE4, mevalonic acid, aminoadipic acid), while in the WH group, it correlated with 10 metabolites (5-hydroxy-L-tryptophan, dihyroxy-1H-indole glucuronide I, 11-trans-LTE4, isovalerylglucuronide, 18-oxocortisol, 3-hydroxydecanedioic acid, S-3-oxodecanoyl cysteamine, L-arginine, p-cresol glucuronide, thromboxane B2). Furthermore, nutrient intake demonstrated a positive association with 3 metabolites in the WL group (inosine, deoxyuridine, glutamine) and the WH group (inosine, N-acetyl-L-aspartic acid, tetrahydrodeoxycorticosterone). Altering the intake of nutrients involved in iAs metabolism could be a pivotal factor in reducing the negative impact of arsenic exposure on the human body. This study underscores the significance of maintaining adequate nutrient intake, particularly in populations exposed to arsenic.
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Affiliation(s)
- Monika Sijko-Szpańska
- Laboratory of Human Metabolism Research, Department of Dietetics, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, 02776 Warsaw, Poland
| | - Lucyna Kozłowska
- Laboratory of Human Metabolism Research, Department of Dietetics, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, 02776 Warsaw, Poland
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Visintin L, García Nicolás M, Vangeenderhuysen P, Goessens T, Alladio E, Pomian B, Vanhaecke L, De Saeger S, De Boevre M. Unraveling biomarkers of exposure for tenuazonic acid through urinary metabolomics. Food Chem Toxicol 2023; 182:114183. [PMID: 37951345 PMCID: PMC10733712 DOI: 10.1016/j.fct.2023.114183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Abstract
Mycotoxins are secondary metabolites produced by fungi such as Aspergillus, Alternaria, and Penicillium, affecting nearly 80% of global food crops. Tenuazonic acid (TeA) is the major mycotoxin produced by Alternaria alternata, a prevalent pathogen affecting plants, fruits, and vegetables. TeA is notably prevalent in European diets, however, TeA biomarkers of exposure and metabolites remain unknown. This research aims to bridge this knowledge-gap by gaining insights about human TeA exposure and metabolization. Nine subjects were divided into two groups. The first group received a single bolus of TeA at the Threshold of Toxicological Concern (TTC) to investigate the presence of TeA urinary biomarkers, while the second group served as a control. Sixty-nine urinary samples were prepared and analyzed using UPLC-Xevo TQ-XS for TeA quantification and UPLC-Orbitrap Exploris for polar metabolome acquisition. TeA was rapidly excreted during the first 13 h and the fraction extracted was 0.39 ± 0.22. The polar metabolome compounds effectively discriminating the two groups were filtered using Orthogonal Partial Least Squares-Discriminant Analysis and subsequently annotated (n = 122) at confidence level 4. Finally, the urinary metabolome was compared to in silico predicted TeA metabolites. Nine metabolites, including oxidized, N-alkylated, desaturated, glucuronidated, and sulfonated forms of TeA were detected.
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Affiliation(s)
- Lia Visintin
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, B-9000, Ghent, Belgium.
| | - María García Nicolás
- Department of Analytical Chemistry, Faculty of Chemistry, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, E-30100, Murcia, Spain
| | - Pablo Vangeenderhuysen
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, B-9820, Merelbeke, Belgium
| | - Tess Goessens
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, B-9000, Ghent, Belgium
| | - Eugenio Alladio
- Regional Anti-doping and Toxicological Centre, 10043, Orbassano, Italy; Department of Chemistry, University of Torino, 10125, Torino, Italy
| | - Beata Pomian
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, B-9820, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, B-9820, Merelbeke, Belgium; Institute for Global Food Security, School of Biological Sciences, Queen's University, BT9 5DL, Belfast, United Kingdom
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, B-9000, Ghent, Belgium; Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng, South Africa
| | - Marthe De Boevre
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, B-9000, Ghent, Belgium.
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Karolkowski A, Meudec E, Bruguière A, Mitaine-Offer AC, Bouzidi E, Levavasseur L, Sommerer N, Briand L, Salles C. Faba Bean ( Vicia faba L. minor) Bitterness: An Untargeted Metabolomic Approach to Highlight the Impact of the Non-Volatile Fraction. Metabolites 2023; 13:964. [PMID: 37623907 PMCID: PMC10456379 DOI: 10.3390/metabo13080964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
In the context of climate change, faba beans are an interesting alternative to animal proteins but are characterised by off-notes and bitterness that decrease consumer acceptability. However, research on pulse bitterness is often limited to soybeans and peas. This study aimed to highlight potential bitter non-volatile compounds in faba beans. First, the bitterness of flours and air-classified fractions (starch and protein) of three faba bean cultivars was evaluated by a trained panel. The fractions from the high-alkaloid cultivars and the protein fractions exhibited higher bitter intensity. Second, an untargeted metabolomic approach using ultra-high-performance liquid chromatography-diode array detector-tandem-high resolution mass spectrometry (UHPLC-DAD-HRMS) was correlated with the bitter perception of the fractions. Third, 42 tentatively identified non-volatile compounds were associated with faba bean bitterness by correlated sensory and metabolomic data. These compounds mainly belonged to different chemical classes such as alkaloids, amino acids, phenolic compounds, organic acids, and terpenoids. This research provided a better understanding of the molecules responsible for bitterness in faba beans and the impact of cultivar and air-classification on the bitter content. The bitter character of these highlighted compounds needs to be confirmed by sensory and/or cellular analyses to identify removal or masking strategies.
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Affiliation(s)
- Adeline Karolkowski
- Centre des Sciences du Goût et de L’Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France; (A.K.); (A.B.); (A.-C.M.-O.)
- Groupe Soufflet-Invivo, F-10400 Nogent-sur-Seine, France;
| | - Emmanuelle Meudec
- SPO, Université de Montpellier, INRAE, Institut Agro, F-34000 Montpellier, France; (E.M.); (N.S.)
- INRAE, PROBE Research Infrastructure, PFP Polyphenol Analysis Facility, F-34060 Montpellier, France
| | - Antoine Bruguière
- Centre des Sciences du Goût et de L’Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France; (A.K.); (A.B.); (A.-C.M.-O.)
| | - Anne-Claire Mitaine-Offer
- Centre des Sciences du Goût et de L’Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France; (A.K.); (A.B.); (A.-C.M.-O.)
| | - Emilie Bouzidi
- Vivien Paille (Groupe Avril), F-59300 Valenciennes, France;
| | | | - Nicolas Sommerer
- SPO, Université de Montpellier, INRAE, Institut Agro, F-34000 Montpellier, France; (E.M.); (N.S.)
- INRAE, PROBE Research Infrastructure, PFP Polyphenol Analysis Facility, F-34060 Montpellier, France
| | - Loïc Briand
- Centre des Sciences du Goût et de L’Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France; (A.K.); (A.B.); (A.-C.M.-O.)
| | - Christian Salles
- Centre des Sciences du Goût et de L’Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France; (A.K.); (A.B.); (A.-C.M.-O.)
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Zhang W, Gao J, Fan L, Wang J, He B, Wang Y, Zhang X, Mao H. ac4C acetylation regulates mRNA stability and translation efficiency in osteosarcoma. Heliyon 2023; 9:e17103. [PMID: 37484432 PMCID: PMC10361233 DOI: 10.1016/j.heliyon.2023.e17103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
Objective N4-acetylcytidine (ac4C) acetylation can promote target gene expression through improved mRNA stability. To explore the role of ac4C acetylation in osteosarcoma, U2OS and MG63 cell lines were treated with the N-acetyltransferase 10 (NAT10) inhibitor Remodelin. Reverse transcription-polymerase chain reaction (RT-PCR) and Western blot were used to test the gene and protein expression efficiency. Methods The proliferation rate of osteosarcoma cells was measured by a cell counting kit-8 (CCK8) assay. The cell cycle and apoptosis were analyzed by flow cytometry. The invasiveness of osteosarcoma cells was detected by a transwell invasion assay. The ac4C acetylation of target genes was screened by acetylated RNA immunoprecipitation and sequencing (acRIP-seq). Results We found that when osteosarcoma cells were treated with Remodelin at the optimal concentration, their NAT10 expression and the cell proliferation was inhibited, the cells in the G1 phase increased (P < 0.05) but those in the S phase decreased, the apoptotic cells in the early and late stages increased, and the cells invasiveness decreased (P < 0.05). Conclusions The farnesyltransferase subunit beta gene (FNTB) was identified by acRIP-seq as one of the target genes of ac4C acetylation and was further verified by RT-PCR and Western blot analyses. Remodelin was demonstrated to reduce the stability and protein translation efficiency of target gene mRNA in osteosarcoma cells. In conclusion, inhibition of ac4C acetylation in osteosarcoma can block proliferation and metastasis as well as promote apoptosis and cell cycle arrest. Ac4C acetylation contributes to the stability and protein translation efficiency of the downstream target gene mRNA.
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Affiliation(s)
- Wenjie Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | - Jia Gao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | - Lei Fan
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | - Juan Wang
- Department of Ultrasonic Diagnosis, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | - Bin He
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | - Yunhua Wang
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, PR China
| | | | - Hui Mao
- Nanjing Medical University, Nanjing, 211166, PR China
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Zhang M, Yang K, Wang QH, Xie L, Liu Q, Wei R, Tao Y, Zheng HL, Lin N, Xu H, Yang L, Wang H, Zhang T, Xue Z, Cao JL, Pan Z. The Cytidine N-Acetyltransferase NAT10 Participates in Peripheral Nerve Injury-Induced Neuropathic Pain by Stabilizing SYT9 Expression in Primary Sensory Neurons. J Neurosci 2023; 43:3009-3027. [PMID: 36898834 PMCID: PMC10146489 DOI: 10.1523/jneurosci.2321-22.2023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
RNA N4-acetylcytidine (ac4C) modification is increasingly recognized as an important layer of gene regulation; however, the involvement of ac4C in pain regulation has not been studied. Here, we report that N-acetyltransferase 10 protein (NAT10; the only known ac4C "writer") contributes to the induction and development of neuropathic pain in an ac4C-dependent manner. Peripheral nerve injury increases the levels of NAT10 expression and overall ac4C in injured dorsal root ganglia (DRGs). This upregulation is triggered by the activation of upstream transcription factor 1 (USF1), a transcription factor that binds to the Nat10 promoter. Knock-down or genetic deletion of NAT10 in the DRG abolishes the gain of ac4C sites in Syt9 mRNA and the augmentation of SYT9 protein, resulting in a marked antinociceptive effect in nerve-injured male mice. Conversely, mimicking NAT10 upregulation in the absence of injury evokes the elevation of Syt9 ac4C and SYT9 protein and induces the genesis of neuropathic-pain-like behaviors. These findings demonstrate that USF1-governed NAT10 regulates neuropathic pain by targeting Syt9 ac4C in peripheral nociceptive sensory neurons. Our findings establish NAT10 as a critical endogenous initiator of nociceptive behavior and a promising new target for treating neuropathic pain.SIGNIFICANCE STATEMENT The cytidine N4-acetylcytidine (ac4C), a new epigenetic RNA modification, is crucial for the translation and stability of mRNA, but its role for chronic pain remains unclear. Here, we demonstrate that N-acetyltransferase 10 (NAT10) acts as ac4C N-acetyltransferase and plays an important role in the development and maintenance of neuropathic pain. NAT10 was upregulated via the activation of the transcription factor upstream transcription factor 1 (USF1) in the injured dorsal root ganglion (DRG) after peripheral nerve injury. Since pharmacological or genetic deleting NAT10 in the DRG attenuated the nerve injury-induced nociceptive hypersensitivities partially through suppressing Syt9 mRNA ac4C and stabilizing SYT9 protein level, NAT10 may serve as an effective and novel therapeutic target for neuropathic pain.
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Affiliation(s)
- Ming Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Kehui Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Qi-Hui Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Ling Xie
- Department of Anesthesiology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Qiaoqiao Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Runa Wei
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Yang Tao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Hong-Li Zheng
- Department of Pain, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Ninghua Lin
- Department of Anesthesiology, Yantai affiliated Hospital of Binzhou Medical University, Yantai 264000, China
| | - Hengjun Xu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Li Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Hongjun Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Tingruo Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Zhouya Xue
- Department of Anesthesiology, Yancheng affiliated Hospital of Xuzhou Medical University, Yancheng 224008, China
| | - Jun-Li Cao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
| | - Zhiqiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou 221004, China
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10
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Zhang X, Zeng J, Wang J, Yang Z, Gao S, Liu H, Li G, Zhang X, Gu Y, Pang D. Revealing the Potential Markers of N(4)-Acetylcytidine through acRIP-seq in Triple-Negative Breast Cancer. Genes (Basel) 2022; 13:genes13122400. [PMID: 36553667 PMCID: PMC9777589 DOI: 10.3390/genes13122400] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding the causes of tumorigenesis and progression in triple-receptor negative breast cancer (TNBC) can help the design of novel and personalized therapies and prognostic assessments. Abnormal RNA modification is a recently discovered process in TNBC development. TNBC samples from The Cancer Genome Atlas database were categorized according to the expression level of NAT10, which drives acetylation of cytidine in RNA to N(4)-acetylcytidine (ac4C) and affects mRNA stability. A total of 703 differentially expressed long non-coding RNAs (lncRNAs) were found between high- and low-expressed NAT10 groups in TNBC. Twenty of these lncRNAs were significantly associated with prognosis. Two breast cancer tissues and their paired normal tissues were sequenced at the whole genome level using acetylated RNA immunoprecipitation sequencing (acRIP-seq) technology to identify acetylation features in TNBC, and 180 genes were significantly differentially ac4c acetylated in patients. We also analyzed the genome-wide lncRNA expression profile and constructed a co-expression network, containing 116 ac4C genes and 1080 lncRNAs. Three of these lncRNAs were prognostic risk lncRNAs affected by NAT10 and contained in the network. The corresponding reciprocal pairs were "LINC01614-COL3A1", "OIP5-AS1-USP8", and "RP5-908M14.9-TRIR". These results indicate that RNA ac4c acetylation involves lncRNAs and affects the tumor process and prognosis of TNBC. This will aid the prediction of drug targets and drug sensitivity.
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Affiliation(s)
- Xingda Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Jiaqi Zeng
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Jianyu Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Zihan Yang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Song Gao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Honghao Liu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Guozheng Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Xin Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
| | - Yue Gu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
- Correspondence: (Y.G.); (D.P.)
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital,150 Haping Road, Harbin 150081, China
- Correspondence: (Y.G.); (D.P.)
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11
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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12
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Liu X, Zhang J, Li Y, Yao C, An Y, Wei W, Yao S, Yang L, Huang Y, Qu H, Guo DA. In-depth profiling, nontargeted metabolomic and selective ion monitoring of eight chemical markers for simultaneous identification of different part of Eucommia ulmoides in 12 commercial products by UPLC/QDa. Food Chem 2022; 393:133346. [DOI: 10.1016/j.foodchem.2022.133346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/04/2022]
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13
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Liang JK, Lu Y, Song ZM, Ye B, Wu QY, Hu HY. Effects of chlorine dose on the composition and characteristics of chlorinated disinfection byproducts in reclaimed water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153739. [PMID: 35149072 DOI: 10.1016/j.scitotenv.2022.153739] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
During chlorination of reclaimed water, the dose of chlorine used can influence the formation of chlorinated disinfection by-products (Cl-DBPs). We used non-targeted screening by Orbitrap mass spectrometry to identify Cl-DBPs in samples of chlorinated reclaimed water, and found that chlorination was likely to form slightly oxidized unsaturated aliphatic compounds and polycyclic aromatic compounds. Increasing the chlorine dose increased the proportion of polycyclic aromatic Cl-DBPs containing one chlorine atom (Cl1-DBPs) and highly oxidized unsaturated aliphatic Cl-DBPs containing two chlorine atoms (Cl2-DBPs). In addition, increasing the chlorine dose first decreased and then increased the proportion of Cl1-DBPs with aromatic index values >0.5 and increased the proportion of Cl2-DBPs with aromatic index values <0.5. Increasing the chlorine dose increased double bond equivalent minus oxygen values of Cl1-DBPs and decreased the double bond equivalent minus oxygen values of Cl2-DBPs, while the nominal oxidant state of carbon decreased for Cl1-DBPs and increased for Cl2-DBPs. In considering the possible precursors of Cl-DBPs and their reaction pathways, substitution reactions occurred more readily with aliphatic compounds and addition reactions occurred more readily with aromatic precursors. When the chlorine dose is increased, more Cl2-DBPs may be formed by substitution. Overall, the chlorine dose influences Cl-DBP formation and composition and should be taken into account during water treatment.
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Affiliation(s)
- Jun-Kun Liang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Institute of Environment and Ecology, Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Yao Lu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Institute of Environment and Ecology, Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhi-Min Song
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Institute of Environment and Ecology, Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Bei Ye
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Institute of Environment and Ecology, Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Qian-Yuan Wu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Institute of Environment and Ecology, Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Environmental Simulation and Pollution Control State Key Joint Laboratory, Beijing Laboratory for Environmental Frontier Technologies, School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Hong-Ying Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, Beijing Laboratory for Environmental Frontier Technologies, School of Environment, Tsinghua University, Beijing 100084, PR China.
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Zhang C, Liu M, Xu X, Wu J, Li X, Wang H, Gao X, Guo D, Tian X, Yang W. Application of Large-Scale Molecular Prediction for Creating the Preferred Precursor Ions List to Enhance the Identification of Ginsenosides from the Flower Buds of Panax ginseng. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5932-5944. [PMID: 35503923 DOI: 10.1021/acs.jafc.2c01435] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This work was designed to evaluate the coverage of data-dependent acquisition (DDA) extensively utilized in the untargeted metabolite/component identification in the food sciences and pharmaceutical analysis. Using saponins from the flower buds of Panax ginseng (PGF) as an example, precursor ions list (PIL)-including DDA on a Q-Orbitrap mass spectrometer could enable higher coverage than the other four MS2 acquisition approaches in characterizing PGF ginsenosides. A "Virtual Library of Ginsenoside" containing 13,536 ginsenoside molecules was established by C-language-programmed large-scale molecular prediction, which in combination with mass defect filtering could create a new PIL involving 1859 PGF saponin precursors. We could newly obtain the MS2 spectra of at least 17 components and characterize 36 ginsenosides with unknown masses, among the 164 compounds identified from PGF. Conclusively, a molecular-prediction-oriented PIL in DDA can assist to discover more potentially novel molecules benefiting to the development of functional foods and new drugs.
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Affiliation(s)
- Chunxia Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Meiyu Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Xiaoyan Xu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Jia Wu
- Shanghai Standard Technology Co., Ltd., 58 Xinhao Road, Shanghai 201314, China
| | - Xue Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Hongda Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Xiumei Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Dean Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Wenzhi Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
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15
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Chen YC, Wu HY, Chang CW, Liao PC. Post-Deconvolution MS/MS Spectra Extraction with Data-Independent Acquisition for Comprehensive Profiling of Urinary Glucuronide-Conjugated Metabolome. Anal Chem 2022; 94:2740-2748. [PMID: 35119834 DOI: 10.1021/acs.analchem.1c03557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conjugation reactions are of critical significance in human metabolism. Identification of these conjugated metabolites is still challenging. Here, we propose a strategy, post-deconvolution MS/MS spectra extraction with data-independent acquisition (PDMS2E-DIA), to comprehensively profile the glucuronide-conjugated metabolome. PDMS2E-DIA enables the identification of conjugated and unconjugated metabolite pairs through neutral loss filtering combined with a significant change in abundance after the deconjugation reaction. Purified DIA MS/MS spectra were constructed by extracting MS/MS fragments shared between spectra derived from conjugated and unconjugated metabolites. The feasibility of this approach was first demonstrated by the identification of two glucuronide-conjugated metabolite standards spiked in urine samples. For human urine samples, 479 features were structurally annotated as potential glucuronide-conjugated metabolites, resulting in the identification of 211 metabolites. Fragment peaks derived from interferents were found to be removed by PDMS2E-DIA, which increased about 6 times the number of identified urine metabolites compared with those calculated from raw DIA deconvoluted MS/MS spectra. This approach was found to have great potential for identifying glucuronide-conjugated metabolites, as well as other kinds of chemical conjugations.
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Affiliation(s)
- Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei 106, Taiwan
| | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
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16
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Twins labeling derivatization-based LC-MS/MS strategy for absolute quantification of paired prototypes and modified metabolites. Anal Chim Acta 2022; 1193:339399. [DOI: 10.1016/j.aca.2021.339399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
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17
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Jensen RH, Rønn M, Thorsteinsson M, Olijhoek DW, Nielsen MO, Nørskov NP. Untargeted Metabolomics Combined with Solid Phase Fractionation for Systematic Characterization of Bioactive Compounds in Hemp with Methane Mitigation Potential. Metabolites 2022; 12:metabo12010077. [PMID: 35050199 PMCID: PMC8779194 DOI: 10.3390/metabo12010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
This study systematically evaluates the presence of methane mitigating metabolites in two hemp (Cannabis sativa L.) varieties, Futura 75 and Finola. Hemp metabolites were extracted with methanol and fractionated using Solid Phase Extraction (SPE). Extracts, fractions, and the remaining pulp were screened for their methane mitigating potential using an in vitro model of rumen fermentation. The bioactive metabolites were identified with Liquid Chromatography-Mass Spectrometry (LC-MS). When incubated with a standard feed (maize silage), the extract of Futura 75 significantly reduced methane production compared to that of control (without added extract) and without negative effects on feed degradability and volatile fatty acid patterns. The compounds responsible for the methane mitigating effect were assigned to flavonoid glycosides. However, none of the fractions of Futura 75 or the pulp exhibited similar effect on methane emission. Butyric acid concentration in the fermentation inoculum was significantly increased, which could indicate why methane production was higher, when incubated with the fractions and the pulp. The extract of Finola did not show a similar significant effect, however, there was a numerical tendency towards lower methane production. The difference in methane mitigating properties between Cannabis sativa L. Futura 75 and Finola, could be related to the content of bioactive flavonoids.
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NAT10 promotes cell proliferation by acetylating CEP170 mRNA to enhance translation efficiency in multiple myeloma. Acta Pharm Sin B 2022; 12:3313-3325. [PMID: 35967285 PMCID: PMC9366180 DOI: 10.1016/j.apsb.2022.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
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19
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Pan-cancer analysis of N4-acetylcytidine adaptor THUMPD1 as a predictor for prognosis and immunotherapy. Biosci Rep 2021; 41:230196. [PMID: 34762107 PMCID: PMC8655504 DOI: 10.1042/bsr20212300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background: THUMPD1 is a specific RNA adaptor that assists acetylation of mRNA and production of N4-acetylcytidine (ac4C). However, it remains unclear whether THUMPD1 plays a part in tumorigenesis and therapeutic efficacy. Here, we analyzed the expression profiles and prognostic value of THUMPD1 in pan-cancer and gained insights into the correlation between THUMPD1 expression level and immunotherapy efficacy. Methods: Gene expression pattern and its correlation with prognosis, immune cell infiltration in pan-cancer were obtained from Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA) databases, with Kaplan–Meier method and Spearman correlation analysis used. Western blotting and immunofluorescence on clinical samples were performed to validate our database-derived results. Correlation between THUMPD1 expression level and immunotherapy responses was also explored, based on clinical cohorts receiving programmed cell death protein 1 ligand (PD-L1) antibody therapy. Finally, gene set enrichment analysis (GSEA) was performed to show the possible tumorigenic mechanism. Results: THUMPD1 was highly expressed in most cancer types, and this elevated expression indicated poor or improved prognosis for different cancers. In kidney renal clear cell carcinoma (KIRC) and rectum adenocarcinoma (READ), patients with higher THUMPD1 expression exhibited a better prognosis, while liver hepatocellular carcinoma (LIHC) patients had worse prognosis. Besides, THUMPD1 was significantly associated with immune cell infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), immune checkpoints and neoantigen in many cancer types. Further, more clinical advantages and therapeutic responses were observed in patients with high THUMPD1 expression. Conclusions: THUMPD1 may serve as a novel predictor to evaluate cancer prognosis and immune therapy efficacy in diverse cancer types.
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Tian T, Zhou BW, Wu LH, Zhang F, Chou GX, Feng CG, Lin GQ. Non-targeted screening of pyranosides in Rhodiola crenulata using an all ion fragmentation-exact neutral loss strategy combined with liquid chromatography-quadrupole time-of-flight mass spectrometry. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:1039-1050. [PMID: 33779008 DOI: 10.1002/pca.3045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/08/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Pyranosides as one kind of natural glycosides contain a pyran ring linked to an aglycone in the structure. They occur widely in plants and possess diverse biological activities. The discovery of new pyranosides not only contributes to research on natural products but also may promote pharmaceutical development. OBJECTIVES A non-targeted liquid chromatography-quadrupole time-of-flight mass spectrometry method coupled with an all ion fragmentation-exact neutral loss (AIF-ENL) strategy was developed for the screening of pyranosides in plants. METHODS Pyranosides in various types were collected as a model. The AIF-ENL strategy comprised three steps: AIF spectrum acquisition and generation, ENL-based searching and identification, and confirmation of structural type using target second-stage mass spectrometry (MS/MS). The strategy was systematically evaluated based on the matrix effects, fragmentation stability, scan rate and screening efficiency and finally applied to Rhodiola crenulata (Hook. f. et Thoms) H. Ohba. RESULTS The method was proved to be an efficient tool for the screening of pyranosides. When it was applied to R. crenulata, a total of 24 pyranoside candidates were detected. Among them, six were tentatively identified on the basis of the agreement of their elemental composition with the reported. The other 18 were detected in R. crenulata for the first time. CONCLUSION The method offers a new platform for discovering pyranosides. In addition, the developed non-targeted strategy can also be used for other natural products, such as flavonoids and coumarins, as long as there is a common fragmentation behaviour in their MS/MS to generate characteristic neutral losses or fragments.
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Affiliation(s)
- Tian Tian
- The Research Centre of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bo-Wen Zhou
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Li-Hong Wu
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fang Zhang
- The Research Centre of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Gui-Xin Chou
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chen-Guo Feng
- The Research Centre of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Qiang Lin
- The Research Centre of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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21
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Zheng S, Zhang X, Li Z, Hoene M, Fritsche L, Zheng F, Li Q, Fritsche A, Peter A, Lehmann R, Zhao X, Xu G. Systematic, Modifying Group-Assisted Strategy Expanding Coverage of Metabolite Annotation in Liquid Chromatography-Mass Spectrometry-Based Nontargeted Metabolomics Studies. Anal Chem 2021; 93:10916-10924. [PMID: 34328315 DOI: 10.1021/acs.analchem.1c01715] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
From microbes to human beings, nontargeted metabolic profiling by liquid chromatography (LC)-mass spectrometry (MS) has been commonly used to investigate metabolic alterations. Still, a major challenge is the annotation of metabolites from thousands of detected features. The aim of our research was to go beyond coverage of metabolite annotation in common nontargeted metabolomics studies by an integrated multistep strategy applying data-dependent acquisition (DDA)-based ultrahigh-performance liquid chromatography (UHPLC)-high-resolution mass spectrometry (HRMS) analysis followed by comprehensive neutral loss matches for characteristic metabolite modifications and database searches in a successive manner. Using pooled human urine as a model sample for method establishment, we found 22% of the detected compounds having modifying structures. Major types of metabolite modifications in urine were glucuronidation (33%), sulfation (20%), and acetylation (6%). Among the 383 annotated metabolites, 100 were confirmed by standard compounds and 50 modified metabolites not present in common databases such as human metabolite database (HMDB) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were structurally elucidated. Practicability was tested by the investigation of urines from pregnant women diagnosed with gestational diabetes mellitus vs healthy controls. Overall, 83 differential metabolites were annotated and 67% of them were modified metabolites including five previously unreported compounds. To conclude, the systematic modifying group-assisted strategy can be taken as a useful tool to extend the number of annotated metabolites in biological and biomedical nontargeted studies.
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Affiliation(s)
- Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miriam Hoene
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany
| | - Louise Fritsche
- German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany.,Internal Medicine 4, University Hospital Tuebingen, Otfried-Mueller-Str. 10, Tuebingen 72076, Germany
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Andreas Fritsche
- German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany.,Internal Medicine 4, University Hospital Tuebingen, Otfried-Mueller-Str. 10, Tuebingen 72076, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany.,German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tuebingen, Hoppe-Seyler-Str. 3, Tuebingen 72076, Germany.,German Center for Diabetes Research (DZD), Tuebingen 72076, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum Muenchen at the University of Tuebingen, Tuebingen 72076, Germany
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Yang C, Wu T, Zhang J, Liu J, Zhao K, Sun W, Zhou X, Kong X, Shi J. Prognostic and Immunological Role of mRNA ac4C Regulator NAT10 in Pan-Cancer: New Territory for Cancer Research? Front Oncol 2021; 11:630417. [PMID: 34094911 PMCID: PMC8170476 DOI: 10.3389/fonc.2021.630417] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background NAT10 (also known as human N-acetyltransferase-like protein) is a critical gene that regulates N4-acetylcytidine formation in RNA, similar to the multiple regulators of N6-methyladenosine. However, the underlying functions and mechanisms of NAT10 in tumor progression and immunology are unclear. Methods In this study, we systematically analyzed the pan-cancer expression and correlations of NAT10, using databases including Oncomine, PrognoScan, GEPIA2, and Kaplan-Meier Plotter. The potential correlations of NAT10 with immune infiltration stages and gene marker sets were analyzed using the Tumor Immune Estimation Resource and GEPIA2. Results Compared with normal tissues, NAT10 showed higher expression in most cancers based on combined data from TCGA and GTEx. In different datasets, high NAT10 expression was significantly correlated with poor prognosis in adrenocortical carcinoma, head and neck squamous cell carcinoma, liver hepatocellular carcinoma, kidney renal papillary cell carcinoma, and pheochromocytoma and paraganglioma. Moreover, there were significant positive correlations between NAT10 expression and immune infiltrates, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, endothelial cells, and fibroblasts in LIHC. NAT10 expression showed strong correlations with diverse immune marker gene sets in LIHC. Conclusion NAT10 expression affects the prognosis of pan-cancer patients and is significantly correlated with tumor immune infiltration. Furthermore, it represents a potential target for cancer therapy.
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Affiliation(s)
- Chuanxi Yang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kun Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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23
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Feng K, Wang S, Han L, Qian Y, Li H, Li X, Jia L, Hu Y, Wang H, Liu M, Hu W, Guo D, Yang W. Configuration of the ion exchange chromatography, hydrophilic interaction chromatography, and reversed-phase chromatography as off-line three-dimensional chromatography coupled with high-resolution quadrupole-Orbitrap mass spectrometry for the multicomponent characterization of Uncaria sessilifructus. J Chromatogr A 2021; 1649:462237. [PMID: 34034106 DOI: 10.1016/j.chroma.2021.462237] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
Herbs represent complex chemical systems involving various primary and secondary metabolites that are featured by large spans of acid-base property, polarity, molecular mass, and content, etc., which thus poses great challenges to characterize the metabolites contained. Here, the combination of multiple-mechanism chromatography coupled with improved data-dependent-MS2 acquisition (DDA-MS2) is presented as a strategy to support the deep metabolites characterization. Targeting Uncaria sessilifructus, a reputable medicinal herb containing alkaloids and triterpenic acids (TAs) as the main pharmacologically bioactive ingredients, a three-dimensional liquid chromatography (3D-LC) system was established by integrating ion exchange chromatography, hydrophilic interaction chromatography, and reversed-phase chromatography (IEC-HILIC-RPC). The first-dimensional chromatography, configuring a PhenoSphere SCX column eluted by methanol/20 mM ammonium acetate-0.05% formic acid in water, could well fractionate the total extract into two fractions (unretained ingredients and alkaloids). The subsequent HILIC using an XAmide column and RPC by a CSH Phenyl-Hexyl column achieved the sufficient resolution of the total TAs and total alkaloids, respectively. A polarity-switching precursor ions list-including DDA approach by Q-Orbitrap-MS enabled the high-efficiency, coverage-enhanced identification of alkaloids and TAs. This 3D-LC/Q-Orbitrap-MS system was validated as precise (RSD < 5% for intra-day/inter-day precision), Up to 308 components were separated from U. sessilifructus, and 128 thereof (including 85 alkaloids, 29 TAs, and 14 others) were identified or tentatively characterized, exhibiting superiority over the conventional one-dimensional LC/MS. Conclusively, 3D-LC/MS in an off-line mode can facilitate the flexible configuration of multiple chromatography to accomplish the fit-for-purpose characterization of the metabolites from an herbal extract or a biosample.
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Affiliation(s)
- Keyu Feng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Simiao Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Lifeng Han
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Yuexin Qian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Huifang Li
- Thermo Fisher Scientific, Building #6, No.27, Xinjinqiao Road, Pudong, Shanghai 201206, China
| | - Xue Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Li Jia
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Ying Hu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Huimin Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Meiyu Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Wandi Hu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China
| | - Dean Guo
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China.
| | - Wenzhi Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China.
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24
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Lu Y, Song ZM, Wang C, Liang JK, Xu N, Hu Q, Wu QY. Combination of high resolution mass spectrometry and a halogen extraction code to identify chlorinated disinfection byproducts formed from aromatic amino acids. WATER RESEARCH 2021; 190:116710. [PMID: 33285452 DOI: 10.1016/j.watres.2020.116710] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/04/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Chlorination can lead to the formation of hazardous chlorinated disinfection byproducts (Cl-DBPs). We identified tyrosine (Tyr) and tryptophan (Trp) as precursors of toxic Cl-DBPs and developed a halogen extraction code to complement ultra performance liquid chromatography in tandem with high resolution mass spectrometry (UPLC-HRMS) in detecting and identifying Cl-DBPs. We detected 20 and 11 Cl-DBPs formed from chlorination of Tyr and Trp, respectively, and identified the structures of 15 Cl-DBPs. Fourteen structures were previously unreported. We also proposed the tentative formation pathways of these newly identified Cl-DBPs. Their incidence in real water sources demonstrated that these Cl-DBPs are likely to form during chlorination of reclaimed water. We computationally predicted the toxicity of these Cl-DBPs, which was relatively high, indicating that these Cl-DBPs could be hazardous and were of valid concern. Combining analytical data with the halogen extraction code can identify Cl-DBPs accurately from complex compounds. This analytical method can be used to identify Cl-DBPs of water treatment procedures in further studies.
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Affiliation(s)
- Yao Lu
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China; Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhi-Min Song
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Jun-Kun Liang
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China
| | - Nan Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Qing Hu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Qian-Yuan Wu
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
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25
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Lu Y, Wang C, Zhang XY, Wang ZW, Song ZM, Du Y, Hu Q, Wu QY, Hu HY. Tracing nitrogenous byproducts during ozonation in the presence of bromide and ammonia using stable isotope labeling and high resolution mass spectrometry. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123612. [PMID: 32814238 DOI: 10.1016/j.jhazmat.2020.123612] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Ammonia has been widely used to inhibit bromate formation during ozonation. However, our recent study found that during ozonation in the presence of bromide and ammonia, toxicity increased under certain conditions that might be attributed to the formation of nitrogenous byproducts. Herein, a typical structural moiety of natural organic matter (NOM), hydroquinone, was evaluated for its potential to form nitrogenous byproducts. During ozonation of the hydroquinone solution containing bromide and ammonia, toxicity of organic byproducts increased significantly. As organic bromine was hardly detected, organic nitrogen was responsible for the increased toxicity. An effective method combining ultra-performance liquid chromatography in tandem with high resolution mass spectrometry (UPLC-HRMS) with an isotope labeling strategy was used to trace nitrogenous byproducts. Four newly formed nitrogenous byproducts were detected, two of which were also detected in Suwannee River natural organic matter (SRNOM) solution treated under the same ozonation condition. Furthermore, the molecular structures and formation pathways of these nitrogenous byproducts were proposed. This study highlights that, despite the widespread use, adding ammonia to inhibit bromate formation during ozonation might increase the toxicity posed by nitrogenous byproducts. During ozonation in the presence of bromide and ammonia, particular attention should be paid to nitrogenous byproducts.
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Affiliation(s)
- Yao Lu
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China; Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Xin-Yang Zhang
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Zhi-Wei Wang
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China
| | - Zhi-Min Song
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Ye Du
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China
| | - Qing Hu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Qian-Yuan Wu
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China.
| | - Hong-Ying Hu
- Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China; Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
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Duan X, Feng F, Chen F, Wang E, Liu T, Wu H, Feng X, Zhang F. Multi-marker scans coupled to high-resolution mass spectrometry strategy for global profiling combined with structure recognition of unknown trace chlorogenic acids in Lonicera Flos. Talanta 2021; 226:122134. [PMID: 33676688 DOI: 10.1016/j.talanta.2021.122134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/07/2023]
Abstract
Deep investigation, profiling of chemical diversity of constituent compounds and discovery of novel structures is a great challenge. A novel comprehensive and effective approach to mine trace unknown compounds combined with structure recognition in complex matrix is developed, in order to profiling potential Chlorogenic acids (CGAs) in Lonicera Flos (LFs): using multiple neutral loss/precursor ion (NL/PI) markers scans combined with high resolution mass spectrometry (HRMS). The workflow included (i) Fragmentation rules deduced by Q-orbitrap and selection of multiple NL/PI markers. (ii) Multiple NL/PI marker scans and grouping of peaks that had responses on two or more channels. (iii) Alignment of peaks in Full-MS scan and multiple NL/PI scans. (iv) The precursor ions list was introduced to mine novel CGAs according to simulated molecular formula. (v) Identification and structure recognition with the aid of HRMS. The procedure proved to be valid to screen and identify 51 CGAs from Lonicera Flos (LFs) with 16 categories, especially dihydroxyphenyl and glucoside for the first time. Its application could also be extended for global profiling of other complicated chemical systems, such as Chinese medicinal formulas.
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Affiliation(s)
- Xiaoyi Duan
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China; School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Feng Feng
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China
| | - Fengming Chen
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China
| | - Enting Wang
- ChongQing Academy of Metrology and Quality Inspection, Chongqing, 401121, China
| | - Tong Liu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China
| | - Hanqiu Wu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China
| | - Xuesong Feng
- School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing, 100176, China.
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27
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Esperanza MG, Wrobel K, Ojeda AG, Garay-Sevilla ME, Escobosa ARC, Barrientos EY, Wrobel K. Liquid chromatography-mass spectrometry untargeted metabolomics reveals increased levels of tryptophan indole metabolites in urine of metabolic syndrome patients. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:379-387. [PMID: 33295818 DOI: 10.1177/1469066720964632] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Metabolic syndrome (MetS) is a multifactor condition predisposing for diabetes, cardiovascular diseases and other degenerative disorders. Although several diagnostic criteria have been established, none of them is specific and there is a call for better pathophysiological explanation of MetS and for the discovery of molecular biomarkers. Phenotype characterization at metabolome level might be useful for both purposes. To this end, our aim was to perform comparative untargeted metabolomics of urines from MetS patients and from the control group. The study participants included 52 diagnosticated and 50 healthy individuals from Leon city in central Mexico; 23 anthropometric and clinical parameters were measured and submitted to Principal Component Analysis (PCA). The obtained PCA model allowed us for selection of 11 MetS patients and 13 control subjects, correspondingly representative for each of the two groups (clearly separated in PCA). The first morning urines from these subjects were ambulatory collected and, after methanol extraction and acidification, were submitted to capillary liquid chromatography-high resolution mass spectrometry (LC-HRMS). The obtained data were analyzed on MetaboScape® platform (Bruker Daltonics). Specifically, t-test applied to LC-HRMS data revealed several ions presenting at least 3-fold higher intensities in MetS with respect to the control samples (p < 0.05). Data analysis and complementary experiments yielded the identification of the following metabolites: indole-3-acetic acid, indole-3-acetic acid-O-glucuronide, N-(indol-3-ylacetyl) glutamine, indole-3-carbaldehyde and hydroxyhexanoycarnitine. Additionally, indole-3-carboxylic acid was annotated with 2.13-fold higher abundance in MetS patients. To assess the contribution of individual metabolites in the difference between two groups of subjects, partial least square discriminant analysis was performed for LC-HRMS data and the obtained values of variable importance in projection (VIP), confirmed the association of six above mentioned compounds with MetS. Overall, this study provides direct evidence on the disturbed catabolism of tryptophan in metabolic syndrome.
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Affiliation(s)
| | - Katarzyna Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
| | | | | | | | | | - Kazimierz Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
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28
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Karthiya R, Wasil SM, Khandelia P. Emerging role of N4-acetylcytidine modification of RNA in gene regulation and cellular functions. Mol Biol Rep 2020; 47:9189-9199. [PMID: 33174082 DOI: 10.1007/s11033-020-05963-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
Post-transcriptional chemical modification of RNA is rapidly emerging as a key player in regulating gene expression and has propelled the development of 'epitranscriptomics' or 'RNA epigenetics' as a frontier area of research. Several RNA modifications are known to decorate RNAs and impact its structure and function. One such recently discovered modification is acetylation of RNA i.e. N4-acetylcytidine (ac4C) chemical modification. N4-acetylcytidine is an ancient and evolutionarily conserved modification, which maps to a wide spectrum of RNAs from archaea bacteria to humans. This modification results in a variety of functional outcomes which impact normal development and disease. In this review, we summarize the recent progress, emerging methods, biological implications and the future challenges for ac4C modification.
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Affiliation(s)
- R Karthiya
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - S Mohammed Wasil
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
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29
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Qiu J, Li T, Zhu ZJ. Multi-dimensional characterization and identification of sterols in untargeted LC-MS analysis using all ion fragmentation technology. Anal Chim Acta 2020; 1142:108-117. [PMID: 33280688 DOI: 10.1016/j.aca.2020.10.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
Sterols are an important type of lipids, and play many important roles in physiological and pathological processes. However, comprehensive analysis of sterols especially identification of unknown sterols is challenging. In this work, LC-MS with all ion fragmentation (AIF) technology was developed for untargeted analysis of sterols in biological samples. AIF technology provided holistic and multi-dimensional characterization for both knowns and unknowns sterols, including accurate m/z, isotope pattern, retention time (RT), and co-eluted peak profiles between MS1 and MS2 ions in one analysis. We further developed an analysis strategy by integrating the multi-dimensional properties to support unambiguous identification of sterols, including distinguishing sterol isomers. The developed strategy enabled to identify a total of 23 sterols in mouse samples, and quantified 19 sterols in mouse liver tissues. More importantly, we demonstrated that AIF based multi-dimensional analysis provided a possibility to identify sterols without chemical standards and facilitated to discover novel compounds with sterol-like structures in biological samples. In summary, we employed the LC-MS based AIF technology to develop multi-dimensional characterization and identification of both known and unknown sterols in complex biological samples. The comprehensive analysis of sterols facilitates to provide molecular insights to many physiological and pathological activities in biology.
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Affiliation(s)
- Jiaqian Qiu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tongzhou Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China.
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Li H, Xu R, Yang L, Luan H, Chen S, Chen L, Cai Z, Tian R. Combinatory Data-Independent Acquisition and Parallel Reaction Monitoring Method for Deep Profiling of Gangliosides. Anal Chem 2020; 92:10830-10838. [PMID: 32648742 DOI: 10.1021/acs.analchem.0c02313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ganglioside is an important class of lipid species involved in intercellular signaling and various diseases, especially for neurodegenerative diseases. Systematic ganglioside profiling is challenging because of their naturally low abundance and highly diverse species. Herein, a new data-independent acquisition and parallel reaction monitoring (DIA/PRM) method with superior sensitivity was developed. The untargeted DIA acquisition consecutively records all the precursor ion and fragment ions at the same time, while the targeted PRM analysis with versatile higher collisional dissociation generates full MS/MS spectra for structure elucidation and verification. As compared with traditional data-dependent acquisition (DDA), the DIA/PRM method unbiasedly detected the majority of abundant ganglioside species and as low as 50 pg of ganglioside in an untargeted manner. Gangliosides in four kinds of biological samples including the mouse brain, mouse plasma, HeLa cell, and human colon cancer tissue were systematically identified, and low-abundance ganglioside species were further extended on the basis of linear chromatography retention rules of the most frequently detected ganglioside species. A total of 383 ganglioside features were defined with 329 of them derived from 32 ganglioside species. Taking advantage of the high-resolution MS analysis, rare ganglioside species were further elucidated according to their characteristic fragment ions and neutral losses. In total, 18 gangliosides with a ceramide carbon number from 20 to 25 and modified gangliosides, including 18 acetylated, 8 diacetylated, 1 phosphorylated, 36 N-glycolyneuraminic acid (NeuGc)-containing, and 7 di-NeuGc-containing gangliosides, were newly identified. The developed DIA/PRM method therefore generated a rich ganglioside resource for further functional exploration and is a unique alternative for DDA analysis for global ganglioside profiling in various biological systems.
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Affiliation(s)
- Hua Li
- SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ruilian Xu
- Department of Oncology, The First Affiliated Hospital of SUSTech and Shenzhen People's Hospital, Shenzhen 518020, China
| | - Lijun Yang
- Department of Oncology, The First Affiliated Hospital of SUSTech and Shenzhen People's Hospital, Shenzhen 518020, China.,Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hemi Luan
- SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shili Chen
- Department of General Surgery and Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lan Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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31
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Zhang CX, Wang XY, Lin ZZ, Wang HD, Qian YX, Li WW, Yang WZ, Guo DA. Highly selective monitoring of in-source fragmentation sapogenin product ions in positive mode enabling group-target ginsenosides profiling and simultaneous identification of seven Panax herbal medicines. J Chromatogr A 2020; 1618:460850. [DOI: 10.1016/j.chroma.2020.460850] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/28/2019] [Accepted: 01/02/2020] [Indexed: 01/17/2023]
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32
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Jin G, Xu M, Zou M, Duan S. The Processing, Gene Regulation, Biological Functions, and Clinical Relevance of N4-Acetylcytidine on RNA: A Systematic Review. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:13-24. [PMID: 32171170 PMCID: PMC7068197 DOI: 10.1016/j.omtn.2020.01.037] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/24/2022]
Abstract
N4-acetylcytidine (ac4C) is often considered to be a conservative, chemically modified nucleoside present on tRNA and rRNA. Recent studies have shown extensive ac4C modifications in human and yeast mRNAs. ac4C helps to correctly read codons during translation and improves translation efficiency and the stability of mRNA. At present, the research of ac4C involves a variety of detection methods. The formation of ac4C is closely related to N-acetyltransferase 10 (NAT10) and its helpers, such as putative tRNA acetyltransferase (TAN1) for tRNA ac4C and small nucleolar RNA (snoRNA) for rRNA ac4C. Also, ac4C is associated with the development, progression, and prognosis of a variety of human diseases. Here, we summarize the history of ac4C research and the detection technologies of ac4C. We then summarized the role and mechanism of ac4C in gene-expression regulation and demonstrated the relevance of ac4C to a variety of human diseases, especially cancer. Finally, we list the future challenges of the ac4C research and demonstrate a research strategy for the interactions among several abundant modified nucleosides on mRNA.
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Affiliation(s)
- Gehui Jin
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Mengsha Zou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
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33
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In-depth profiling, characterization, and comparison of the ginsenosides among three different parts (the root, stem leaf, and flower bud) of Panax quinquefolius L. by ultra-high performance liquid chromatography/quadrupole-Orbitrap mass spectrometry. Anal Bioanal Chem 2019; 411:7817-7829. [DOI: 10.1007/s00216-019-02180-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/18/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
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