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Zhang X, An M, Zhang J, Zhao Y, Liu Y. Nano-medicine therapy reprogramming metabolic network of tumour microenvironment: new opportunity for cancer therapies. J Drug Target 2024; 32:241-257. [PMID: 38251656 DOI: 10.1080/1061186x.2024.2309565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/26/2023] [Indexed: 01/23/2024]
Abstract
Metabolic heterogeneity is one of the characteristics of tumour cells. In order to adapt to the tumour microenvironment of hypoxia, acidity and nutritional deficiency, tumour cells have undergone extensive metabolic reprogramming. Metabolites involved in tumour cell metabolism are also very different from normal cells, such as a large number of lactate and adenosine. Metabolites play an important role in regulating the whole tumour microenvironment. Taking metabolites as the target, it aims to change the metabolic pattern of tumour cells again, destroy the energy balance it maintains, activate the immune system, and finally kill tumour cells. In this paper, the regulatory effects of metabolites such as lactate, glutamine, arginine, tryptophan, fatty acids and adenosine were reviewed, and the related targeting strategies of nano-medicines were summarised, and the future therapeutic strategies of nano-drugs were discussed. The abnormality of tumour metabolites caused by tumour metabolic remodelling not only changes the energy and material supply of tumour, but also participates in the regulation of tumour-related signal pathways, which plays an important role in the survival, proliferation, invasion and metastasis of tumour cells. Regulating the availability of local metabolites is a new aspect that affects tumour progress. (The graphical abstract is by Figdraw).
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Affiliation(s)
- Xiaojie Zhang
- Department of Pharmaceutics, School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Min An
- Department of Pharmaceutics, School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Juntao Zhang
- Department of Pharmaceutics, School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Yumeng Zhao
- Department of Pharmaceutics, School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Yanhua Liu
- Department of Pharmaceutics, School of Pharmacy, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Hui Ethnic Medicine Modernization, Ningxia Medical University, Yinchuan, China
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2
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Dong Y, Li Y, Su W, Sun P, Yang H, Li Q, Du S, Yu X. Differential metabolic networks in three energy substances of flaxseed (Linum usitatissimum L.) during germination. Food Chem 2024; 443:138463. [PMID: 38280366 DOI: 10.1016/j.foodchem.2024.138463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/29/2024]
Abstract
Germinated flaxseed (Linum usitatissimum L.) is an essential potential food ingredient, but the major energy substances (proteins, lipids, and carbohydrates) metabolites and metabolic pathways are unknown. Comprehensive metabolomic analyses were performed using Fourier transform infrared spectroscopy and high-performance liquid chromatography mass spectrometry on flaxseed from 0 to 7 d. Additionally, the critical metabolites pathways networks of three energy substances metabolites during flaxseed germination were exhibited. The results showed that arginine was the most active metabolite during germination, strongly associated with the arginine biosynthesis and arginine and proline metabolism pathways. Carbohydrates predominantly comprised sucrose on 0-3 d, which participated in galactose metabolism and starch and sucrose metabolism. The main flaxseed phospholipid molecules were phosphatidic acid, phosphatidylethanolamine, lysophosphatidic acid, and lysophosphatidylcholine during germination. This study underscores the paramount metabolic pathways in proteins, lipids and carbohydrates were arginine and proline metabolism, linoleic acid metabolism, arachidonic acid metabolism, and ascorbate and aldarate metabolism during germination.
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Affiliation(s)
- Yaoyao Dong
- Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, PR China
| | - Yonglin Li
- Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, PR China
| | - Weidong Su
- Ningxia Xingling Grain & Oil Co., Ltd, Yinchuan 751400, Ningxia, PR China
| | - Pengda Sun
- Ningxia Xingling Grain & Oil Co., Ltd, Yinchuan 751400, Ningxia, PR China
| | - Huijun Yang
- Shaanxi Guanzhongyoufang Oil Co., Ltd, Baoji 721000, Shaanxi, PR China
| | - Qi Li
- Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, PR China
| | - Shuangkui Du
- Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, PR China
| | - Xiuzhu Yu
- Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, PR China.
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3
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Li X, Zhang W, Niu D, Liu X. Effects of abiotic stress on chlorophyll metabolism. Plant Sci 2024; 342:112030. [PMID: 38346561 DOI: 10.1016/j.plantsci.2024.112030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
Chlorophyll, an essential pigment in the photosynthetic machinery of plants, plays a pivotal role in the absorption of light energy and its subsequent transfer to reaction centers. Given that the global production of chlorophyll reaches billions of tons annually, a comprehensive understanding of its biosynthetic pathways and regulatory mechanisms is important. The metabolic pathways governing chlorophyll biosynthesis and catabolism are complex, encompassing a series of interconnected reactions mediated by a spectrum of enzymes. Environmental fluctuations, particularly abiotic stressors such as drought, extreme temperature variations, and excessive light exposure, can significantly perturb these processes. Such disruptions in chlorophyll metabolism have profound implications for plant growth and development. This review delves into the core aspects of chlorophyll metabolism, encompassing both biosynthetic and degradative pathways. It elucidates key genes and enzymes instrumental in these processes and underscores the impact of abiotic stress on chlorophyll metabolism. Furthermore, the review aims to deepen the understanding of the interplay between chlorophyll metabolic dynamics and stress responses, thereby shedding light on potential regulatory mechanisms.
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Affiliation(s)
- Xu Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Di Niu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiaomin Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Chen Y, Gustafsson J, Yang J, Nielsen J, Kerkhoven EJ. Single-cell omics analysis with genome-scale metabolic modeling. Curr Opin Biotechnol 2024; 86:103078. [PMID: 38359604 DOI: 10.1016/j.copbio.2024.103078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
Single-cell technologies have been widely used in biological studies and generated a plethora of single-cell data to be interpreted. Due to the inclusion of the priori metabolic network knowledge as well as gene-protein-reaction associations, genome-scale metabolic models (GEMs) have been a powerful tool to integrate and thereby interpret various omics data mostly from bulk samples. Here, we first review two common ways to leverage bulk omics data with GEMs and then discuss advances on integrative analysis of single-cell omics data with GEMs. We end by presenting our views on current challenges and perspectives in this field.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Johan Gustafsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jingyu Yang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; BioInnovation Institute, DK-2200 Copenhagen, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technology University of Denmark, DK-2800 Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
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5
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Yu Z, Lin Y, Wu L, Wang L, Fan Y, Xu L, Zhang L, Wu W, Tao J, Huan F, Liu W, Wang J, Gao R. Bisphenol F exposure induces depression-like changes: Roles of the kynurenine metabolic pathway along the "liver-brain" axis. Environ Pollut 2024; 346:123356. [PMID: 38266696 DOI: 10.1016/j.envpol.2024.123356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 01/02/2024] [Accepted: 01/13/2024] [Indexed: 01/26/2024]
Abstract
Bisphenol F (BPF), one of the major alternatives of Bisphenol A (BPA), is becoming extensively used in industrial production with great harm to human beings and environment. Recent studies have revealed that environmental exposure is crucial to the initiation and development of depression. Thereby, the aim the present study is to ascertain the correlationship between the BPF exposure and depression occurrence. In the current study, BPF strikingly triggered depression-like changes in mice through the sucrose preference test (SPT), tail suspension test (TST) and forced swim test (FST), accompanied by the perturbation of the kynurenine (KYN) metabolic pathway along the "liver-brain" axis. Mechanistically, the neurotransmitters from the tryptophan metabolic pathway were converted to the toxic KYN pathway after BPF treatment. With the ELISA assay, it revealed that the toxic KYN metabolites, including KYN and 3-hydroxykynurenine (3-HK), were strikingly increased in the mouse brains which was ascribed to the enhanced expression of the rate-limiting enzymes Indoleamine 2,3-dioxygenase (IDO1) and Kynurenine 3-monooxygenase (KMO) respectively. Interestingly, the increased brain KYN induced by BPF was also validated partially from the periphery, since the ELISA and western blotting results indicated the significantly increased KYN in the serum and L-type amino acid transporter 1 (LAT1) in the brain, the key transporter responsible for KYN and 3-HK crossing the blood-brain barrier. Intriguingly, the liver-derived KYN metabolic pathway was the important source of the peripheral KYN and 3-HK, as BPF substantially enhanced hepatic IDO1, Tryptophan, 2, 3-dioxygenase (TDO2), and KMO levels indicated by western blotting. This study is the first to delineate previously unrecognized BPF-induced depression by regulating the KYN metabolic pathway along the "liver-brain" axis; therefore, targeting LAT1 or hepatic KYN signaling may provide a potentially unique therapeutic intervention in BPF-induced depression.
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Affiliation(s)
- Zheng Yu
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Yuxin Lin
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Linlin Wu
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China; The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China
| | - Luyao Wang
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Yichun Fan
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Liuting Xu
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Linwei Zhang
- Department of Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Weilan Wu
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Jingxian Tao
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Fei Huan
- Department of Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
| | - Wenwei Liu
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China
| | - Jun Wang
- Department of Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China; China International Cooperation Center for Environment and Human Health, Nanjing Medical University, 818 Tianyuan East Road, Nanjing, 211166, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Rong Gao
- Department of Hygienic Analysis and Detection, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China.
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6
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Li Z, Sang R, Feng G, Feng Y, Zhang R, Yan X. Microbiological and metabolic pathways analysing the mechanisms of alfalfa polysaccharide and sulfated alfalfa polysaccharide in alleviating obesity. Int J Biol Macromol 2024; 263:130334. [PMID: 38387635 DOI: 10.1016/j.ijbiomac.2024.130334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/10/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Alfalfa polysaccharide (AP) and sulfated alfalfa polysaccharide (SAP) exhibit potential for alleviating obesity. This study aimed to analyze the mechanism of action of AP and SAP in alleviating obesity through combined microbiomics and metabolomics. The research selected validated optimal AP and SAP concentration for experiment. The results showed that AP and SAP down-regulated colonic inflammatory gene expression, regulated intestinal pH to normal, and restored intestinal growth. Microbial sequencing showed that AP and SAP altered the microbial composition ratio. AP increased the relative abundance of Muribaculaceae and Romboutsia. SAP increased the relative abundance of Dubosiella, Fecalibaculum and Desulfovibrionaceae. Metabolomic analysis showed that AP regulated steroid hormone biosynthesis, neuroactive ligand-receptor interactions and bile secretion pathways. SAP focuses more on pathways related to amino acid metabolism. Meanwhile, AP and SAP down-regulated the mRNA expression of colonic COX-2, PepT-1 and HK2 and up-regulated the mRNA expression of TPH1. Correlation analysis showed a strong correlation between metabolites and gut bacteria. Dubosiella, Faecalibaculum may be the critical marker flora for polysaccharides to alleviate obesity. This study indicates that AP and SAP alleviate obesity through different pathways and that specific polysaccharide modifications affect characteristic microbial and metabolic pathways, providing new insights into polysaccharide modifications.
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Affiliation(s)
- Zhiwei Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Ruxue Sang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Guilan Feng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Yuxi Feng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Ran Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province 225009, China.
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7
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Jiménez AG, Paul KD, Benson M, Lalwani S, Cipolli W. Cellular metabolic pathways of aging in dogs: could p53 and SIRT1 be at play? GeroScience 2024; 46:1895-1908. [PMID: 37768524 PMCID: PMC10828300 DOI: 10.1007/s11357-023-00942-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Aging and cancer seem to be closely associated, such that cancer is generally considered a disease of the elderly in both humans and dogs. Additionally, cancer is a metabolic shift in itself towards aerobic glycolysis. Larger dog breeds with shorter lifespans, and increased glycolytic cellular metabolic rates, die of cancer more often than smaller breeds. The tumor suppressor p53 factor is a key suppressor oncogene, and the p53 pathway arrests cellular proliferation and prevents DNA mutations from accumulating during cellular stress. The p53 pathway is also associated with the control of cellular metabolism to prevent cellular metabolic shifts common to cancerous phenotypes. SIRT1 deacetylates the p53 tumor suppressor protein, downregulating p53 via effects on stability and activity during stress. Here, we used primary fibroblast cells from small and large puppies and old dogs. Using UV radiation to upregulate the p53 system (100 J/m2), control cells and UV-treated cells were used to measure aerobic and glycolytic metabolic rates using a Seahorse XFe96 oxygen flux analyzer. We also quantified p53 expression and SIRT1 concentration in canine primary fibroblasts before and after UV treatment. We demonstrate that, due to a higher p53 nuclear to cytoplasmic ratio in large breed dogs after UV treatment, p53 could have a more regulatory effect on large breed dogs' metabolism compared with smaller breeds. Thus, there may be a link between p53 upregulation and inhibition of glycolysis in large breed dogs during times of cellular stress compared with small breed dogs. However, SIRT1 concentrations decrease with age in domestic dogs of both size classes, suggesting a possible release of inhibition of p53 through the SIRT1 pathway with age. This may lead to increased incidences of cancer, especially due to the more pronounced upregulation of p53 with cellular stress.
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Affiliation(s)
- Ana Gabriela Jiménez
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA.
| | - Kailey D Paul
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA
| | - Mitchel Benson
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA
| | - Sahil Lalwani
- Stanford Law School, Crown Quadrangle, 559 Nathan Abbott Way, Stanford, CA, 94305, USA
| | - William Cipolli
- Department of Mathematics, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA
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Coffey NJ, Simon MC. Metabolic alterations in hereditary and sporadic renal cell carcinoma. Nat Rev Nephrol 2024; 20:233-250. [PMID: 38253811 DOI: 10.1038/s41581-023-00800-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.
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Affiliation(s)
- Nathan J Coffey
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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de Dios-Pérez I, González-Garcinuño Á, Muñoz-Barroso I, Martín Del Valle EM. A Synergistic Approach Therapy for Colorectal Cancer Based on Exosomes and Exploitation of Metabolic Pathways. J Pharm Sci 2024; 113:1038-1046. [PMID: 37844760 DOI: 10.1016/j.xphs.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
In order to reduce the side effects of traditional chemotherapy in the treatment of colorectal cancer (CRC), a new drug delivery system has been developed in this work, based on exosomes that can host two drugs that act synergistically: farnesol (that stops the cell cycle) and paclitaxel (prevents microtubule system depolymerization). Firstly, exosomes were isolated from different cell cultures (from colorectal cancer and from fibroblast as example of normal cell line) by different methods and characterized by western blot, TEM and DLS, and results showed that they express classical protein markers such as CD9 and HSP-70 and they showed spherical morphology with sizes from 93 nm to 129 nm depending on the source. These exosomes were loaded with both drugs and its effect was studied in vitro. The efficacy was studied by comparing the viability of cell cultures with a colorectal cancer cell line (HCT-116) and a normal cell line (fibroblast HS-5). Results showed that exosomes present a specific effect with more reduction in cell viability in tumour cultures than healthy ones. In summary, exosomes are presented in this work as a promising strategy for colorectal cancer treatment.
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Affiliation(s)
| | - Álvaro González-Garcinuño
- Department of Chemical Engineering, University of Salamanca, Salamanca, Spain; Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Isabel Muñoz-Barroso
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - Eva María Martín Del Valle
- Department of Chemical Engineering, University of Salamanca, Salamanca, Spain; Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
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Biran A, Santos TCB, Dingjan T, Futerman AH. The Sphinx and the egg: Evolutionary enigmas of the (glyco)sphingolipid biosynthetic pathway. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159462. [PMID: 38307322 DOI: 10.1016/j.bbalip.2024.159462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
In eukaryotes, the de novo synthesis of sphingolipids (SLs) consists of multiple sequential steps which are compartmentalized between the endoplasmic reticulum and the Golgi apparatus. Studies over many decades have identified the enzymes in the pathway, their localization, topology and an array of regulatory mechanisms. However, little is known about the evolutionary forces that underly the generation of this complex pathway or of its anteome, i.e., the metabolic pathways that converge on the SL biosynthetic pathway and are essential for its activity. After briefly describing the pathway, we discuss the mechanisms by which the enzymes of the SL biosynthetic pathway are targeted to their different subcellular locations, how the pathway per se may have evolved, including its compartmentalization, and the relationship of the pathway to eukaryogenesis. We discuss the circular interdependence of the evolution of the SL pathway, and comment on whether current Darwinian evolutionary models are able to provide genuine mechanistic insight into how the pathway came into being.
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Affiliation(s)
- Assaf Biran
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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11
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Peng Y, Zhang Z, He L, Li C, Liu M. NMR spectroscopy for metabolomics in the living system: recent progress and future challenges. Anal Bioanal Chem 2024; 416:2319-2334. [PMID: 38240793 PMCID: PMC10950998 DOI: 10.1007/s00216-024-05137-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/08/2023] [Accepted: 01/10/2024] [Indexed: 03/21/2024]
Abstract
Metabolism is a fundamental process that underlies human health and diseases. Nuclear magnetic resonance (NMR) techniques offer a powerful approach to identify metabolic processes and track the flux of metabolites at the molecular level in living systems. An in vitro study through in-cell NMR tracks metabolites in real time and investigates protein structures and dynamics in a state close to their most natural environment. This technique characterizes metabolites and proteins involved in metabolic pathways in prokaryotic and eukaryotic cells. In vivo magnetic resonance spectroscopy (MRS) enables whole-organism metabolic monitoring by visualizing the spatial distribution of metabolites and targeted proteins. One limitation of these NMR techniques is the sensitivity, for which a possible improved approach is through isotopic enrichment or hyperpolarization methods, including dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP). DNP involves the transfer of high polarization from electronic spins of radicals to surrounding nuclear spins for signal enhancements, allowing the detection of low-abundance metabolites and real-time monitoring of metabolic activities. PHIP enables the transfer of nuclear spin polarization from parahydrogen to other nuclei for signal enhancements, particularly in proton NMR, and has been applied in studies of enzymatic reactions and cell signaling. This review provides an overview of in-cell NMR, in vivo MRS, and hyperpolarization techniques, highlighting their applications in metabolic studies and discussing challenges and future perspectives.
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Affiliation(s)
- Yun Peng
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zeting Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Optics Valley Laboratory, Wuhan, 430074, Hubei, China.
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12
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Wang L, Qu F, Yu X, Yang S, Zhao B, Chen Y, Li P, Zhang Z, Zhang J, Han X, Wei D. Cortical lipid metabolic pathway alteration of early Alzheimer's disease and candidate drugs screen. Eur J Med Res 2024; 29:199. [PMID: 38528586 DOI: 10.1186/s40001-024-01730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/12/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Lipid metabolism changes occur in early Alzheimer's disease (AD) patients. Yet little is known about metabolic gene changes in early AD cortex. METHODS The lipid metabolic genes selected from two datasets (GSE39420 and GSE118553) were analyzed with enrichment analysis. Protein-protein interaction network construction and correlation analyses were used to screen core genes. Literature analysis and molecular docking were applied to explore potential therapeutic drugs. RESULTS 60 lipid metabolic genes differentially expressed in early AD patients' cortex were screened. Bioinformatics analyses revealed that up-regulated genes were mainly focused on mitochondrial fatty acid oxidation and mediating the activation of long-chain fatty acids, phosphoproteins, and cholesterol metabolism. Down-regulated genes were mainly focused on lipid transport, carboxylic acid metabolic process, and neuron apoptotic process. Literature reviews and molecular docking results indicated that ACSL1, ACSBG2, ACAA2, FABP3, ALDH5A1, and FFAR4 were core targets for lipid metabolism disorder and had a high binding affinity with compounds including adenosine phosphate, oxidized Photinus luciferin, BMS-488043, and candidate therapeutic drugs especially bisphenol A, benzo(a)pyrene, ethinyl estradiol. CONCLUSIONS AD cortical lipid metabolism disorder was associated with the dysregulation of the PPAR signaling pathway, glycerophospholipid metabolism, adipocytokine signaling pathway, fatty acid biosynthesis, fatty acid degradation, ferroptosis, biosynthesis of unsaturated fatty acids, and fatty acid elongation. Candidate drugs including bisphenol A, benzo(a)pyrene, ethinyl estradiol, and active compounds including adenosine phosphate, oxidized Photinus luciferin, and BMS-488043 have potential therapeutic effects on cortical lipid metabolism disorder of early AD.
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Affiliation(s)
- Linshuang Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fengxue Qu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Xueyun Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Sixia Yang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Binbin Zhao
- Institute of Gerontology, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Yaojing Chen
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Pengbo Li
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Zhanjun Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Junying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- BABRI Centre, Beijing Normal University, Beijing, 100875, China.
| | - Xuejie Han
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Dongfeng Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Dos Reis JBA, Lorenzi AS, Pinho DB, Cortelo PC, do Vale HMM. The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications. Arch Microbiol 2024; 206:185. [PMID: 38506928 DOI: 10.1007/s00203-024-03911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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14
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Long X, Zhang C, Yang Q, Zhang X, Chen W, Zhu X, Xu Q, Tan Q. Photoheterotroph improved the growth and nutrient levels of Chlorella vulgaris and the related molecular mechanism. Appl Microbiol Biotechnol 2024; 108:269. [PMID: 38507095 PMCID: PMC10954984 DOI: 10.1007/s00253-024-13090-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/16/2024] [Accepted: 02/25/2024] [Indexed: 03/22/2024]
Abstract
Microalgae are rich in fatty acids, proteins, and other nutrients, which have gained the general attention of researchers all over the world. For the development of Chlorella vulgaris in food and feed industry, this study was conducted to investigate the differences in C. vulgaris' growth and nutritional components under different culture conditions (autotrophic, heterotrophic, photoheterotrophic) and the internal factors through cell counting in combination with transcriptome and nutrient analyses. The results showed that, under the photoheterotrophic condition, Chlorella's growth and the contents of lipid and protein were significantly higher than that under the heterotrophic condition, and the moisture content was lower than that under the heterotrophic condition. The saturated fatty acid content under the photoheterotrophic condition was the lowest, while the polyunsaturated fatty acid content was significantly higher than those under the other two conditions. There were 46,583 differentially expressed genes (DEGs), including 33,039 up-regulated DEGs (70.93%) and 13,544 down-regulated DEGs (29.07%), under the photoheterotrophic condition in comparison with the autotrophic condition. The fold change between the two conditions of samples of up-regulated genes was higher than that of the down-regulated genes. The KEGG enrichment showed that the up-regulated DEGs in the photoheterotrophic condition were significantly enriched in 5 pathways, including protein processing in endoplasmic reticulum pathway, photosynthesis pathway, photosynthesis-antenna protein pathway, endocytosis pathway, and phosphonate and phosphinate metabolism pathway. DEGs related to fatty acid metabolic pathways were significantly enriched in the fatty acid biosynthesis pathway and the biosynthesis of unsaturated fatty acid pathway. The qPCR analysis showed that the expression pattern of the selected genes was consistent with that of transcriptome analysis. The results of this study lay a theoretical foundation for the large-scale production of Chlorella and its application in food, feed, and biodiesel. KEY POINTS: • Nutrient levels under photoheterotrophic condition were higher than other conditions. • Six important pathways were discovered that affect changes in nutritional composition. • Explored genes encode important enzymes in the differential metabolic pathways.
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Affiliation(s)
- Xianmei Long
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Cancan Zhang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qian Yang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xiaorui Zhang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Wangwang Chen
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xiaofang Zhu
- Hubei Vocational College of Bio-Technology, Wuhan, 430070, China
| | - Qing Xu
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qingsong Tan
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
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15
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Yu Y, Ji X, Song L, Cao Y, Feng J, Zhang R, Tao F, Zhang F, Xue P. Saponins from Chenopodium quinoa Willd. husks alleviated high-fat-diet-induced hyperlipidemia via modulating the gut microbiota and multiple metabolic pathways. J Sci Food Agric 2024; 104:2417-2428. [PMID: 37989713 DOI: 10.1002/jsfa.13127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Hyperlipidemia is characterized by abnormally elevated blood lipids. Quinoa saponins (QS) have multiple pharmacological activities, including antitumor, bactericidal and immune-enhancing effects. However, the lipid-lowering effect and mechanisms of QS in vivo have been scarcely reported. METHODS The effect of QS against hyperlipidemia induced by high-fat diet in rats was explored based on gut microbiota and serum non-targeted metabolomics. RESULTS The study demonstrated that the supplementation of QS could reduce serum lipids, body weight, liver injury and inflammation. 16S rRNA sequencing demonstrated that QS mildly increased alpha-diversity, altered the overall structure of intestinal flora, decreased the relative richness of Firmicutes, the ratio of Firmicutes/Bacteroidetes (P < 0.05) and increased the relative richness of Actinobacteria, Bacteroidetes, Bifidobacterium, Roseburia and Coprococcus (P < 0.05). Simultaneously, metabolomics analysis showed that QS altered serum functional metabolites with respect to bile acid biosynthesis, arachidonic acid metabolism and taurine and hypotaurine metabolism, which were closely related to bile acid metabolism and fatty acid β-oxidation. Furthermore, QS increased protein levels of farnesoid X receptor, peroxisome proliferator-activated receptor α and carnitine palmitoyltransferase 1, which were related to the screened metabolic pathways. Spearman correlation analysis showed that there was a correlation between gut microbiota and differential metabolites. CONCLUSION QS could prevent lipid metabolism disorders in hyperlipidemic rats, which may be closely associated with the regulation of the gut microbiota and multiple metabolic pathways. This study may provide new evidence for QS as natural active substances for the prevention of hyperlipidemia. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yuan Yu
- Clinical Nutrition Department, First Affiliated Hospital of Weifang Medical, University (Weifang People's Hospital), Weifang, People's Republic of China
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Xueying Ji
- Clinical Nutrition Department, First Affiliated Hospital of Weifang Medical, University (Weifang People's Hospital), Weifang, People's Republic of China
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Linmeng Song
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Yuqing Cao
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Jing Feng
- School of Rehabilitation, Weifang Medical University, Weifang, People's Republic of China
| | - Ruoyu Zhang
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Feiyan Tao
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Fengxiang Zhang
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
| | - Peng Xue
- Clinical Nutrition Department, First Affiliated Hospital of Weifang Medical, University (Weifang People's Hospital), Weifang, People's Republic of China
- School of Public Health, Weifang Medical University, Weifang, People's Republic of China
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16
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Li X, Li G, Wang J, Li X, Yang Y, Song D. Elucidating polyethylene microplastic degradation mechanisms and metabolic pathways via iron-enhanced microbiota dynamics in marine sediments. J Hazard Mater 2024; 466:133655. [PMID: 38310843 DOI: 10.1016/j.jhazmat.2024.133655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/06/2024]
Abstract
The extensive use of plastics has given rise to microplastics, a novel environmental contaminant that has sparked considerable ecological and environmental concerns. Biodegradation offers a more environmentally friendly approach to eliminating microplastics, but their degradation by marine microbial communities has received little attention. In this study, we used iron-enhanced marine sediment to augment the natural bacterial community and facilitate the decomposition of polyethylene (PE) microplastics. The introduction of iron-enhanced sediment engendered an augmented bacterial biofilm formation on the surface of polyethylene (PE), thereby leading to a more pronounced degradation effect. This novel observation has been ascribed to the oxidative stress-induced generation of a variety of oxygenated functional groups, including hydroxyl (-OH), carbonyl (-CO), and ether (-C-O) moieties, within the microplastic substrate. The analysis of succession in the community structure of sediment bacteria during the degradation phase disclosed that Acinetobacter and Pseudomonas emerged as the principal bacterial players in PE degradation. These taxa were directly implicated in oxidative metabolic pathways facilitated by diverse oxidase enzymes under iron-facilitated conditions. The present study highlights bacterial community succession as a new pivotal factor influencing the complex biodegradation dynamics of polyethylene (PE) microplastics. This investigation also reveals, for the first time, a unique degradation pathway for PE microplastics orchestrated by the multifaceted marine sediment microbiota. These novel insights shed light on the unique functional capabilities and internal biochemical mechanisms employed by the marine sediment microbiota in effectively degrading polyethylene microplastics.
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Affiliation(s)
- Xionge Li
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guangbi Li
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jiaxin Wang
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinyi Li
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuru Yang
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Donghui Song
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin 300457, China.
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17
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Lefèvre-Morand RYL, Nikel PI, Acevedo-Rocha CG. How many Mutations are needed to Evolve the Chemical Makeup of a Synthetic Cell? Chembiochem 2024; 25:e202300829. [PMID: 38226957 DOI: 10.1002/cbic.202300829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
The chemical evolution of a synthetic cell endowed with a synthetic amino acid as building block, analog to tryptophan, required the emergence of key mutations in genes involved in, inter alia, the general stress response, amino acid metabolism, stringent response, and chemotaxis. Understanding adaptation mechanisms to non-canonical biomass components will inform strategies for engineering synthetic metabolic pathways and cells.
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Affiliation(s)
- Rodrigue Yves Louis Lefèvre-Morand
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
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18
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Chen Y, Li F. Metabolomes evolve faster than metabolic network structures. Proc Natl Acad Sci U S A 2024; 121:e2400519121. [PMID: 38457519 PMCID: PMC10945805 DOI: 10.1073/pnas.2400519121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024] Open
Affiliation(s)
- Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Feiran Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen518055, China
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Simula L, Fumagalli M, Vimeux L, Rajnpreht I, Icard P, Birsen G, An D, Pendino F, Rouault A, Bercovici N, Damotte D, Lupo-Mansuet A, Alifano M, Alves-Guerra MC, Donnadieu E. Mitochondrial metabolism sustains CD8 + T cell migration for an efficient infiltration into solid tumors. Nat Commun 2024; 15:2203. [PMID: 38467616 PMCID: PMC10928223 DOI: 10.1038/s41467-024-46377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
The ability of CD8+ T cells to infiltrate solid tumors and reach cancer cells is associated with improved patient survival and responses to immunotherapy. Thus, identifying the factors controlling T cell migration in tumors is critical, so that strategies to intervene on these targets can be developed. Although interstitial motility is a highly energy-demanding process, the metabolic requirements of CD8+ T cells migrating in a 3D environment remain unclear. Here, we demonstrate that the tricarboxylic acid (TCA) cycle is the main metabolic pathway sustaining human CD8+ T cell motility in 3D collagen gels and tumor slices while glycolysis plays a more minor role. Using pharmacological and genetic approaches, we report that CD8+ T cell migration depends on the mitochondrial oxidation of glucose and glutamine, but not fatty acids, and both ATP and ROS produced by mitochondria are required for T cells to migrate. Pharmacological interventions to increase mitochondrial activity improve CD8+ T cell intratumoral migration and CAR T cell recruitment into tumor islets leading to better control of tumor growth in human xenograft models. Our study highlights the rationale of targeting mitochondrial metabolism to enhance the migration and antitumor efficacy of CAR T cells in treating solid tumors.
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Affiliation(s)
- Luca Simula
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France.
| | - Mattia Fumagalli
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Lene Vimeux
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Irena Rajnpreht
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Philippe Icard
- Université de Normandie, UNICAEN, Inserm U1086 Interdisciplinary Research Unit for Cancer Prevention and Treatment, Caen, France
- Thoracic Surgery Department, Cochin Hospital, APHP-Centre, Université Paris-Cité, Paris, France
| | - Gary Birsen
- Department of Pneumology, Thoracic Oncology Unit, Cochin Hospital, APHP-Centre, Université Paris-Cité, 75014, Paris, France
| | - Dongjie An
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Frédéric Pendino
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Adrien Rouault
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Nadège Bercovici
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France
| | - Diane Damotte
- Department of Pathology, Cochin Hospital, APHP-Centre, Université Paris-Cité, 75014, Paris, France
| | - Audrey Lupo-Mansuet
- Department of Pathology, Cochin Hospital, APHP-Centre, Université Paris-Cité, 75014, Paris, France
| | - Marco Alifano
- Thoracic Surgery Department, Cochin Hospital, APHP-Centre, Université Paris-Cité, Paris, France
- Inserm U1138, Integrative Cancer Immunology Unit, 75006, Paris, France
| | | | - Emmanuel Donnadieu
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, Equipe labellisée "Ligue contre le Cancer", Paris, 75014, France.
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Ferreira MADM, Silveira WBD, Nikoloski Z. Protein constraints in genome-scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes. Biotechnol Bioeng 2024; 121:915-930. [PMID: 38178617 DOI: 10.1002/bit.28650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Genome-scale metabolic models provide a valuable resource to study metabolism and cell physiology. These models are employed with approaches from the constraint-based modeling framework to predict metabolic and physiological phenotypes. The prediction performance of genome-scale metabolic models can be improved by including protein constraints. The resulting protein-constrained models consider data on turnover numbers (kcat ) and facilitate the integration of protein abundances. In this systematic review, we present and discuss the current state-of-the-art regarding the estimation of kinetic parameters used in protein-constrained models. We also highlight how data-driven and constraint-based approaches can aid the estimation of turnover numbers and their usage in improving predictions of cellular phenotypes. Finally, we identify standing challenges in protein-constrained metabolic models and provide a perspective regarding future approaches to improve the predictive performance.
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Affiliation(s)
| | | | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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21
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Zou Y, Zhang J, Wang J, Gong X, Jiang T, Yan Y. A self-regulated network for dynamically balancing multiple precursors in complex biosynthetic pathways. Metab Eng 2024; 82:69-78. [PMID: 38316239 PMCID: PMC10947840 DOI: 10.1016/j.ymben.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Microbial synthesis has emerged as a promising and sustainable alternative to traditional chemical synthesis and plant extraction. However, the competition between synthetic pathways and central metabolic pathways for cellular resources may impair final production efficiency. Moreover, when the synthesis of target product requires multiple precursors from the same node, the conflicts of carbon flux have further negative impacts on yields. In this study, a self-regulated network was developed to relieve the competition of precursors in complex synthetic pathways. Using 4-hydroxycoumarin (4-HC) synthetic pathway as a proof of concept, we employed an intermediate as a trigger to dynamically rewire the metabolic flux of pyruvate and control the expression levels of genes in 4-HC synthetic pathway, achieving self-regulation of multiple precursors and enhanced titer. Transcriptomic analysis results additionally demonstrated that the gene transcriptional levels of both pyruvate kinase PykF and synthetic pathway enzyme SdgA dynamically changed according to the intermediate concentrations. Overall, our work established a self-regulated network to dynamically balance the metabolic flux of two precursors in 4-HC biosynthesis, providing insight into balancing biosynthetic pathways where multiple precursors compete and interfere with each other.
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Affiliation(s)
- Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Jianli Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Xinyu Gong
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.
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22
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Wang S, Zhao F, Yang M, Lin Y, Han S. Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals. Crit Rev Biotechnol 2024; 44:163-190. [PMID: 36596577 DOI: 10.1080/07388551.2022.2153008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 01/05/2023]
Abstract
In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.
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Affiliation(s)
- Shuai Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
| | - Manli Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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23
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Zou S, Zhang B, Han Y, Liu J, Zhao K, Xue Y, Zheng Y. Design of a cofactor self-sufficient whole-cell biocatalyst for enzymatic asymmetric reduction via engineered metabolic pathways and multi-enzyme cascade. Biotechnol J 2024; 19:e2300744. [PMID: 38509791 DOI: 10.1002/biot.202300744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/22/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
NAD(P)H-dependent oxidoreductases are crucial biocatalysts for synthesizing chiral compounds. Yet, the industrial implementation of enzymatic redox reactions is often hampered by an insufficient supply of expensive nicotinamide cofactors. Here, a cofactor self-sufficient whole-cell biocatalyst was developed for the enzymatic asymmetric reduction of 2-oxo-4-[(hydroxy)(-methyl)phosphinyl] butyric acid (PPO) to L-phosphinothricin (L-PPT). The endogenous NADP+ pool was significantly enhanced by regulating Preiss-Handler pathway toward NAD(H) synthesis and, in the meantime, introducing NAD kinase to phosphorylate NAD(H) toward NADP+. The intracellular NADP(H) concentration displayed a 2.97-fold increase with the strategy compared with the wild-type strain. Furthermore, a recombinant multi-enzyme cascade biocatalytic system was constructed based on the Escherichia coli chassis. In order to balance multi-enzyme co-expression levels, the strategy of modulating rate-limiting enzyme PmGluDH by RBS strengths regulation successfully increased the catalytic efficiency of PPO conversion. Finally, the cofactor self-sufficient whole-cell biocatalyst effectively converted 300 mM PPO to L-PPT in 2 h without the need to add exogenous cofactors, resulting in a 2.3-fold increase in PPO conversion (%) from 43% to 100%, with a high space-time yield of 706.2 g L-1 d-1 and 99.9% ee. Overall, this work demonstrates a technological example for constructing a cofactor self-sufficient system for NADPH-dependent redox biocatalysis.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Bing Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuyue Han
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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24
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Chumin EJ, Burton CP, Silvola R, Miner EW, Persohn SC, Veronese M, Territo PR. Brain metabolic network covariance and aging in a mouse model of Alzheimer's disease. Alzheimers Dement 2024; 20:1538-1549. [PMID: 38032015 DOI: 10.1002/alz.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD), the leading cause of dementia worldwide, represents a human and financial impact for which few effective drugs exist to treat the disease. Advances in molecular imaging have enabled assessment of cerebral glycolytic metabolism, and network modeling of brain region have linked to alterations in metabolic activity to AD stage. METHODS We performed 18 F-FDG positron emission tomography (PET) imaging in 4-, 6-, and 12-month-old 5XFAD and littermate controls (WT) of both sexes and analyzed region data via brain metabolic covariance analysis. RESULTS The 5XFAD model mice showed age-related changes in glucose uptake relative to WT mice. Analysis of community structure of covariance networks was different across age and sex, with a disruption of metabolic coupling in the 5XFAD model. DISCUSSION The current study replicates clinical AD findings and indicates that metabolic network covariance modeling provides a translational tool to assess disease progression in AD models.
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Affiliation(s)
- Evgeny J Chumin
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana, USA
- Indiana University Network Science Institute, Indiana University, Bloomington, Indiana, USA
| | - Charles P Burton
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rebecca Silvola
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Ethan W Miner
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Scott C Persohn
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Mattia Veronese
- Department of Information Engineering, University of Padua, Padua, Italy
- Department of Neuroimaging, King's College London, London, UK
| | - Paul R Territo
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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25
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Zhou N, Guo H, Zhang Z, Wang H. The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions. Chemosphere 2024; 351:141230. [PMID: 38237784 DOI: 10.1016/j.chemosphere.2024.141230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.
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Affiliation(s)
- Nan Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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26
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Woo H, Kim Y, Kim D, Yoon SH. Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources. Mol Syst Biol 2024; 20:170-186. [PMID: 38291231 PMCID: PMC10912204 DOI: 10.1038/s44320-024-00017-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Carbon source-dependent control of bacterial growth is fundamental to bacterial physiology and survival. However, pinpointing the metabolic steps important for cell growth is challenging due to the complexity of cellular networks. Here, the elastic net model and multilayer perception model that integrated genome-wide gene-deletion data and simulated flux distributions were constructed to identify metabolic reactions beneficial or detrimental to Escherichia coli grown on 30 different carbon sources. Both models outperformed traditional in silico methods by identifying not just essential reactions but also nonessential ones that promote growth. They successfully predicted metabolic reactions beneficial to cell growth, with high convergence between the models. The models revealed that biosynthetic pathways generally promote growth across various carbon sources, whereas the impact of energy-generating pathways varies with the carbon source. Intriguing predictions were experimentally validated for findings beyond experimental training data and the impact of various carbon sources on the glyoxylate shunt, pyruvate dehydrogenase reaction, and redundant purine biosynthesis reactions. These highlight the practical significance and predictive power of the models for understanding and engineering microbial metabolism.
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Affiliation(s)
- Hyunjae Woo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngshin Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dohyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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27
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Andrews SS, Wiley HS, Sauro HM. Design patterns of biological cells. Bioessays 2024; 46:e2300188. [PMID: 38247191 PMCID: PMC10922931 DOI: 10.1002/bies.202300188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
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Affiliation(s)
- Steven S. Andrews
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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28
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Huang L, Li H, Zhang C, Chen Q, Liu Z, Zhang J, Luo P, Wei T. Unlocking the potential of T-cell metabolism reprogramming: Advancing single-cell approaches for precision immunotherapy in tumour immunity. Clin Transl Med 2024; 14:e1620. [PMID: 38468489 PMCID: PMC10928360 DOI: 10.1002/ctm2.1620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
As single-cell RNA sequencing enables the detailed clustering of T-cell subpopulations and facilitates the analysis of T-cell metabolic states and metabolite dynamics, it has gained prominence as the preferred tool for understanding heterogeneous cellular metabolism. Furthermore, the synergistic or inhibitory effects of various metabolic pathways within T cells in the tumour microenvironment are coordinated, and increased activity of specific metabolic pathways generally corresponds to increased functional activity, leading to diverse T-cell behaviours related to the effects of tumour immune cells, which shows the potential of tumour-specific T cells to induce persistent immune responses. A holistic understanding of how metabolic heterogeneity governs the immune function of specific T-cell subsets is key to obtaining field-level insights into immunometabolism. Therefore, exploring the mechanisms underlying the interplay between T-cell metabolism and immune functions will pave the way for precise immunotherapy approaches in the future, which will empower us to explore new methods for combating tumours with enhanced efficacy.
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Affiliation(s)
- Lihaoyun Huang
- Department of OncologyZhujiang HospitalSouthern Medical UniversityGuangzhouChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouChina
| | - Haitao Li
- Department of OncologyTaishan People's HospitalGuangzhouChina
| | - Cangang Zhang
- Department of Pathogenic Microbiology and ImmunologySchool of Basic Medical SciencesXi'an Jiaotong UniversityXi'anShaanxiChina
| | - Quan Chen
- Department of NeurosurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zaoqu Liu
- Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (Beijing)Beijing Institute of LifeomicsBeijingChina
- Key Laboratory of Medical Molecular BiologyChinese Academy of Medical SciencesDepartment of PathophysiologyPeking Union Medical CollegeInstitute of Basic Medical SciencesBeijingChina
| | - Jian Zhang
- Department of OncologyZhujiang HospitalSouthern Medical UniversityGuangzhouChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouChina
| | - Peng Luo
- Department of OncologyZhujiang HospitalSouthern Medical UniversityGuangzhouChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouChina
| | - Ting Wei
- Department of OncologyZhujiang HospitalSouthern Medical UniversityGuangzhouChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouChina
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29
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Xue B, Liu Y, Yang C, Liu H, Yuan Q, Wang S, Su H. Co-Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction. Adv Sci (Weinh) 2024; 11:e2306662. [PMID: 38093511 PMCID: PMC10916542 DOI: 10.1002/advs.202306662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/23/2023] [Indexed: 03/07/2024]
Abstract
Synthetic consortia have emerged as a promising biosynthetic platform that offers new opportunities for biosynthesis. Genome-scale metabolic network models (GEMs) with complex constraints are extensively utilized to guide the synthesis in monocultures. However, few methods are currently available to guide the rational construction of synthetic consortia for predicting the optimal allocation strategy of synthetic pathways aimed at enhancing product synthesis. A standardized method to construct the co-cultivated Enzyme Constraint metabolic network model (CulECpy) is proposed, which integrates enzyme constraints and modular interaction scale constraints based on the research concept of "independent + global". This method is applied to construct several synthetic consortia models, which encompassed different target products, strains, synthetic pathways, and compositional structures. Analyzing the model, the optimal pathway allocation and initial inoculum ratio that enhance the synthesis of target products by synthetic consortia are predicted and verified. When comparing with the constructed co-culture synthesis system, the normalized root mean square error of all optimal theoretical yield simulations is found to be less than or equal to 0.25. The analyses and verifications demonstrate that the method CulECpy can guide the rational construction of synthetic consortia systems to facilitate biochemical synthesis.
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Affiliation(s)
- Boyuan Xue
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Yu Liu
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Chen Yang
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Hao Liu
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Qianqian Yuan
- Biodesign CenterKey Laboratory of Engineering Biology for Low‐carbon ManufacturingTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308P. R. China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Haijia Su
- Beijing Key Laboratory of Bioprocessand Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical TechnologyBeijing100029P. R. China
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30
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Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J, Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. Nat Protoc 2024; 19:629-667. [PMID: 38238583 DOI: 10.1038/s41596-023-00931-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 10/13/2023] [Indexed: 03/10/2024]
Abstract
Genome-scale metabolic models (GEMs) are computational representations that enable mathematical exploration of metabolic behaviors within cellular and environmental constraints. Despite their wide usage in biotechnology, biomedicine and fundamental studies, there are many phenotypes that GEMs are unable to correctly predict. GECKO is a method to improve the predictive power of a GEM by incorporating enzymatic constraints using kinetic and omics data. GECKO has enabled reconstruction of enzyme-constrained metabolic models (ecModels) for diverse organisms, which show better predictive performance than conventional GEMs. In this protocol, we describe how to use the latest version GECKO 3.0; the procedure has five stages: (1) expansion from a starting metabolic model to an ecModel structure, (2) integration of enzyme turnover numbers into the ecModel structure, (3) model tuning, (4) integration of proteomics data into the ecModel and (5) simulation and analysis of ecModels. GECKO 3.0 incorporates deep learning-predicted enzyme kinetics, paving the way for improved metabolic models for virtually any organism and cell line in the absence of experimental data. The time of running the whole protocol is organism dependent, e.g., ~5 h for yeast.
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Affiliation(s)
- Yu Chen
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Johan Gustafsson
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Albert Tafur Rangel
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technology University of Denmark, Lyngby, Denmark
| | - Mihail Anton
- Department of Life Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Feiran Li
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Le Yuan
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technology University of Denmark, Lyngby, Denmark.
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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31
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Arikawa LM, Mota LFM, Schmidt PI, Frezarim GB, Fonseca LFS, Magalhães AFB, Silva DA, Carvalheiro R, Chardulo LAL, Albuquerque LGD. Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle. Meat Sci 2024; 209:109402. [PMID: 38056170 DOI: 10.1016/j.meatsci.2023.109402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.
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Affiliation(s)
- Leonardo Machestropa Arikawa
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Patrícia Iana Schmidt
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Jequitinhonha and Mucuri Valleys, Department of Animal Science, Rod. MG 367, Diamantina, MG 39100-000, Brazil
| | - Delvan Alves Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Viçosa, Department of Animal Science, Av. PH Rolfs, Viçosa, MG 36570-900, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Luis Artur Loyola Chardulo
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil
| | - Lucia Galvão de Albuquerque
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil.
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Maucourt F, Doumèche B, Nazaret S, Fraissinet-Tachet L. Under explored roles of microbial ligninolytic enzymes in aerobic polychlorinated biphenyl transformation. Environ Sci Pollut Res Int 2024; 31:19071-19084. [PMID: 38372925 DOI: 10.1007/s11356-024-32291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants in the environment that are responsible for many adverse health effects. Bioremediation appears to be a healthy and cost-effective alternative for remediating PCB-contaminated environments. While some microbial species have been observed to be capable of transforming PCBs, only two different microbial pathways (rdh and bph pathways) have been described to be involved in PCB transformations. Ligninolytic enzymes have been observed or are under suspicion in some microbial PCB transformations. However, the role of these promising PCB-transforming enzymes, which are produced by fungi and some aerobic bacteria, is still unclear. The present review describes their role by identifying microbial PCB-transforming species and their reported ligninolytic enzymes whether proven or suspected to be involved in PCB transformations. There are several lines of evidence that ligninolytic enzymes are responsible for PCB transformations such as (1) the ability of purified laccases from Myceliophthora thermophila, Pycnoporus cinnabarinus, Trametes versicolor, Cladosporium sp, and Coprinus cumatus to transform hydroxy-PCBs; (2) the increased production of laccases and peroxidases by many fungi in the presence of PCBs; and (3) the enhanced PCB transformation by Pseudomonas stutzeri and Sinorhizobium meliloti NM after the addition of ligninolytic enzyme enhancers. However, if the involvement of ligninolytic enzymes in PCB transformation is clearly demonstrated in some fungal species, it does not seem to be implicated in all microbial species suggesting other still unknown metabolic pathways involved in PCB transformation and different from the bph and rdh pathways. Therefore, PCB transformation may involve several metabolic pathways, some involving ligninolytic enzymes, bph or rdh genes, and some still unknown, depending on the microbial species. In addition, current knowledge does not fully clarify the role of ligninolytic enzymes in PCB oxidation and dechlorination. Therefore, further studies focusing on purified ligninolytic enzymes are needed to clearly elucidate their role in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
- ENVISOL, 2-4 rue Hector Berlioz, F-38110, La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-7 69622, Villeurbanne, France
| | - Sylvie Nazaret
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France.
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Zhou M, Wang Q, Lu X, Zhang P, Yang R, Chen Y, Xia J, Chen D. Exhaled breath and urinary volatile organic compounds (VOCs) for cancer diagnoses, and microbial-related VOC metabolic pathway analysis: a systematic review and meta-analysis. Int J Surg 2024; 110:1755-1769. [PMID: 38484261 PMCID: PMC10942174 DOI: 10.1097/js9.0000000000000999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 03/17/2024]
Abstract
BACKGROUND The gradual evolution of the detection and quantification of volatile organic compounds (VOCs) has been instrumental in cancer diagnosis. The primary objective of this study was to assess the diagnostic potential of exhaled breath and urinary VOCs in cancer detection. As VOCs are indicative of tumor and human metabolism, our work also sought to investigate the metabolic pathways linked to the development of cancerous tumors. MATERIALS AND METHODS An electronic search was performed in the PubMed database. Original studies on VOCs within exhaled breath and urine for cancer detection with a control group were included. A meta-analysis was conducted using a bivariate model to assess the sensitivity and specificity of the VOCs for cancer detection. Fagan's nomogram was designed to leverage the findings from our diagnostic analysis for the purpose of estimating the likelihood of cancer in patients. Ultimately, MetOrigin was employed to conduct an analysis of the metabolic pathways associated with VOCs in relation to both human and/or microbiota. RESULTS The pooled sensitivity, specificity and the area under the curve for cancer screening utilizing exhaled breath and urinary VOCs were determined to be 0.89, 0.88, and 0.95, respectively. A pretest probability of 51% can be considered as the threshold for diagnosing cancers with VOCs. As the estimated pretest probability of cancer exceeds 51%, it becomes more appropriate to emphasize the 'ruling in' approach. Conversely, when the estimated pretest probability of cancer falls below 51%, it is more suitable to emphasize the 'ruling out' approach. A total of 14, 14, 6, and 7 microbiota-related VOCs were identified in relation to lung, colorectal, breast, and liver cancers, respectively. The enrichment analysis of volatile metabolites revealed a significant enrichment of butanoate metabolism in the aforementioned tumor types. CONCLUSIONS The analysis of exhaled breath and urinary VOCs showed promise for cancer screening. In addition, the enrichment analysis of volatile metabolites revealed a significant enrichment of butanoate metabolism in four tumor types, namely lung, colorectum, breast and liver. These findings hold significant implications for the prospective clinical application of multiomics correlation in disease management and the exploration of potential therapeutic targets.
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Affiliation(s)
- Min Zhou
- Department of Breast Surgery, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi Maternity and Child Health Care Hospital
| | - Qinghua Wang
- Research Institute for Reproductive Health and Genetic Diseases, Women’s Hospital of Jiangnan University
| | - Xinyi Lu
- Department of Breast Surgery, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi Maternity and Child Health Care Hospital
| | - Ping Zhang
- Department of Breast Surgery, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi Maternity and Child Health Care Hospital
| | - Rui Yang
- Research Institute for Reproductive Health and Genetic Diseases, Women’s Hospital of Jiangnan University
| | - Yu Chen
- Research Institute for Reproductive Health and Genetic Diseases, Women’s Hospital of Jiangnan University
| | - Jiazeng Xia
- Department of General Surgery and Translational Medicine Center, The Affiliated Wuxi No. 2 People’s Hospital of Nanjing Medical University, Jiangnan University Medical Center, Wuxi, People’s Republic of China
| | - Daozhen Chen
- Department of Breast Surgery, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi Maternity and Child Health Care Hospital
- Research Institute for Reproductive Health and Genetic Diseases, Women’s Hospital of Jiangnan University
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Sala S, Nitschke P, Masuda R, Gray N, Lawler NG, Wood JM, Buckler JN, Berezhnoy G, Bolaños J, Boughton BA, Lonati C, Rössler T, Singh Y, Wilson ID, Lodge S, Morillon AC, Loo RL, Hall D, Whiley L, Evans GB, Grove TL, Almo SC, Harris LD, Holmes E, Merle U, Trautwein C, Nicholson JK, Wist J. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients. J Proteome Res 2024; 23:956-970. [PMID: 38310443 PMCID: PMC10913068 DOI: 10.1021/acs.jproteome.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/29/2023] [Indexed: 02/05/2024]
Abstract
We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel endogenous cytosine metabolites with potential antiviral activities. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif, indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally enabled the characterization and quantification of the most abundant serum metabolites, showing the potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine- and uracil-based) analogue structures, eight of which were previously unknown in humans allowing us to propose a new extended viperin pathway for the innate production of antiviral compounds. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ, and IL-10, suggest an association with the viperin enzyme contributing to an ancient endogenous innate immune defense mechanism against viral infection.
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Affiliation(s)
- Samuele Sala
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Philipp Nitschke
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Reika Masuda
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nicola Gray
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nathan G. Lawler
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - James M. Wood
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Joshua N. Buckler
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
| | - Georgy Berezhnoy
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jose Bolaños
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
| | - Berin A. Boughton
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Caterina Lonati
- Center
for Preclinical Research, Fondazione IRCCS
Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Titus Rössler
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Yogesh Singh
- Institute
of Medical Genetics and Applied Genomics, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Ian D. Wilson
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Samantha Lodge
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Aude-Claire Morillon
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Ruey Leng Loo
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Drew Hall
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Luke Whiley
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Gary B. Evans
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Lawrence D. Harris
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Elaine Holmes
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Uta Merle
- Department
of Internal Medicine IV, University Hospital
Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Trautwein
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jeremy K. Nicholson
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Institute
of Global Health Innovation, Faculty of
Medicine, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, U.K.
| | - Julien Wist
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
- Faculty of Medicine, Department of Metabolism,
Digestion and Reproduction,
Division of Digestive Diseases at Imperial College, London SW7 2AZ, U.K.
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Stockbauer A, Beyer L, Huber M, Kreuzer A, Palleis C, Katzdobler S, Rauchmann BS, Morbelli S, Chincarini A, Bruffaerts R, Vandenberghe R, Kramberger MG, Trost M, Garibotto V, Nicastro N, Lathuilière A, Lemstra AW, van Berckel BNM, Pilotto A, Padovani A, Ochoa-Figueroa MA, Davidsson A, Camacho V, Peira E, Bauckneht M, Pardini M, Sambuceti G, Aarsland D, Nobili F, Gross M, Vöglein J, Perneczky R, Pogarell O, Buerger K, Franzmeier N, Danek A, Levin J, Höglinger GU, Bartenstein P, Cumming P, Rominger A, Brendel M. Metabolic network alterations as a supportive biomarker in dementia with Lewy bodies with preserved dopamine transmission. Eur J Nucl Med Mol Imaging 2024; 51:1023-1034. [PMID: 37971501 PMCID: PMC10881642 DOI: 10.1007/s00259-023-06493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE Metabolic network analysis of FDG-PET utilizes an index of inter-regional correlation of resting state glucose metabolism and has been proven to provide complementary information regarding the disease process in parkinsonian syndromes. The goals of this study were (i) to evaluate pattern similarities of glucose metabolism and network connectivity in dementia with Lewy bodies (DLB) subjects with subthreshold dopaminergic loss compared to advanced disease stages and to (ii) investigate metabolic network alterations of FDG-PET for discrimination of patients with early DLB from other neurodegenerative disorders (Alzheimer's disease, Parkinson's disease, multiple system atrophy) at individual patient level via principal component analysis (PCA). METHODS FDG-PETs of subjects with probable or possible DLB (n = 22) without significant dopamine deficiency (z-score < 2 in putamen binding loss on DaT-SPECT compared to healthy controls (HC)) were scaled by global-mean, prior to volume-of-interest-based analyses of relative glucose metabolism. Single region metabolic changes and network connectivity changes were compared against HC (n = 23) and against DLB subjects with significant dopamine deficiency (n = 86). PCA was applied to test discrimination of patients with DLB from disease controls (n = 101) at individual patient level. RESULTS Similar patterns of hypo- (parietal- and occipital cortex) and hypermetabolism (basal ganglia, limbic system, motor cortices) were observed in DLB patients with and without significant dopamine deficiency when compared to HC. Metabolic connectivity alterations correlated between DLB patients with and without significant dopamine deficiency (R2 = 0.597, p < 0.01). A PCA trained by DLB patients with dopamine deficiency and HC discriminated DLB patients without significant dopaminergic loss from other neurodegenerative parkinsonian disorders at individual patient level (area-under-the-curve (AUC): 0.912). CONCLUSION Disease-specific patterns of altered glucose metabolism and altered metabolic networks are present in DLB subjects without significant dopaminergic loss. Metabolic network alterations in FDG-PET can act as a supporting biomarker in the subgroup of DLB patients without significant dopaminergic loss at symptoms onset.
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Affiliation(s)
- Anna Stockbauer
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Leonie Beyer
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Maria Huber
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Annika Kreuzer
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Carla Palleis
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Sabrina Katzdobler
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Boris-Stephan Rauchmann
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Department of Neuroradiology, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Silvia Morbelli
- Nuclear Medicine Uni, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Andrea Chincarini
- National Institute of Nuclear Physics (INFN), Genoa Section, Genoa, Italy
| | - Rose Bruffaerts
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Louvain, Belgium
- Neurology Department, University Hospitals Leuven, Louvain, Belgium
- Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Louvain, Belgium
- Neurology Department, University Hospitals Leuven, Louvain, Belgium
| | - Milica G Kramberger
- Department of Neurology and Department for Nuclear Medicine, University Medical Centre, Ljubljana, Slovenia
| | - Maja Trost
- Department of Neurology and Department for Nuclear Medicine, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Valentina Garibotto
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospitals and NIMTLab, Geneva University, Geneva, Switzerland
| | - Nicolas Nicastro
- Department of Clinical Neurosciences, Geneva University Hospitals, Geneva, Switzerland
| | - Aurélien Lathuilière
- LANVIE (Laboratoire de Neuroimagerie du Vieillissement), Department of Psychiatry, Geneva University Hospitals, Geneva, Switzerland
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Bart N M van Berckel
- Department of Radiology & Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Andrea Pilotto
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- Parkinson's Disease Rehabilitation Centre, FERB ONLUS - S. Isidoro Hospital, Trescore Balneario, BG, Italy
| | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Miguel A Ochoa-Figueroa
- Department of Clinical Physiology in Linköping, Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Department of Diagnostic Radiology, Linköping University Hospital, Linköping, Sweden
- Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Anette Davidsson
- Department of Clinical Physiology in Linköping, Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Valle Camacho
- Servicio de Medicina Nuclear, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Enrico Peira
- National Institute of Nuclear Physics (INFN), Genoa Section, Genoa, Italy
- Department of Neuroscience (DINOGMI), University of Genoa, Genoa, Italy
| | - Matteo Bauckneht
- Nuclear Medicine Uni, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Matteo Pardini
- Department of Neuroscience (DINOGMI), University of Genoa, Genoa, Italy
- Clinical Neurology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gianmario Sambuceti
- Nuclear Medicine Uni, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Dag Aarsland
- Centre of Age-Related Medicine (SESAM), Stavanger University Hospital, Stavanger, Norway
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College, London, UK
| | - Flavio Nobili
- Department of Neuroscience (DINOGMI), University of Genoa, Genoa, Italy
- Clinical Neurology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mattes Gross
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Jonathan Vöglein
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Robert Perneczky
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, S10 2HQ, UK
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College, London, UK
| | - Oliver Pogarell
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Katharina Buerger
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institut for Stroke and Dementia Research, University of Munich, Munich, Germany
| | | | - Adrian Danek
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Johannes Levin
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Günter U Höglinger
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Peter Bartenstein
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Paul Cumming
- Department of Nuclear Medicine, University of Bern, Inselspital Bern, Bern, Switzerland
- School of Psychology and Counselling and IHBI, Queensland University of Technology, Brisbane, Australia
| | - Axel Rominger
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
- Department of Nuclear Medicine, University of Bern, Inselspital Bern, Bern, Switzerland
| | - Matthias Brendel
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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Patil N, Mirveis Z, Byrne HJ. Kinetic modelling of the cellular metabolic responses underpinning in vitro glycolysis assays. FEBS Open Bio 2024; 14:466-486. [PMID: 38217078 PMCID: PMC10909989 DOI: 10.1002/2211-5463.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
This study aims to demonstrate the benefits of augmenting commercially available, real-time, in vitro glycolysis assays with phenomenological rate equation-based kinetic models, describing the contributions of the underpinning metabolic pathways. To this end, a commercially available glycolysis assay, sensitive to changes in extracellular acidification (extracellular pH), was used to derive the glycolysis pathway kinetics. The pathway was numerically modelled using a series of ordinary differential rate equations, to simulate the obtained experimental results. The sensitivity of the model to the key equation parameters was also explored. The cellular glycolysis pathway kinetics were determined for three different cell-lines, under nonmodulated and modulated conditions. Over the timescale studied, the assay demonstrated a two-phase metabolic response, representing the differential kinetics of glycolysis pathway rate as a function of time, and this behaviour was faithfully reproduced by the model simulations. The model enabled quantitative comparison of the pathway kinetics of three cell lines, and also the modulating effect of two known drugs. Moreover, the modelling tool allows the subtle differences between different cell lines to be better elucidated and also allows augmentation of the assay sensitivity. A simplistic numerical model can faithfully reproduce the differential pathway kinetics for three different cell lines, with and without pathway-modulating drugs, and furthermore provides insights into the cellular metabolism by elucidating the underlying mechanisms leading to the pathway end-product. This study demonstrates that augmenting a relatively simple, real-time, in vitro assay with a model of the underpinning metabolic pathway provides considerable insights into the observed differences in cellular systems.
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Affiliation(s)
- Nitin Patil
- FOCAS Research InstituteTU DublinIreland
- School of Physics, Optometric and Clinical SciencesTU DublinIreland
| | - Zohreh Mirveis
- FOCAS Research InstituteTU DublinIreland
- School of Physics, Optometric and Clinical SciencesTU DublinIreland
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Hu M, Suthers PF, Maranas CD. KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states. Metab Eng 2024; 82:123-133. [PMID: 38336004 DOI: 10.1016/j.ymben.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty in obtaining flux and/or concentration data but also due to the computational difficulties of the underlying parameter identification problem. Both the computational demands for parameterization, degeneracy of obtained parameter solutions and interpretability of results has so far limited widespread adoption of large-scale kinetic models despite their potential. Herein, we introduce the Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the (non)steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP is benchmarked against previously parameterized large-scale kinetic models demonstrating an at least an order of magnitude faster convergence than the tool K-FIT while at the same time attaining better data fits. This versatile toolbox accepts different kinetic descriptions, metabolic fluxes, enzyme levels and metabolite concentrations, under either steady-state or instationary conditions to enable robust kinetic model construction and parameterization. KETCHUP supports the SBML format and can be accessed at https://github.com/maranasgroup/KETCHUP.
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Affiliation(s)
- Mengqi Hu
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, USA.
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Huldani H, Malviya J, Rodrigues P, Hjazi A, Deorari MM, Al-Hetty HRAK, Qasim QA, Alasheqi MQ, Ihsan A. Discovering the strength of immunometabolism in cancer therapy: Employing metabolic pathways to enhance immune responses. Cell Biochem Funct 2024; 42:e3934. [PMID: 38379261 DOI: 10.1002/cbf.3934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
Immunometabolism, which studies cellular metabolism and immune cell function, is a possible cancer treatment. Metabolic pathways regulate immune cell activation, differentiation, and effector functions, crucial to tumor identification and elimination. Immune evasion and tumor growth can result from tumor microenvironment metabolic dysregulation. These metabolic pathways can boost antitumor immunity. This overview discusses immune cell metabolism, including glycolysis, oxidative phosphorylation, amino acid, and lipid metabolism. Amino acid and lipid metabolic manipulations may improve immune cell activity and antitumor immunity. Combination therapy using immunometabolism-based strategies may enhance therapeutic efficacy. The complexity of the metabolic network, biomarker development, challenges, and future approaches are all covered, along with a summary of case studies demonstrating the effectiveness of immunometabolism-based therapy. Metabolomics, stable isotope tracing, single-cell analysis, and computational modeling are also reviewed for immunometabolism research. Personalized and combination treatments are considered. This review adds to immunometabolism expertise and sheds light on metabolic treatments' ability to boost cancer treatment immunological response. Also, in this review, we discussed the immune response in cancer treatment and altering metabolic pathways to increase the immune response against malignancies.
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Affiliation(s)
- Huldani Huldani
- Department of Physiology, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
| | - Jitendra Malviya
- Institute of Advance Bioinformatics, Bhopal, Madhya Pradesh, India
| | - Paul Rodrigues
- Department of Computer Engineering, King Khalid University, Al-Faraa, Asir-Abha, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, Prince Sattam bin Abdulaziz University College of Applied Medical Sciences, Al-Kharj, Saudi Arabia
| | - Maha Medha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | | | | | - Ali Ihsan
- Department of Medical Laboratories Techniques, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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Wang C, Cui W, Yu B, Zhou H, Cui Z, Guo P, Yu T, Feng Y. Role of succinylation modification in central nervous system diseases. Ageing Res Rev 2024; 95:102242. [PMID: 38387517 DOI: 10.1016/j.arr.2024.102242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Diseases of the central nervous system (CNS), including stroke, brain tumors, and neurodegenerative diseases, have a serious impact on human health worldwide, especially in elderly patients. The brain, which is one of the body's most metabolically dynamic organs, lacks fuel stores and therefore requires a continuous supply of energy substrates. Metabolic abnormalities are closely associated with the pathogenesis of CNS disorders. Post-translational modifications (PTMs) are essential regulatory mechanisms that affect the functions of almost all proteins. Succinylation, a broad-spectrum dynamic PTM, primarily occurs in mitochondria and plays a crucial regulatory role in various diseases. In addition to directly affecting various metabolic cycle pathways, succinylation serves as an efficient and rapid biological regulatory mechanism that establishes a connection between metabolism and proteins, thereby influencing cellular functions in CNS diseases. This review offers a comprehensive analysis of succinylation and its implications in the pathological mechanisms of CNS diseases. The objective is to outline novel strategies and targets for the prevention and treatment of CNS conditions.
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Affiliation(s)
- Chao Wang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Weigang Cui
- Department of Cardiology, People's Hospital of Rizhao, Rizhao 276800, People's Republic of China
| | - Bing Yu
- Qingdao University, Qingdao 266000, People's Republic of China
| | - Han Zhou
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Zhenwen Cui
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Pin Guo
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China.
| | - Yugong Feng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China.
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Yue M, Liu M, Gao S, Ren X, Zhou S, Rao Y, Zhou J. High-Level De Novo Production of (2 S)-Eriodictyol in Yarrowia Lipolytica by Metabolic Pathway and NADPH Regeneration Engineering. J Agric Food Chem 2024; 72:4292-4300. [PMID: 38364826 DOI: 10.1021/acs.jafc.3c08861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
(2S)-Eriodictyol, a polyphenolic flavonoid, has found widespread applications in health supplements and food additives. However, the limited availability of plant-derived (2S)-eriodictyol cannot meet the market demand. Microbial production of (2S)-eriodictyol faces challenges, including the low catalytic efficiency of flavone 3'-hydroxylase/cytochrome P450 reductase (F3'H/CPR), insufficient precursor supplementation, and inadequate NADPH regeneration. This study systematically engineered Yarrowia lipolytica for high-level (2S)-eriodictyol production. In doing this, the expression of F3'H/CPR was balanced, and the supply of precursors was enhanced by relieving feedback inhibition of the shikimate pathway, promoting fatty acid β-oxidation, and increasing the copy number of synthetic pathway genes. These strategies, combined with NADPH regeneration, achieved an (2S)-eriodictyol titer of 423.6 mg/L. Finally, in fed-batch fermentation, a remarkable 6.8 g/L (2S)-eriodictyol was obtained, representing the highest de novo microbial titer reported to date and paving the way for industrial production.
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Affiliation(s)
- Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuefeng Ren
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yijian Rao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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41
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Islam SR, Manna SK. Identification of glucose-independent and reversible metabolic pathways associated with anti-proliferative effect of metformin in liver cancer cells. Metabolomics 2024; 20:29. [PMID: 38413541 DOI: 10.1007/s11306-024-02096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024]
Abstract
INTRODUCTION Despite the ability of cancer cells to survive glucose deprivation, most studies on anti-cancer effect of metformin explored its impact on glucose metabolism. No study ever examined whether its anti-cancer effect is reversible. Existing evidences warrant understanding of glucose-independent non-cytotoxic anti-proliferative effect of metformin to rationalize its role in liver cancer. OBJECTIVES Characterization of glucose-independent anti-proliferative metabolic effects of metformin as well as analysis of their reversibility in liver cancer cells. METHODOLOGY The dose-dependent effects of metformin on HepG2 cells were examined in presence and absence of glucose. The longitudinal evolution of metabolome was analyzed along with gene and protein expression as well as their correlations with and reversibility of cellular phenotype and metabolic signatures. RESULTS Metformin concentrations up to 2.5 mM were found to be anti-proliferative irrespective of presence of glucose without significant increase in cytotoxicity. Apart from mitochondrial impairment, derangement of fatty acid desaturation, one-carbon, glutathione, and polyamine metabolism were associated with metformin treatment irrespective of glucose supplementation. Depletion of pantothenic acid, downregulation of essential amino acid uptake and metabolism alongside purine salvage were identified as novel glucose-independent effects of metformin. These were significantly correlated with cMyc expression and reduction in proliferation. Rescue experiments established reversibility upon metformin withdrawal and tight association between proliferation, metabotype, and cMyc expression. CONCLUSIONS The derangement of multiple glucose-independent metabolic pathways, which are often upregulated in therapy-resistant cancer, and concomitant cMyc downregulation coordinately contribute to the anti-proliferative effect of metformin in liver cancer cells. These are reversible and may influence its therapeutic utility.
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Affiliation(s)
- Sk Ramiz Islam
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal, 700 064, India
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400 094, India
| | - Soumen Kanti Manna
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal, 700 064, India.
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400 094, India.
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42
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Mandwal A, Bishop SL, Castellanos M, Westlund A, Chaconas G, Davidsen J, Lewis IA. MINNO: An Open Source Software for Refining Metabolic Networks and Investigating Complex Network Activity Using Empirical Metabolomics Data. Anal Chem 2024; 96:3382-3388. [PMID: 38359900 PMCID: PMC10902815 DOI: 10.1021/acs.analchem.3c04501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
Metabolomics is a powerful tool for uncovering biochemical diversity in a wide range of organisms. Metabolic network modeling is commonly used to frame metabolomics data in the context of a broader biological system. However, network modeling of poorly characterized nonmodel organisms remains challenging due to gene homology mismatches which lead to network architecture errors. To address this, we developed the Metabolic Interactive Nodular Network for Omics (MINNO), a web-based mapping tool that uses empirical metabolomics data to refine metabolic networks. MINNO allows users to create, modify, and interact with metabolic pathway visualizations for thousands of organisms, in both individual and multispecies contexts. Herein, we illustrate the use of MINNO in elucidating the metabolic networks of understudied species, such as those of the Borrelia genus, which cause Lyme and relapsing fever diseases. Using a hybrid genomics-metabolomics modeling approach, we constructed species-specific metabolic networks for threeBorrelia species. Using these empirically refined networks, we were able to metabolically differentiate these species via their nucleotide metabolism, which cannot be predicted from genomic networks. Additionally, using MINNO, we identified 18 missing reactions from the KEGG database, of which nine were supported by the primary literature. These examples illustrate the use of metabolomics for the empirical refining of genetically constructed networks and show how MINNO can be used to study nonmodel organisms.
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Affiliation(s)
- Ayush Mandwal
- Department
of Physics and Astronomy, University of
Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - Stephanie L. Bishop
- Alberta
Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - Mildred Castellanos
- Department
of Biochemistry and Molecular Biology, Cumming School of Medicine,
Snyder Institute for Chronic Diseases, University
of Calgary, 2500 University
Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - Anika Westlund
- Alberta
Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - George Chaconas
- Department
of Biochemistry and Molecular Biology, Cumming School of Medicine,
Snyder Institute for Chronic Diseases, University
of Calgary, 2500 University
Dr NW, Calgary T2N 1N4, Alberta, Canada
- Department
of Microbiology, Immunology and Infectious Diseases, Cumming School
of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - Jörn Davidsen
- Department
of Physics and Astronomy, University of
Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
- Hotchkiss
Brain Institute, University of Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
| | - Ian A. Lewis
- Alberta
Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary T2N 1N4, Alberta, Canada
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Kumano T. Specialized metabolites degradation by microorganisms. Biosci Biotechnol Biochem 2024; 88:270-275. [PMID: 38169014 DOI: 10.1093/bbb/zbad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024]
Abstract
Secondary metabolites are specialized metabolic products synthesized by plants, insects, and bacteria, some of which exhibit significant physiological activities against other organisms. Plants containing bioactive secondary metabolites have been used in traditional medicine for centuries. In developed countries, one-fourth of medicines directly contain plant-derived compounds or indirectly contain them via semi-synthesis. These compounds have contributed considerably to the development of not only medicine but also molecular biology. Moreover, the biosynthesis of these physiologically active secondary metabolites has attracted substantial interest and has been extensively studied. However, in many cases, the degradation mechanisms of these secondary metabolites remain unclear. In this review, some unique microbial degradation pathways for lignans and C-glycosides are explored.
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Affiliation(s)
- Takuto Kumano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Hu J, Wan K, Deng X, Liu X, Fang Y, Zhou F, Yu J, Chi R, Xiao C. Metagenomic analysis revealed the evolution of microbial communities, metabolic pathways, and functional genes in the heterotrophic nitrification-aerobic denitrification process under La 3+ stress. Sci Total Environ 2024; 912:169243. [PMID: 38101649 DOI: 10.1016/j.scitotenv.2023.169243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Trivalent lanthanum (La3+) exists widely in ammonia nitrogen (NH4+-N) tailing water from ionic rare earth mines; however, its effect on heterotrophic nitrification-aerobic denitrification (HN-AD) is unknown, thereby limiting the application of the HN-AD process in this field. In this study, we conducted an HN-AD process using a sequencing batch reactor (5 L) that was continuously operated to directly treat acidic (NH4)2SO4 wastewater (influent NH4+-N concentration of approximately 110 mg/L and influent pH of 5) containing different La3+ concentrations (0-100 mg/L). The NH4+-N removal efficiency of the reactor reached 98.25 % at a La3+ concentration of 100 mg/L. The reactor was in a neutral-to-alkaline environment, which favored La3+ precipitation and complexation. Metagenomic analysis revealed that the relative abundance of Thauera in the reactor remained high (88.62-92.27 %) under La3+ stress. The relative abundances of Pannonobacter and Hyphomonas significantly increased, whereas that of Azoarcus significantly decreased. Metabolic functions in the reactor were mainly contributed by Thauera, and the abundance of metabolic functions under low La3+ stress (≤5 mg/L) significantly differed from that under high La3+ stress (≥10 mg/L). The relative abundance of ammonia assimilation-related genes in the reactor was high and significantly correlated with ammonia removal. However, traditional ammonia oxidation genes were not annotated, and unknown ammonia oxidation pathways may have been present in the reactor. Moreover, La3+ stimulated amino acid biosynthesis and translocation, the citrate cycle, sulfur metabolism, and oxidative phosphorylation and promoted the overproduction of extracellular polymeric substances, which underwent complexation and adsorbed La3+ to reduce its toxicity. Our results showed that the HN-AD process had a strong tolerance to La3+, stable NH4+-N removal efficiency, the potential to recover La3+, and considerable application prospects in treating NH4+-N tailing water from ionic rare earth mines.
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Affiliation(s)
- Jingang Hu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Kai Wan
- Hubei Three Gorges Laboratory, Yichang 443007, China
| | - Xiangyi Deng
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xuemei Liu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yun Fang
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Fang Zhou
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Junxia Yu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Ruan Chi
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Three Gorges Laboratory, Yichang 443007, China
| | - Chunqiao Xiao
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Three Gorges Laboratory, Yichang 443007, China.
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ZOU S, LI N, ZHANG T, GENG Q. [Research Progress on Tumor Metabolic Biomarkers in Liquid Biopsy of Lung Cancer]. Zhongguo Fei Ai Za Zhi 2024; 27:126-132. [PMID: 38453444 PMCID: PMC10918242 DOI: 10.3779/j.issn.1009-3419.2023.106.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Indexed: 03/09/2024]
Abstract
Liquid biopsy is gradually being applied in the clinical diagnosis and treatment of lung cancer. At present, with the development of metabolomics, more and more metabolic biomarkers are considered as potential sensitive markers reflecting the occurrence and development of tumors. This article summarizes the changes in the main metabolic pathways of lung cancer, including glucose metabolism, amino acid metabolism, lipid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and purine metabolism. Meanwhile, this article reviews the role of metabolic biomarkers in the early diagnosis of lung cancer, predicting disease progression, and evaluating the efficacy of chemotherapy and immunotherapy, aiming to provide effective biomarkers for tumor diagnosis and treatment.
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Rana B, Chandola R, Sanwal P, Joshi GK. Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing. Sci Rep 2024; 14:4031. [PMID: 38369518 PMCID: PMC10874962 DOI: 10.1038/s41598-024-53350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.
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Affiliation(s)
- Babita Rana
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Renu Chandola
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Pankaj Sanwal
- Department of Biochemical Engineering, BTKIT, Dwarahat, Uttarakhand, India
| | - Gopal Krishna Joshi
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India.
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47
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Watanabe T, Kimura Y, Umeno D. MetJ-Based Mutually Interfering SAM-ON/SAM-OFF Biosensors. ACS Synth Biol 2024; 13:624-633. [PMID: 38286030 DOI: 10.1021/acssynbio.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
SAM (S-adenosylmethionine) is an important metabolite that operates as a major donor of methyl groups and is a controller of various physiological processes. Its availability is also believed to be a major bottleneck in the biological production of numerous high-value metabolites. Here, we constructed SAM-sensing systems using MetJ, an SAM-dependent transcriptional regulator, as a core component. SAM is a corepressor of MetJ, which suppresses the MetJ promoter with an increasing cellular concentration of SAM (SAM-OFF sensor). The application of transcriptional interference and evolutionary tuning effectively inverted its response, yielding a SAM-ON sensor (signal increases with increasing SAM concentration). By linking two genes encoding fluorescent protein reporters in such a way that their transcription events interfere with each other's and by placing one of them under the control of MetJ, we could increase the effective signal-to-noise ratio of the SAM sensor while decreasing the batch-to-batch deviation in signal output, likely by canceling out the growth-associated fluctuation in translational resources. By taking the ratio of SAM-ON/SAM-OFF signals and by resetting the default pool size of SAM, we could rapidly identify SAM synthetase (MetK) mutants with increased cellular activity from a random library. The strategy described herein should be widely applicable for identifying activity mutants, which would be otherwise overlooked because of the strong homeostasis of metabolic networks.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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48
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Abooshahab R, Razavi F, Ghorbani F, Hooshmand K, Zarkesh M, Hedayati M. Thyroid cancer cell metabolism: A glance into cell culture system-based metabolomics approaches. Exp Cell Res 2024; 435:113936. [PMID: 38278284 DOI: 10.1016/j.yexcr.2024.113936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Thyroid cancer is the most common malignancy of the endocrine system and the seventh most prevalent cancer in women worldwide. It is a complex and diverse disease characterized by heterogeneity, underscoring the importance of understanding the underlying metabolic alterations within tumor cells. Metabolomics technologies offer a powerful toolset to explore and identify endogenous and exogenous biochemical reaction products, providing crucial insights into the intricate metabolic pathways and processes within living cells. Metabolism plays a central role in cell function, making metabolomics a valuable reflection of a cell's phenotype. In the OMICs era, metabolomics analysis of cells brings numerous advantages over existing methods, propelling cell metabolomics as an emerging field with vast potential for investigating metabolic pathways and their perturbation in pathophysiological conditions. This review article aims to look into recent developments in applying metabolomics for characterizing and interpreting the cellular metabolome in thyroid cancer cell lines, exploring their unique metabolic characteristics. Understanding the metabolic alterations in tumor cells can lead to the identification of critical nodes in the metabolic network that could be targeted for therapeutic intervention.
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Affiliation(s)
- Raziyeh Abooshahab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Curtin Medical School, Curtin University, Bentley 6102, Australia
| | - Fatemeh Razavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ghorbani
- Department of Molecular Immunology, Ruhr University Bochum, Bochum, Germany
| | | | - Maryam Zarkesh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Páez-Watson T, van Loosdrecht MCM, Wahl SA. From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake. Water Res 2024; 250:121028. [PMID: 38128304 DOI: 10.1016/j.watres.2023.121028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.
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Affiliation(s)
- Timothy Páez-Watson
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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Yang M, Du D, Zhu F, Qin H. Metabolic network and proteomic expression perturbed by cyclosporine A to model microbe Escherichia coli. J Hazard Mater 2024; 464:132975. [PMID: 38044020 DOI: 10.1016/j.jhazmat.2023.132975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]
Abstract
Cyclosporine A (CsA) is a model drug that has caused great concern due to its widespread use and abuse in the environment. However, the potential harm of CsA to organisms also remains largely unknown, and this issue is exceptionally important for the health risk assessment of antibiotics. To address this concern, the crosstalk between CsA stress and cellular metabolism at the proteomic level in Escherichia coli was investigated and dissected in this study. The results showed that CsA inhibited E. coli growth in a time-dependent manner. CsA induced reactive oxygen species (ROS) overproduction in a dose- and time-dependent manner, leading to membrane depolarization followed by cell apoptosis. In addition, translation, the citric acid cycle, amino acid biosynthesis, glycolysis and responses to oxidative stress and heat were the central metabolic pathways induced by CsA stress. The upregulated proteins, including PotD, PotF and PotG, controlled cell growth. The downregulated proteins, including SspA, SspB, CstA and DpS, were regulators of self-feedback during the starvation process. And the up- and downregulated proteins, including AtpD, Adk, GroS, GroL and DnaK, controlled energy production. These results provide an important reference for the environmental health risk assessment of CsA.
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Affiliation(s)
- Meng Yang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daolin Du
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fang Zhu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Huaming Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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