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Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Biomark Res 2024; 12:107. [PMID: 39294728 DOI: 10.1186/s40364-024-00654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/10/2024] [Indexed: 09/21/2024] Open
Abstract
As one of the most common tumors in women, the pathogenesis and tumor heterogeneity of breast cancer have long been the focal point of research, with the emergence of tumor metastasis and drug resistance posing persistent clinical challenges. The emergence of single-cell sequencing (SCS) technology has introduced novel approaches for gaining comprehensive insights into the biological behavior of malignant tumors. SCS is a high-throughput technology that has rapidly developed in the past decade, providing high-throughput molecular insights at the individual cell level. Furthermore, the advent of multitemporal point sampling and spatial omics also greatly enhances our understanding of cellular dynamics at both temporal and spatial levels. The paper provides a comprehensive overview of the historical development of SCS, and highlights the most recent advancements in utilizing SCS and spatial omics for breast cancer research. The findings from these studies will serve as valuable references for future advancements in basic research, clinical diagnosis, and treatment of breast cancer.
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Affiliation(s)
- Xin Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xin Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Dong Z, Su R, Fu Y, Wang Y, Chang L. Recent Progress in DNA Biosensors for Detecting Biomarkers in Living Cells. ACS Biomater Sci Eng 2024; 10:5595-5608. [PMID: 39143919 DOI: 10.1021/acsbiomaterials.4c01339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Analysis of biomarkers in living cells is crucial for deciphering the dynamics of cells as well as for precise diagnosis of diseases. DNA biosensors employ DNA sequences as probes to offer insights into living cells, and drive progress in disease diagnosis and drug development. In this review, we present recent advances in DNA biosensors for detecting biomarkers in living cells. The basic structural components of DNA biosensors and the signal output method are presented. The strategies of DNA biosensors crossing the cell membrane are also described, including coincubation, nanocarriers, and nanoelectroporation techniques. Based on biomarker categorization, we detail recent applications of DNA biosensors for detecting small molecules, RNAs, proteins, and integrated targets in living cells. Furthermore, the future development directions of DNA biosensors are summarized to encourage further research in this growing field.
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Affiliation(s)
- Zaizai Dong
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Rongtai Su
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yao Fu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Yupei Wang
- Gansu Provincial Maternity and Child-Care Hospital (Gansu Provincial Central Hospital), Lanzhou 730050, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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Zhang YM, Li T, Xu CC, Qian JY, Guo H, Zhang X, Zhan ZJ, Lu JJ. Uncover the anticancer potential of lycorine. Chin Med 2024; 19:121. [PMID: 39245716 PMCID: PMC11382518 DOI: 10.1186/s13020-024-00989-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Natural products have a long history in drug discovery. Lycorine is an alkaloid derived from Amaryllidaceae plants, demonstrating significant pharmacological potential. Lycorine and its hydrochloride salt, lycorine hydrochloride, have shown outstanding anticancer effects both in vitro and in vivo. PURPOSE This review aims to comprehensively summarize recent research advancements regarding the anticancer potential of lycorine and lycorine hydrochloride. It intends to elucidate current research limitations, optimization strategies, and future research directions to guide clinical translation. METHODS Various databases, e.g., Web of Science, PubMed, and Chinese National Knowledge Infrastructure, are systematically searched for relevant articles using keywords such as lycorine, cancer, pharmacokinetics, and toxicity. The retrieved literature is then categorized and summarized to provide an overview of the research advancements in the anticancer potential of lycorine and lycorine hydrochloride. RESULTS Lycorine and lycorine hydrochloride demonstrate significant anticancer activities against various types of cancer both in vitro and in vivo, employing diverse mechanisms such as inducing cell cycle arrest, triggering cellular senescence, regulating programmed cell death, inhibiting angiogenesis, suppressing metastasis, and modulating immune system. Furthermore, pharmacokinetic profiles and toxicity data are summarized. Additionally, this review discusses the druggability, limitations, optimization strategies, and target identification of lycorine, offering insights for future preclinical studies. CONCLUSION The anticancer effects and safety profile of lycorine and lycorine hydrochloride suggest promising potential for clinical applications. Further research on their in-depth mechanisms and optimization strategies targeting their limitations will enhance the understanding and druggability of lycorine and lycorine hydrochloride.
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Affiliation(s)
- Yan-Ming Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao SAR, 999078, China
| | - Chun-Cao Xu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
| | - Jia-Yu Qian
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hongwei Guo
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China.
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao SAR, 999078, China.
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China.
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4
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Hao Y, Hao Z, Zeng X, Lin Y. Gut microbiota and metabolites of cirrhotic portal hypertension: a novel target on the therapeutic regulation. J Gastroenterol 2024; 59:788-797. [PMID: 39028343 DOI: 10.1007/s00535-024-02134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/06/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The regulatory role of gut microbiota and gut-derived metabolites through the gut-liver axis in the development of cirrhotic portal hypertension (PH) has received increasing attention. METHODS The review summarized a series of investigations on effects of metabolites derived from microbiota and medicines targeting microbiome including rifaximin, VSL#3, statins, propranolol, FXR agonists as well as drugs derived from bile acids (BAs) on PH progression. RESULTS Patients with PH exhibit alterations in gut microbial richness and differential overall microbiota community, and several results clearly displayed the correlation of PH with enrichment of Veillonella dispar or depletion of Clostridiales, Peptostreptococcaceae, Alistipes putredinis, Roseburia faecis and Clostridium cluster IV. The gut-derived metabolites including hydrogen sulfide, tryptophan metabolites, butyric acid, secondary BAs and phenylacetic acid (PAA) participate in a range of pathophysiology process of PH through modulating intrahepatic vascular resistance and portal blood flow associated with the formation and progression of PH. Established and emerging drugs targeting on bacterial translocation and intestinal eubiosis are gradually identified as potential strategies for treatments of liver cirrhosis and PH by modulating intestinal inflammation, splanchnic arterial vasodilation and endothelial dysfunction. CONCLUSIONS Future explorations should further characterize the alteration of the fecal microbiome and metabolite profiles in PH and elucidate the regulatory mechanism of the intestinal microbiome, gut-derived metabolites and gut microbiota targeted pharmaceutical treatments involved in PH.
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Affiliation(s)
- Yarong Hao
- Department of Gastroenterology, Shanghai Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Zhiyuan Hao
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Xin Zeng
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China.
| | - Yong Lin
- Department of Gastroenterology, Shanghai Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China.
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Dong W, Lu J, Li Y, Zeng J, Du X, Yu A, Zhao X, Chi F, Xi Z, Cao S. SIRT1: a novel regulator in colorectal cancer. Biomed Pharmacother 2024; 178:117176. [PMID: 39059350 DOI: 10.1016/j.biopha.2024.117176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/08/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024] Open
Abstract
The class-III histone deacetylase SIRT1 is the most extensively investigated sirtuin deacetylase. It is resistant to the broad deacetylase inhibitor trichostatin A and depends on oxidized nicotinamide adenine nucleotide (NAD+). SIRT1 plays a crucial role in the tumorigenesis of numerous types of cancers, including colorectal cancer (CRC). Accumulating evidence indicates that SIRT1 is a therapeutic target for CRC; however, the function and underlying mechanism of SIRT1 in CRC still need to be elucidated. Herein, we provide a detailed and updated review to illustrate that SIRT1 regulates many processes that go awry in CRC cells, such as apoptosis, autophagy, proliferation, migration, invasion, metastasis, oxidative stress, resistance to chemo-radio therapy, immune evasion, and metabolic reprogramming. Moreover, we closely link our review to the clinical practice of CRC treatment, summarizing the mechanisms and prospects of SIRT1 inhibitors in CRC therapy. SIRT1 inhibitors as monotherapy in CRC or in combination with chemotherapy, radiotherapy, and immune therapies are comprehensively discussed. From epigenetic regulation to its potential therapeutic effect, we hope to offer novel insights and a comprehensive understanding of SIRT1's role in CRC.
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Affiliation(s)
- Weiwei Dong
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - Jinjing Lu
- Department of Health Management, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - You Li
- Nursing Department, Liaoning Jinqiu Hospital, Shenyang, Liaoning Province 110016, China
| | - Juan Zeng
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - Xiaoyun Du
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - Ao Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - Xuechan Zhao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China
| | - Feng Chi
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China.
| | - Zhuo Xi
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China.
| | - Shuo Cao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province 110004, China.
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6
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Pitti E, Vanni D, Viceconte N, Lembo A, Tanzilli G, Raparelli V, Petrella G, Cicero DO. Metabolic Crosstalk in Multimorbidity: Identifying Compensatory Effects Among Diabetes, Hypertension, and Dyslipidemia. J Endocr Soc 2024; 8:bvae152. [PMID: 39262573 PMCID: PMC11388003 DOI: 10.1210/jendso/bvae152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Indexed: 09/13/2024] Open
Abstract
Context Metabolomics is becoming increasingly popular for detecting markers that indicate the presence of a specific disease. However, it is usually applied to studying individual ailments, yielding results that may not be directly relevant to people with multiple health conditions. Objective Our study proposes a different approach to explore metabolic crosstalk between various disease states. Design Setting and Patients We conducted a study on subjects at medium to high risk of developing coronary artery disease. We measured the plasma levels of 83 metabolites using nuclear magnetic resonance and analyzed the connections between these metabolites and various risk factors such as diabetes, hypertension, and dyslipidemia. Linear regression and multivariate analysis were combined for this purpose. Results Inspection of the metabolic maps created by our analysis helped us efficiently compare profiles. In this way, it was possible to discover opposing metabolic features among single conditions and their combination. Furthermore, we found compensating metabolic effects between diabetes, hypertension, and dyslipidemia involving mainly ketone body metabolism and fatty acid β-oxidation. Conclusion Our study introduces a novel approach to investigating how metabolism reacts to the simultaneous presence of multiple health conditions. This has allowed the detection of potential compensatory effects between diabetes, hypertension, and dyslipidemia, highlighting the complexity of metabolic crosstalk in patients with comorbidities. A better understanding of metabolic crosstalk like this could aid in developing focused treatments, resulting in improved therapeutic results.
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Affiliation(s)
- Erica Pitti
- Department of Chemical Science and Technology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Domitilla Vanni
- Department of Chemical Science and Technology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Nicola Viceconte
- Department of Cardiovascular, Respiratory, Nephrological, Anesthesiologic and Geriatric Sciences, Sapienza University of Rome, Policlinic Umberto I, 00161 Rome, Italy
| | - Angelo Lembo
- Department of Chemical Science and Technology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Gaetano Tanzilli
- Department of Cardiovascular, Respiratory, Nephrological, Anesthesiologic and Geriatric Sciences, Sapienza University of Rome, Policlinic Umberto I, 00161 Rome, Italy
| | - Valeria Raparelli
- Department of Translational and Precision Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Greta Petrella
- Department of Chemical Science and Technology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Daniel O Cicero
- Department of Chemical Science and Technology, University of Rome "Tor Vergata," 00133 Rome, Italy
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Bhandari D, Adepu KK, Anishkin A, Kay CD, Young EE, Baumbauer KM, Ghosh A, Chintapalli SV. Unraveling Protein-Metabolite Interactions in Precision Nutrition: A Case Study of Blueberry-Derived Metabolites Using Advanced Computational Methods. Metabolites 2024; 14:430. [PMID: 39195526 DOI: 10.3390/metabo14080430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Metabolomics, the study of small-molecule metabolites within biological systems, has become a potent instrument for understanding cellular processes. Despite its profound insights into health, disease, and drug development, identifying the protein partners for metabolites, especially dietary phytochemicals, remains challenging. In the present study, we introduced an innovative in silico, structure-based target prediction approach to efficiently predict protein targets for metabolites. We analyzed 27 blood serum metabolites from nutrition intervention studies' blueberry-rich diets, known for their health benefits, yet with elusive mechanisms of action. Our findings reveal that blueberry-derived metabolites predominantly interact with Carbonic Anhydrase (CA) family proteins, which are crucial in acid-base regulation, respiration, fluid balance, bone metabolism, neurotransmission, and specific aspects of cellular metabolism. Molecular docking showed that these metabolites bind to a common pocket on CA proteins, with binding energies ranging from -5.0 kcal/mol to -9.0 kcal/mol. Further molecular dynamics (MD) simulations confirmed the stable binding of metabolites near the Zn binding site, consistent with known compound interactions. These results highlight the potential health benefits of blueberry metabolites through interaction with CA proteins.
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Affiliation(s)
| | - Kiran Kumar Adepu
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colin D Kay
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Erin E Young
- KU Medical Center, Department of Anesthesiology, Pain and Perioperative Medicine, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Kyle M Baumbauer
- KU Medical Center, Department of Anesthesiology, Pain and Perioperative Medicine, University of Kansas School of Medicine, Kansas City, KS 66160, USA
- KU Medical Center, Department of Cell Biology and Physiology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Anuradha Ghosh
- Department of Environmental Health, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Luo J, Guo M, Xie K, Han TL, Ai S. Metabolomic analysis of Agkistrodon haly venom poisoning mouse treatment by Jidesheng snake pill based on GC-MS. Front Pharmacol 2024; 15:1419609. [PMID: 39148553 PMCID: PMC11324443 DOI: 10.3389/fphar.2024.1419609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/10/2024] [Indexed: 08/17/2024] Open
Abstract
Introduction Snakebites are acute systemic toxic diseases caused by snake venom entering the body through wounds. Failure to use antivenom immediately and difficulty in obtaining antivenoms are frequently responsible for worsening disease. Traditional Chinese medicine is commonly used to supplement and replace antivenom in treating snakebites. The Jidesheng snake pill (JDS) is a widely used traditional Chinese medicine that has achieved good clinical therapeutic effects; however, its mechanism remains unclear. Therefore, metabolomics techniques were employed to explore the pathophysiological mechanisms of JDS treatment of Agkistrodon halys (Ah) snake venom-poisoned mice. Methods The Ah group mouse model was established by intramuscular injection of Ah venom into the hind legs of the mice. The Ah venom + JDS group model was established using JDS after the affected area was treated with Ah venom. Hematoxylin and eosin (HE) staining was used to evaluate the severity of gastrocnemius injury. Quantitative polymerase chain reaction (qPCR) was utilized to detect the mRNA expression of vascular cell adhesion molecule-1 (VCAM-1), muscle-specific creatine kinase (CKM), thrombin antithrombin complex (TAT), and tumor necrosis factor-alpha (TNF-α). Gas chromatography-mass spectrometry (GC-MS) was performed with multivariate statistical analysis to provide new insights into the global metabolic profile of Ah venom-poisoned mice. Results HE staining revealed increased red cell necrosis, local hemorrhage, and neutrophil infiltration in the Ah venom group than in the control group. Several compounds were identified, including lipids, amino acids, peptides, and organooxygen. Eighty differential metabolites were screened between the control group and the Ah venom group, and 24 were screened between the Ah venom and JDS groups. The mechanism of Ah venom poisoning in mice may involve aminoacyl-tRNA biosynthesis, various amino acid metabolism disorders, tricarboxylic acid circulation disorders, and abnormal fatty acid metabolism. JDS may reduce symptoms by affecting long-chain fatty acid and amino acid metabolism and promoting nicotinamide-nicotinamide metabolism. Conclusion Our results suggest that metabolomics has huge prospects for elucidating the pathophysiology of Agkistrodon haly venom poisoning and therapeutic mechanisms of JDS.
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Affiliation(s)
- Jie Luo
- Emergency Department, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing, China
| | - Minkang Guo
- Department of Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ke Xie
- Department of Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ting-Li Han
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, Chongqing, China
| | - Shanmu Ai
- Emergency Department, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing, China
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Mayers JR, Varon J, Zhou RR, Daniel-Ivad M, Beaulieu C, Bhosle A, Glasser NR, Lichtenauer FM, Ng J, Vera MP, Huttenhower C, Perrella MA, Clish CB, Zhao SD, Baron RM, Balskus EP. A metabolomics pipeline highlights microbial metabolism in bloodstream infections. Cell 2024; 187:4095-4112.e21. [PMID: 38885650 PMCID: PMC11283678 DOI: 10.1016/j.cell.2024.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024]
Abstract
The growth of antimicrobial resistance (AMR) highlights an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe infections profoundly alter host metabolism, prior studies have largely ignored microbial metabolism in this context. Here, we describe an iterative, comparative metabolomics pipeline to uncover microbial metabolic features in the complex setting of a host and apply it to investigate gram-negative bloodstream infection (BSI) in patients. We find elevated levels of bacterially derived acetylated polyamines during BSI and discover the enzyme responsible for their production (SpeG). Blocking SpeG activity reduces bacterial proliferation and slows pathogenesis. Reduction of SpeG activity also enhances bacterial membrane permeability and increases intracellular antibiotic accumulation, allowing us to overcome AMR in culture and in vivo. This study highlights how tools to study pathogen metabolism in the natural context of infection can reveal and prioritize therapeutic strategies for addressing challenging infections.
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Affiliation(s)
- Jared R Mayers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Ruixuan R Zhou
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA
| | - Martin Daniel-Ivad
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Amrisha Bhosle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Julie Ng
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Mayra Pinilla Vera
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sihai D Zhao
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA
| | - Rebecca M Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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10
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Keshari KR, Heller DA, Boltyanskiy R, Hricak H, Magaldi T, Overholtzer M. Engineering focusing on cancer. Cancer Cell 2024; 42:1138-1141. [PMID: 38848719 DOI: 10.1016/j.ccell.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024]
Abstract
While cancer research and care have benefited from revolutionary advances in the ability to manipulate and study living systems, the field is limited by a lack of synergy to leverage the power of engineering approaches. Cancer engineering is an emerging subfield of biomedical engineering that unifies engineering and cancer biology to better understand, diagnose, and treat cancer. We highlight cancer engineering's unique challenges, the importance of creating dedicated centers and departments that enable translational collaboration, and educational approaches to arm a new generation of scientists with engineering expertise and a fundamental understanding of cancer biology to transform clinical cancer care.
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Affiliation(s)
- Kayvan R Keshari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering School for Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Imaging and Bioengineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Daniel A Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering School for Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Imaging and Bioengineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Rostislav Boltyanskiy
- Center for Molecular Imaging and Bioengineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hedvig Hricak
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering School for Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Imaging and Bioengineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas Magaldi
- Gerstner Sloan Kettering School for Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Overholtzer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering School for Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Imaging and Bioengineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Xie R, Lin J, Li W, Chen H, Zhang J, Zhong M, Xue J, Mo C, Chen L, Zhu Y, Chen X, Xu S. Homogentisic acid metabolism inhibits papillary thyroid carcinoma proliferation through ROS and p21-induced cell cycle arrest. Life Sci 2024; 347:122682. [PMID: 38702025 DOI: 10.1016/j.lfs.2024.122682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Thyroid cancer is one of the most common primary endocrine malignancies worldwide, and papillary thyroid carcinoma (PTC) is the predominant histological type observed therein. Although PTC has been studied extensively, our understanding of the altered metabolism and metabolic profile of PTC tumors is limited. We identified that the content of metabolite homogentisic acid (HGA) in PTC tissues was lower than that in adjacent non-cancerous tissues. We evaluated the potential of HGA as a novel molecular marker in the diagnosis of PTC tumors, as well as its ability to indicate the degree of malignancy. Studies have further shown that HGA contributes to reactive oxygen species (ROS) associated oxidative stress, leading to toxicity and inhibition of proliferation. In addition, HGA caused an increase in p21 expression levels in PTC cells and induced G1 arrest. Moreover, we found that the low HGA content in PTC tumors was due to the low expression levels of tyrosine aminotransferase (TAT) and p-hydroxyphenylpyruvate hydroxylase (HPD), which catalyze the conversion of tyrosine to HGA. The low expression levels of TAT and HPD are strongly associated with a higher probability of PTC tumor invasion and metastasis. Our study demonstrates that HGA could be used to diagnose PTC and provides mechanisms linking altered HGA levels to the biological behavior of PTC tumors.
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Affiliation(s)
- Ruiwang Xie
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Junyu Lin
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Weiwei Li
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Huaying Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Junsi Zhang
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Minjie Zhong
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Jiajie Xue
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Caiqin Mo
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Ling Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Youzhi Zhu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China; Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China.
| | - Xiangjin Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China; Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China.
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China; Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China; Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Fuzhou, China.
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12
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Hilovsky D, Hartsell J, Young JD, Liu X. Stable Isotope Tracing Analysis in Cancer Research: Advancements and Challenges in Identifying Dysregulated Cancer Metabolism and Treatment Strategies. Metabolites 2024; 14:318. [PMID: 38921453 PMCID: PMC11205609 DOI: 10.3390/metabo14060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer, driving the development of therapies targeting cancer metabolism. Stable isotope tracing has emerged as a widely adopted tool for monitoring cancer metabolism both in vitro and in vivo. Advances in instrumentation and the development of new tracers, metabolite databases, and data analysis tools have expanded the scope of cancer metabolism studies across these scales. In this review, we explore the latest advancements in metabolic analysis, spanning from experimental design in stable isotope-labeling metabolomics to sophisticated data analysis techniques. We highlight successful applications in cancer research, particularly focusing on ongoing clinical trials utilizing stable isotope tracing to characterize disease progression, treatment responses, and potential mechanisms of resistance to anticancer therapies. Furthermore, we outline key challenges and discuss potential strategies to address them, aiming to enhance our understanding of the biochemical basis of cancer metabolism.
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Affiliation(s)
- Dalton Hilovsky
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Joshua Hartsell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37212, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
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13
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Lin C, Tian Q, Guo S, Xie D, Cai Y, Wang Z, Chu H, Qiu S, Tang S, Zhang A. Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification. Molecules 2024; 29:2198. [PMID: 38792060 PMCID: PMC11124072 DOI: 10.3390/molecules29102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.
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Affiliation(s)
- Chunsheng Lin
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
| | - Qianqian Tian
- Faculty of Social Sciences, The University of Hong Kong, Hong Kong 999077, China;
| | - Sifan Guo
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Dandan Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Ying Cai
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Zhibo Wang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Hang Chu
- Department of Biomedical Sciences, Beijing City University, Beijing 100193, China;
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Aihua Zhang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
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14
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Jin X, Liu L, Liu D, Wu J, Wang C, Wang S, Wang F, Yu G, Jin X, Xue YW, Jiang D, Ni Y, Yang X, Wang MS, Wang ZW, Orlov YL, Jia W, Melino G, Liu JB, Chen WL. Unveiling the methionine cycle: a key metabolic signature and NR4A2 as a methionine-responsive oncogene in esophageal squamous cell carcinoma. Cell Death Differ 2024; 31:558-573. [PMID: 38570607 PMCID: PMC11094133 DOI: 10.1038/s41418-024-01285-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a deadly malignancy with notable metabolic reprogramming, yet the pivotal metabolic feature driving ESCC progression remains elusive. Here, we show that methionine cycle exhibits robust activation in ESCC and is reversely associated with patient survival. ESCC cells readily harness exogenous methionine to generate S-adenosyl-methionine (SAM), thus promoting cell proliferation. Mechanistically, methionine augments METTL3-mediated RNA m6A methylation through SAM and revises gene expression. Integrative omics analysis highlights the potent influence of methionine/SAM on NR4A2 expression in a tumor-specific manner, mediated by the IGF2BP2-dependent stabilization of methylated NR4A2 mRNA. We demonstrate that NR4A2 facilitates ESCC growth and negatively impacts patient survival. We further identify celecoxib as an effective inhibitor of NR4A2, offering promise as a new anti-ESCC agent. In summary, our findings underscore the active methionine cycle as a critical metabolic characteristic in ESCC, and pinpoint NR4A2 as a novel methionine-responsive oncogene, thereby presenting a compelling target potentially superior to methionine restriction.
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Affiliation(s)
- Xing Jin
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Lei Liu
- Department of Thoracic Surgery, The Affiliated Tumor Hospital of Nantong University, Nantong, 226300, China
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Dan Liu
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Jia Wu
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Congcong Wang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Siliang Wang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Fengying Wang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China
| | - Guanzhen Yu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
- Laboratory of Digital Health and Artificial Intelligence, Zhejiang Digital Content Research Institute, Shaoxing, 312000, China
| | - Xiaoxia Jin
- Department of Pathology, The Affiliated Tumor Hospital of Nantong University, Nantong, 226300, China
| | - Yu-Wen Xue
- Pathology department, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Dan Jiang
- Pathology department, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yan Ni
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310029, China
| | - Xi Yang
- Department of Oncology, Shanxi Provincial Hospital of Traditional Chinese Medicine, Shanxi, 030001, China
| | - Ming-Song Wang
- Department of Thoracic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Zhi-Wei Wang
- Department of Breast, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, 119991, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Life Sciences Department, Novosibirsk State University, Novosibirsk, 630090, Russia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, 690922, Russia
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow, 117198, Russia
| | - Wei Jia
- Department of Pharmacology and Pharmacy, Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Gerry Melino
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Ji-Bin Liu
- Cancer Institute, The Affiliated Tumor Hospital of Nantong University, Nantong, 226361, China
| | - Wen-Lian Chen
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, 200032, China.
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Dong X, Qu Y, Sheng T, Fan Y, Chen S, Yuan Q, Ma G, Ge Y. HCMMD: systematic evaluation of metabolites in body fluids as liquid biopsy biomarker for human cancers. Aging (Albany NY) 2024; 16:7487-7504. [PMID: 38683118 PMCID: PMC11087094 DOI: 10.18632/aging.205779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 05/01/2024]
Abstract
Metabolomics is a rapidly expanding field in systems biology used to measure alterations of metabolites and identify metabolic biomarkers in response to disease processes. The discovery of metabolic biomarkers can improve early diagnosis, prognostic prediction, and therapeutic intervention for cancers. However, there are currently no databases that provide a comprehensive evaluation of the relationship between metabolites and cancer processes. In this review, we summarize reported metabolites in body fluids across pan-cancers and characterize their clinical applications in liquid biopsy. We conducted a search for metabolic biomarkers using the keywords ("metabolomics" OR "metabolite") AND "cancer" in PubMed. Of the 22,254 articles retrieved, 792 were deemed potentially relevant for further review. Ultimately, we included data from 573,300 samples and 17,083 metabolic biomarkers. We collected information on cancer types, sample size, the human metabolome database (HMDB) ID, metabolic pathway, area under the curve (AUC), sensitivity and specificity of metabolites, sample source, detection method, and clinical features were collected. Finally, we developed a user-friendly online database, the Human Cancer Metabolic Markers Database (HCMMD), which allows users to query, browse, and download metabolite information. In conclusion, HCMMD provides an important resource to assist researchers in reviewing metabolic biomarkers for diagnosis and progression of cancers.
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Affiliation(s)
- Xun Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yaoyao Qu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tongtong Sheng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanming Fan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Silu Chen
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinbo Yuan
- Department of Urology, Wuxi Fifth People’s Hospital, Wuxi, China
| | - Gaoxiang Ma
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- The Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, China
- Deparment of Oncology, Pukou Hospital of Chinese Medicine affiliated to China Pharmaceutical University, Nanjing, China
| | - Yuqiu Ge
- Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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Wen S, Lin X, Luo W, Pan Y, Liao F, Wang Z, Zhan B, Feng J, Huang H. Metabolic difference between patient-derived xenograft model of pancreatic ductal adenocarcinoma and corresponding primary tumor. BMC Cancer 2024; 24:485. [PMID: 38632504 PMCID: PMC11022326 DOI: 10.1186/s12885-024-12193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Patients-derived xenograft (PDX) model have been widely used for tumor biological and pathological studies. However, the metabolic similarity of PDX tumor to the primary cancer (PC) is still unknown. METHODS In present study, we established PDX model by engrafting primary tumor of pancreatic ductal adenocarcinoma (PDAC), and then compared the tumor metabolomics of PC, the first generation of PDX tumor (PDXG1), and the third generation of PDX tumor (PDXG3) by using 1H NMR spectroscopy. Then, we assessed the differences in response to chemotherapy between PDXG1 and PDXG3 and corresponding metabolomic differences in drug-resistant tumor tissues. To evaluate the metabolomic similarity of PDX to PC, we also compared the metabolomic difference of cell-derived xenograft (CDX) vs. PC and PDX vs. PC. RESULTS After engraftment, PDXG1 tumor had a low level of lactate, pyruvate, citrate and multiple amino acids (AAs) compared with PC. Metabolite sets enrichment and metabolic pathway analyses implied that glycolysis metabolisms were suppressed in PDXG1 tumor, and tricarboxylic acid cycle (TCA)-associated anaplerosis pathways, such as amino acids metabolisms, were enhanced. Then, after multiple passages of PDX, the altered glycolysis and TCA-associated anaplerosis pathways were partially recovered. Although no significant difference was observed in the response of PDXG1 and PDXG3 to chemotherapy, the difference in glycolysis and amino acids metabolism between PDXG1 and PDXG3 could still be maintained. In addition, the metabolomic difference between PC and CDX models were much larger than that of PDX model and PC, indicating that PDX model still retain more metabolic characteristics of primary tumor which is more suitable for tumor-associated metabolism research. CONCLUSIONS Compared with primary tumor, PDX models have obvious difference in metabolomic level. These findings can help us design in vivo tumor metabolomics research legitimately and analyze the underlying mechanism of tumor metabolic biology thoughtfully.
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Affiliation(s)
- Shi Wen
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Xianchao Lin
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Wei Luo
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Yu Pan
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Fei Liao
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Zhenzhao Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Bohan Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China.
| | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China.
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Wang C, Lou C, Yang Z, Shi J, Niu N. Plasma metabolomic analysis reveals the metabolic characteristics and potential diagnostic biomarkers of spinal tuberculosis. Heliyon 2024; 10:e27940. [PMID: 38571585 PMCID: PMC10987919 DOI: 10.1016/j.heliyon.2024.e27940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 02/16/2024] [Accepted: 03/08/2024] [Indexed: 04/05/2024] Open
Abstract
Objectives This study aimed to conduct a non-targeted metabolomic analysis of plasma from patients with spinal tuberculosis (STB) to systematically elucidate the metabolomic alterations associated with STB, and explore potential diagnostic biomarkers for STB. Methods From January 2020 to January 2022, 30 patients with spinal tuberculosis (STBs) clinically diagnosed at the General Hospital of Ningxia Medical University and 30 age- and sex-matched healthy controls (HCs) were selected for this study. Using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) based metabolomics, we analyzed the metabolic profiles of 60 plasma samples. Statistical analyses, pathway enrichment, and receiver operating characteristic (ROC) analyses were performed to screen and evaluate potential diagnostic biomarkers. Results Metabolomic profiling revealed distinct alterations between the STBs and HCs cohorts. A total of 1635 differential metabolites were screened, functionally clustered, and annotated. The results showed that the differential metabolites were enriched in sphingolipid metabolism, tuberculosis, cutin, suberine and wax biosynthesis, beta-alanine metabolism, methane metabolism, and other pathways. Through the random forest algorithm, LysoPE (18:1(11Z)/0:0), 8-Demethyl-8-formylriboflavin 5'-phosphate, Glutaminyl-Gamma-glutamate, (2R)-O-Phospho-3-sulfolactate, and LysoPE (P-16:0/0:0) were determined to have high independent diagnostic value. Conclusions STBs exhibited significantly altered metabolite profiles compared with HCs. Here, we provide a global metabolomic profile and identify potential diagnostic biomarkers of STB. Five potential independent diagnostic biomarkers with high diagnostic value were screened. This study provides novel insights into the pathogenesis, diagnosis, and treatment strategies of STB.
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Affiliation(s)
- Chaoran Wang
- Department of Orthopedics, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
- School of Clinical Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Caili Lou
- School of Clinical Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Zongqiang Yang
- Department of Orthopedics, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Jiandang Shi
- Department of Orthopedics, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Ningkui Niu
- Department of Orthopedics, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
- Research Center for Prevention and Control of Bone and Joint Tuberculosis, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
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18
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Ye J, Chen H, Wang Y, Chen H, Huang J, Yang Y, Feng Z, Li W. A preliminary metabolomics study of the database for biological samples of schizophrenia among Chinese ethnic minorities. BMC Psychiatry 2024; 24:262. [PMID: 38594695 PMCID: PMC11003042 DOI: 10.1186/s12888-024-05660-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Schizophrenia (SCZ) is a profound mental disorder with a multifactorial etiology, including genetics, environmental factors, and demographic influences such as ethnicity and geography. Among these, the studies of SCZ also shows racial and regional differences. METHODS We first established a database of biological samples for SCZ in China's ethnic minorities, followed by a serum metabolomic analysis of SCZ patients from various ethnic groups within the same region using the LC-HRMS platform. RESULTS Analysis identified 47 metabolites associated with SCZ, with 46 showing significant differences between Miao and Han SCZ patients. These metabolites, primarily fatty acids, amino acids, benzene, and derivatives, are involved in fatty acid metabolism pathways. Notably, L-Carnitine, L-Cystine, Aspartylphenylalanine, and Methionine sulfoxide demonstrated greater diagnostic efficacy in Miao SCZ patients compared to Han SCZ patients. CONCLUSION Preliminary findings suggest that there are differences in metabolic levels among SCZ patients of different ethnicities in the same region, offering insights for developing objective diagnostic or therapeutic monitoring strategies that incorporate ethnic considerations of SCZ.
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Affiliation(s)
- Jun Ye
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Haixia Chen
- Department of Clinical Biochemistry and Laboratory Medicine, Guizhou Medical University, 550001, Guizhou, China
| | - Yang Wang
- Shandong Yingsheng Biotechnology Co., Ltd., 250101, Jinan, Shandong, China
| | - Haini Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Jiang Huang
- Department of Psychiatry, The Second Affiliated Hospital of Guizhou Medical University, Kangfu Road, 556000, Guizhou, China
| | - Yixia Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Zhen Feng
- Shandong Yingsheng Biotechnology Co., Ltd., 250101, Jinan, Shandong, China.
| | - Wenfeng Li
- Department of Psychiatry, The Second Affiliated Hospital of Guizhou Medical University, Kangfu Road, 556000, Guizhou, China.
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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Wufuer R, Liu K, Feng J, Wang M, Hu S, Chen F, Lin S, Zhang Y. Distinct mechanisms by which Nrf1 and Nrf2 as drug targets contribute to the anticancer efficacy of cisplatin on hepatoma cells. Free Radic Biol Med 2024; 213:488-511. [PMID: 38278308 DOI: 10.1016/j.freeradbiomed.2024.01.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
Cisplatin (cis-Dichlorodiamineplatinum[II], CDDP) is generally accepted as a platinum-based alkylating agent type of the DNA-damaging anticancer drug, which is widely administrated in clinical treatment of many solid tumors. The pharmacological effect of CDDP is mainly achieved by replacing the chloride ion (Cl-) in its structure with H2O to form active substances with the strong electrophilic properties and then react with any nucleophilic molecules, primarily leading to genomic DNA damage and subsequent cell death. In this process, those target genes driven by the consensus electrophilic and/or antioxidant response elements (EpREs/AREs) in their promoter regions are also activated or repressed by CDDP. Thereby, we here examined the expression profiling of such genes regulated by two principal antioxidant transcription factors Nrf1 and Nrf2 (both encoded by Nfe2l1 and Nfe2l2, respectively) in diverse cellular signaling responses to this intervention. The results demonstrated distinct cellular metabolisms, molecular pathways and signaling response mechanisms by which Nrf1 and Nrf2 as the drug targets differentially contribute to the anticancer efficacy of CDDP on hepatoma cells and xenograft tumor mice. Interestingly, the role of Nrf1, rather than Nrf2, is required for the anticancer effect of CDDP, to suppress malignant behavior of HepG2 cells by differentially monitoring multi-hierarchical signaling to gene regulatory networks. To our surprise, it was found there exists a closer relationship of Nrf1α than Nrf2 with DNA repair, but the hyperactive Nrf2 in Nrf1α-∕- cells manifests a strong correlation with its resistance to CDDP, albeit their mechanistic details remain elusive.
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Affiliation(s)
- Reziyamu Wufuer
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Keli Liu
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Jing Feng
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China.
| | - Meng Wang
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Shaofan Hu
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Feilong Chen
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China.
| | - Shanshan Lin
- Bioengineering College and Graduate School, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China; Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Yiguo Zhang
- Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
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21
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Liu S, Liu X, Locasale JW. Quantification of metabolic activity from isotope tracing data using automated methodology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581907. [PMID: 38464003 PMCID: PMC10925140 DOI: 10.1101/2024.02.25.581907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Isotope tracing is a widely used technique to study metabolic activities by introducing heavy labeled nutrients into living cells and organisms. However, interpreting isotope tracing data is often heuristic, and application of automated methods using artificial intelligence is limited due to the paucity of evaluative knowledge. Our study developed a new pipeline that efficiently predicts metabolic activity in expansive metabolic networks and systematically quantifies flux uncertainty of traditional computational methods. We further developed an algorithm adept at significantly reducing this uncertainty, enabling robust evaluations of metabolic activity with limited data. Using this technology, we discovered highly reprogrammed mitochondria-cytosol exchange cycles in tumor tissue of patients, and observed similar metabolic patterns influenced by nutritional conditions in cancer cells. Thus, our refined methodology provides robust automated quantification of metabolism allowing for new insight into metabolic network activity.
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Affiliation(s)
- Shiyu Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham NC 27710, USA
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham NC 27710, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham NC 27710, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham NC 27710, USA
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham NC 27710, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
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Wang L, Chen X, Liu X, Miao H, Gong F, Yang H, Duan L, Zhu H, Sun W. Cerebrospinal Fluid Metabolomic Pattern of Different Pituitary Stalk Lesions. J Clin Endocrinol Metab 2024; 109:802-814. [PMID: 37769631 DOI: 10.1210/clinem/dgad559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE To describe the cerebrospinal fluid (CSF) metabolomic pattern of pituitary stalk lesions. METHODS CSF was collected from patients with different pituitary stalk lesions treated at Peking Union Medical College Hospital: germ cell tumor (GCT, n = 27); hypophysitis (n = 10); and Langerhans cell histiocytosis (LCH) or Erdheim-Chester disease (ECD) (LCH + ECD, n = 10). The CSF metabolome profiles were characterized by liquid chromatography-mass spectrometry (LC-MS). RESULTS There were 44 metabolites that significantly differed between patients with GCT and those with hypophysitis (P < .05). Between patients with GCT with CSF level of beta subunit of human chorionic gonadotrophin (β-hCG) < 5 mIU/mL and those with hypophysitis, there were 15 differential metabolites (P < .05, fold change > 1.5 or < 1/1.5). All of the metabolites had an area under the curve (AUC) above 0.7. There were 9 metabolites that significantly differed between patients with GCT and those with LCH + ECD (P < .05) and 7 metabolites had significant differences between GCT (CSF β-hCG < 5 mIU/mL) and LCH + ECD (P < .05, fold change > 1.5 or < 1/1.5). We found 6 metabolites that were significantly different between patients with hypophysitis and those with LCH + ECD (P < .05) and 5 of these had fold change more than 1.5 or less than 1/1.5. Three metabolites, 5-deoxydiplosporin, cloversaponin I, and phytosphingosine, showed excellent capabilities to differentiate the 3 disease categories. Furthermore, we identified 67 metabolites associated with clinical test results (ρ > 0.2, P < .05) and 29 metabolites showed strong correlation (ρ > 0.4, P < .05). CONCLUSION Our study is the first to systematically investigate the metabolomics of CSF in different pituitary stalk lesions. CSF metabolomics is a useful strategy for biomarker discovery.
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Affiliation(s)
- Linjie Wang
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Xiaoxue Chen
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoyan Liu
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100730, China
| | - Hui Miao
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Fengying Gong
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hongbo Yang
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Lian Duan
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Huijuan Zhu
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100730, China
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Dragic H, Chaveroux C, Cosset E, Manie SN. Modelling cancer metabolism in vitro: current improvements and future challenges. FEBS J 2024; 291:402-411. [PMID: 36516350 DOI: 10.1111/febs.16704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Advances in cancer biology over the past decades have revealed that metabolic adaptation of cancer cells is an essential aspect of tumorigenesis. However, recent insights into tumour metabolism in vivo have revealed dissimilarities with results obtained in vitro. This is partly due to the reductionism of in vitro cancer models that struggle to reproduce the complexity of tumour tissues. This review describes some of the discrepancies in cancer cell metabolism between in vitro and in vivo conditions, and presents current methodological approaches and tools used to bridge the gap with the clinically relevant microenvironment. As such, these approaches should generate new knowledge that could be more effectively translated into therapeutic opportunities.
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Affiliation(s)
- Helena Dragic
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Cedric Chaveroux
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Erika Cosset
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Serge N Manie
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
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24
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Chen J, Lu H, Cao D, Sun J, Qi F, Liu X, Liu J, Yang J, Yu M, Zhou H, Cheng N, Wang J, Zhang Y, Peng P, Wang T, Shen K, Sun W. Urine and serum metabolomic analysis of endometrial cancer diagnosis and classification based on ultra-performance liquid chromatography mass spectrometry. Metabolomics 2024; 20:18. [PMID: 38281200 DOI: 10.1007/s11306-023-02085-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
OBJECTIVE This study aimed to reveal the urinary and serum metabolic pattern of endometrial cancer (EC) and establish diagnostic models to identify EC from controls, high-risk from low-risk EC, and type II from type I EC. METHOD This study included 146 EC patients (comprising 79 low-risk and 67 high-risk patients, including 124 type I and 22 type II) and 59 controls. The serum and urine samples were analyzed using ultraperformance liquid chromatography mass spectrometry. Analysis was used to elucidate the distinct metabolites and altered metabolic pathways. Receiver operating characteristic (ROC) analyses were employed to discover and validate the potential biomarker models. RESULTS Serum and urine metabolomes displayed significant differences between EC and controls, with metabolites related to amino acid and nicotinamide metabolisms. The serum and urine panels distinguished these two groups with Area Under the Curve (AUC) of 0.821 and 0.902, respectively. The panel consisting of serum and urine metabolites demonstrated the best predictive ability (AUC = 0.953 and 0.976 in discovering and validation group). In comparing high-risk and low risk EC, differential metabolites were enriched in purine and glutamine metabolism. The AUC values for serum and urine panels were 0.818, and 0.843, respectively. The combined panel exhibited better predictive accuracy (0.881 in discovering group and 0.936 in external validation). In the comparison between type I and type II group, altered folic acid metabolism was identified. The serum, urine and combined panels discriminated these two groups with the AUC of 0.829, 0.913 and 0.922, respectively. CONCLUSION The combined urine and serum metabolome effectively revealed the metabolic patterns in EC patients, offering valuable diagnostic models for EC diagnosis and classification.
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Affiliation(s)
- Junyu Chen
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Hezhen Lu
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Jiameng Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Qi
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiaqi Liu
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiaxin Yang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mei Yu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huimei Zhou
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ninghai Cheng
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jinhui Wang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ying Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Peng Peng
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Wang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Keng Shen
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Sun
- China-Japan Union Hospital of Jilin University, Changchun, China.
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Pan B, Yang Y, Jiang Y, Xiao Q, Chen W, Wang J, Chen F, Yan S, Liu Y. Potential roles of HSYA in attenuating sepsis-induced liver injury through multi-omics analysis. J Pharm Biomed Anal 2024; 238:115801. [PMID: 37924577 DOI: 10.1016/j.jpba.2023.115801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023]
Abstract
Liver injury is a strong independent predictor of mortality in patients with sepsis, in which gut dysbiosis plays a crucial role. Hydroxyl safflower yellow A (HSYA), an important component of safflower, has been used to treat liver injury in animal models. However, its role in sepsis-induced liver dysfunction and the specific molecular mechanisms remain unclear. In the current study, we first discussed the discrepancy in the gut microbiota between the cecal ligation puncture (CLP) and HSYA groups using 16 S RNA sequencing. Our data demonstrated that HSYA supplementation significantly decreased the relative abundance of Proteobacteria, Firmicutes, and Campylobacterota, and further decreased the abundance of Bacteroidota, suggesting that the protective effects of HSYA against sepsis-induced liver injury may be partially attributed to the alteration of these bacteria. In addition, the metabolomic data identified 823 differentially expressed metabolites associated with sepsis-induced liver injury. After HSYA supplementation, the levels of 56 metabolites were restored to sham-like levels. Transcriptomic analysis revealed 4990 differentially expressed genes (DEGs) between the sham and CLP groups, and after HSYA injection, 1613 genes were modulated. Comprehensive analysis demonstrated that the enrichment pathways of the 903 DEGs mainly focused on inflammatory responses, amino acid metabolism, and Lipid reactions. In conclusion, our study revealed the potential mechanism of action of HSYA in sepsis-induced liver injury through a comprehensive analysis of 16 S RNA sequencing, metabolomics, and transcriptomics, thus providing a theoretical basis for further clinical applications of HSYA.
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Affiliation(s)
- Bingbing Pan
- Department of Anesthesiology, Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), China
| | - Ying Yang
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), China
| | - Yu Jiang
- Department of Emergency, Institute of Emergency Medicine, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University) Changsha, Hunan, China
| | - Qianyu Xiao
- Department of Anesthesiology, Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), China
| | - Wenyan Chen
- Department of Anesthesiology, Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), China
| | - Jia Wang
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), China
| | - Fang Chen
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), China
| | - Shifan Yan
- Department of Emergency, Institute of Emergency Medicine, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University) Changsha, Hunan, China; Hunan University of Chinese Medicine,Changsha, Hunan, China.
| | - Yanjuan Liu
- Department of Anesthesiology, Clinical Research Center for Anesthesiology of ERAS in Hunan Province, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), China; Department of Emergency, Institute of Emergency Medicine, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University) Changsha, Hunan, China.
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26
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Wilson ID, Broeckling C, Gethings LA, Munjoma NC, Trengove R, Rainville PD, Lai SK, Isaac G, Plumb RS. Development of a single mobile phase for LC-IM-MS-based discovery lipidomics and metabolic phenotyping: Application to methapyrilene hepatotoxicity in the rat. J Chromatogr A 2024; 1714:464552. [PMID: 38113579 DOI: 10.1016/j.chroma.2023.464552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The untargeted global profiling of endogenous metabolites and lipids has the potential to increase knowledge and understanding in many areas of biology. LC-MS/MS is a key technology for such analyses however, several different LC methodologies, using different mobile phase compositions, are required to cover the diversity in polarity and analyte structure encountered in biological samples. Most notably many lipid screening methods make use of isopropanol (IPA) as a major component of mobile phases employed for comprehensive lipidomic profiling. In order to increase laboratory efficiency, and minimize opportunities for errors, a suite of methods, based on a single acetonitrile (ACN)-aqueous buffer mobile phase combination, has been developed. This mobile phase can be used for hydrophobic interaction liquid chromatography on an amide stationary phase (for polar analytes), reversed-phase (RP) LC analysis on a C8 stationary phase (for moderately polar-non-polar compounds) and RPLC using a CSH phenyl-hexyl bonded column (for lipids). All of these sub 10 minute separations had good throughput and reproducibility with CV's of analyte response <25 % whilst eliminating the need for complex mobile phase preparation and the use of IPA as an organic modifier for lipidomics. Advantages of removing IPA and replacing it with the ACN-based method were a 58 % increase in peak capacity for lipids, with improved resolution for the di- and triglycerides and cholesterol esters compared to current methods. Compared to the IPA-containing solvent system the ACN-based mobile phase also resulted in a 61 % increase in lipid feature detection. The utility of this "universal" mobile phase approach was demonstrated by its application to a rat toxicology study investigating the consequences of methapyrilene administration through on the endogenous metabolite profiles of plasma and urine. Methapyrilene and its metabolites were also profiled in these samples.
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Affiliation(s)
- Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Corey Broeckling
- Bioanalysis and Omics, Colorado State University, Fort Collins, CO 8052, USA
| | | | | | - Robert Trengove
- Curtin Health Innovation Research Institute, Curtin University, Kent St, Bentley WA 6102, Australia.
| | | | | | - Giorgis Isaac
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Maiti KS, Fill E, Strittmatter F, Volz Y, Sroka R, Apolonski A. Standard operating procedure to reveal prostate cancer specific volatile organic molecules by infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123266. [PMID: 37657373 DOI: 10.1016/j.saa.2023.123266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023]
Abstract
The growing number of prostate cancer cases is a real concern in modern society. Over 1.4 million new cases and about 400 thousand (>26%) deaths were registered worldwide in 2020 due to prostate cancer. The high mortality rate of prostate cancer is due to the lack of reliable early detection of the disease. Till now the most reliable diagnosis of cancer is tissue biopsy, which is an invasive process. A non-invasive or minimally invasive technique could lead to a diagnostic tool that will allow for saving or prolonging the lifespan of millions of lives. Metabolite-based diagnostics may have a better chance of early cancer detection. However, reliable detection techniques need to be developed. Infrared spectroscopy based gaseous-biofluid holds great promise towards the development of non-invasive diagnostics. A pilot study based on breath analysis by infrared spectroscopy showed promising results in distinguishing prostate cancer patients from healthy volunteers. Details of the spectral metabolic analysis are presented.
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Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany; Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, Garching, 85747, Germany; Department of Anesthesiology and Intensive Care Medicine/Center for Sepsis Control and Care, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany.
| | - Ernst Fill
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany
| | - Frank Strittmatter
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany
| | - Yannic Volz
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany
| | - Ronald Sroka
- Urologische Klinik und Poliklinik des Klinikums der Ludwig-Maximilians- Universität München in Großhadern, 81377 Munich, Germany; Laser-Forschungslabor, LIFE Center, University Hospital, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Alexander Apolonski
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, 85748 Garching, Germany; Institute of Automation and Electrometry SB RAS, 630090 Novosibirsk, Russia
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Xourafa G, Korbmacher M, Roden M. Inter-organ crosstalk during development and progression of type 2 diabetes mellitus. Nat Rev Endocrinol 2024; 20:27-49. [PMID: 37845351 DOI: 10.1038/s41574-023-00898-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/18/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by tissue-specific insulin resistance and pancreatic β-cell dysfunction, which result from the interplay of local abnormalities within different tissues and systemic dysregulation of tissue crosstalk. The main local mechanisms comprise metabolic (lipid) signalling, altered mitochondrial metabolism with oxidative stress, endoplasmic reticulum stress and local inflammation. While the role of endocrine dysregulation in T2DM pathogenesis is well established, other forms of inter-organ crosstalk deserve closer investigation to better understand the multifactorial transition from normoglycaemia to hyperglycaemia. This narrative Review addresses the impact of certain tissue-specific messenger systems, such as metabolites, peptides and proteins and microRNAs, their secretion patterns and possible alternative transport mechanisms, such as extracellular vesicles (exosomes). The focus is on the effects of these messengers on distant organs during the development of T2DM and progression to its complications. Starting from the adipose tissue as a major organ relevant to T2DM pathophysiology, the discussion is expanded to other key tissues, such as skeletal muscle, liver, the endocrine pancreas and the intestine. Subsequently, this Review also sheds light on the potential of multimarker panels derived from these biomarkers and related multi-omics for the prediction of risk and progression of T2DM, novel diabetes mellitus subtypes and/or endotypes and T2DM-related complications.
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Affiliation(s)
- Georgia Xourafa
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Düsseldorf, Germany
| | - Melis Korbmacher
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Düsseldorf, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Düsseldorf, Germany.
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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Bartman CR, Faubert B, Rabinowitz JD, DeBerardinis RJ. Metabolic pathway analysis using stable isotopes in patients with cancer. Nat Rev Cancer 2023; 23:863-878. [PMID: 37907620 PMCID: PMC11161207 DOI: 10.1038/s41568-023-00632-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 11/02/2023]
Abstract
Metabolic reprogramming is central to malignant transformation and cancer cell growth. How tumours use nutrients and the relative rates of reprogrammed pathways are areas of intense investigation. Tumour metabolism is determined by a complex and incompletely defined combination of factors intrinsic and extrinsic to cancer cells. This complexity increases the value of assessing cancer metabolism in disease-relevant microenvironments, including in patients with cancer. Stable-isotope tracing is an informative, versatile method for probing tumour metabolism in vivo. It has been used extensively in preclinical models of cancer and, with increasing frequency, in patients with cancer. In this Review, we describe approaches for using in vivo isotope tracing to define fuel preferences and pathway engagement in tumours, along with some of the principles that have emerged from this work. Stable-isotope infusions reported so far have revealed that in humans, tumours use a diverse set of nutrients to supply central metabolic pathways, including the tricarboxylic acid cycle and amino acid synthesis. Emerging data suggest that some activities detected by stable-isotope tracing correlate with poor clinical outcomes and may drive cancer progression. We also discuss current challenges in isotope tracing, including comparisons of in vivo and in vitro models, and opportunities for future discovery in tumour metabolism.
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Affiliation(s)
- Caroline R Bartman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Brandon Faubert
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Ralph J DeBerardinis
- Howard Hughes Medical Institute and Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Ritterhoff J, Tian R. Metabolic mechanisms in physiological and pathological cardiac hypertrophy: new paradigms and challenges. Nat Rev Cardiol 2023; 20:812-829. [PMID: 37237146 DOI: 10.1038/s41569-023-00887-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
Cardiac metabolism is vital for heart function. Given that cardiac contraction requires a continuous supply of ATP in large quantities, the role of fuel metabolism in the heart has been mostly considered from the perspective of energy production. However, the consequence of metabolic remodelling in the failing heart is not limited to a compromised energy supply. The rewired metabolic network generates metabolites that can directly regulate signalling cascades, protein function, gene transcription and epigenetic modifications, thereby affecting the overall stress response of the heart. In addition, metabolic changes in both cardiomyocytes and non-cardiomyocytes contribute to the development of cardiac pathologies. In this Review, we first summarize how energy metabolism is altered in cardiac hypertrophy and heart failure of different aetiologies, followed by a discussion of emerging concepts in cardiac metabolic remodelling, that is, the non-energy-generating function of metabolism. We highlight challenges and open questions in these areas and finish with a brief perspective on how mechanistic research can be translated into therapies for heart failure.
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Affiliation(s)
- Julia Ritterhoff
- Molecular and Translational Cardiology, Department of Internal Medicine III, Heidelberg University Hospital, Heidelberg, Germany.
- Mitochondria and Metabolism Center, Department of Anaesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
| | - Rong Tian
- Mitochondria and Metabolism Center, Department of Anaesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
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31
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D'Gama AM, Agrawal PB. Genomic medicine in neonatal care: progress and challenges. Eur J Hum Genet 2023; 31:1357-1363. [PMID: 37789085 PMCID: PMC10689757 DOI: 10.1038/s41431-023-01464-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
During the neonatal period, many genetic disorders present and contribute to neonatal morbidity and mortality. Genomic medicine-the use of genomic information in clinical care- has the potential to significantly reduce morbidity and mortality in the neonatal period and improve outcomes for this population. Diagnostic genomic testing for symptomatic newborns, especially rapid testing, has been shown to be feasible and have diagnostic and clinical utility, particularly in the short-term. Ongoing studies are assessing the feasibility and utility, including personal utility, of implementation in diverse populations. Genomic screening for asymptomatic newborns has also been studied, and the acceptability and feasibility of such an approach remains an active area of investigation. Emerging precision therapies, with examples even at the "n-of-1" level, highlight the promise of precision diagnostics to lead to early intervention and improve outcomes. To sustainably implement genomic medicine in neonatal care in an ethical, effective, and equitable manner, we need to ensure access to genetics and genomics knowledge, access to genomic tests, which is currently limited by payors, feasible processes for ordering these tests, and access to follow up in the clinical and research realms. Future studies will provide further insight into enablers and barriers to optimize implementation strategies.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Holtz Children's Hospital, Jackson Health System, Miami, FL, USA.
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Wu H, Kren BT, Lane AN, Cassel TA, Higashi RM, Fan TWM, Scaria GS, Shekels LL, Klein MA, Albrecht JH. Cyclin D1 extensively reprograms metabolism to support biosynthetic pathways in hepatocytes. J Biol Chem 2023; 299:105407. [PMID: 38152849 PMCID: PMC10687208 DOI: 10.1016/j.jbc.2023.105407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 12/29/2023] Open
Abstract
Cell proliferation requires metabolic reprogramming to accommodate biosynthesis of new cell components, and similar alterations occur in cancer cells. However, the mechanisms linking the cell cycle machinery to metabolism are not well defined. Cyclin D1, along with its main partner cyclin-dependent kinase 4 (Cdk4), is a pivotal cell cycle regulator and driver oncogene that is overexpressed in many cancers. Here, we examine hepatocyte proliferation to define novel effects of cyclin D1 on biosynthetic metabolism. Metabolomic studies reveal that cyclin D1 broadly promotes biosynthetic pathways including glycolysis, the pentose phosphate pathway, and the purine and pyrimidine nucleotide synthesis in hepatocytes. Proteomic analyses demonstrate that overexpressed cyclin D1 binds to numerous metabolic enzymes including those involved in glycolysis and pyrimidine synthesis. In the glycolysis pathway, cyclin D1 activates aldolase and GAPDH, and these proteins are phosphorylated by cyclin D1/Cdk4 in vitro. De novo pyrimidine synthesis is particularly dependent on cyclin D1. Cyclin D1/Cdk4 phosphorylates the initial enzyme of this pathway, carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), and metabolomic analysis indicates that cyclin D1 depletion markedly reduces the activity of this enzyme. Pharmacologic inhibition of Cdk4 along with the downstream pyrimidine synthesis enzyme dihydroorotate dehydrogenase synergistically inhibits proliferation and survival of hepatocellular carcinoma cells. These studies demonstrate that cyclin D1 promotes a broad network of biosynthetic pathways in hepatocytes, and this model may provide insights into potential metabolic vulnerabilities in cancer cells.
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Affiliation(s)
- Heng Wu
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
| | - Betsy T Kren
- Research Service, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Teresa W M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - George S Scaria
- Hematology and Oncology Division, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Laurie L Shekels
- Research Service, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Mark A Klein
- Hematology and Oncology Division, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Jeffrey H Albrecht
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA.
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Al-Shalan HAM, Zhou L, Dong Z, Wang P, Nicholls PK, Boughton B, Stumbles PA, Greene WK, Ma B. Systemic perturbations in amino acids/amino acid derivatives and tryptophan pathway metabolites associated with murine influenza A virus infection. Virol J 2023; 20:270. [PMID: 37990229 PMCID: PMC10664681 DOI: 10.1186/s12985-023-02239-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Influenza A virus (IAV) is the only influenza virus causing flu pandemics (i.e., global epidemics of flu disease). Influenza (the flu) is a highly contagious disease that can be deadly, especially in high-risk groups. Worldwide, these annual epidemics are estimated to result in about 3 to 5 million cases of severe illness and in about 290,000 to 650,000 respiratory deaths. We intend to reveal the effect of IAV infection on the host's metabolism, immune response, and neurotoxicity by using a mouse IAV infection model. METHODS 51 metabolites of murine blood plasma (33 amino acids/amino acid derivatives (AADs) and 18 metabolites of the tryptophan pathway) were analyzed by using Ultra-High-Performance Liquid Chromatography-Mass Spectrometry with Electrospray Ionization at the acute (7 days post-infection (dpi)), resolution (14 dpi), and recovery (21 dpi) stages of the virus infection in comparison with controls. RESULTS Among the 33 biogenic amino acids/AADs, the levels of five amino acids/AADs (1-methylhistidine, 5-oxoproline, α-aminobutyric acid, glutamine, and taurine) increased by 7 dpi, whereas the levels of ten amino acids/AADs (4-hydroxyproline, alanine, arginine, asparagine, cysteine, citrulline, glycine, methionine, proline, and tyrosine) decreased. By 14 dpi, the levels of one AAD (3-methylhistidine) increased, whereas the levels of five amino acids/AADs (α-aminobutyric acid, aminoadipic acid, methionine, threonine, valine) decreased. Among the 18 metabolites from the tryptophan pathway, the levels of kynurenine, quinolinic acid, hydroxykynurenine increased by 7 dpi, whereas the levels of indole-3-acetic acid and nicotinamide riboside decreased. CONCLUSIONS Our data may facilitate understanding the molecular mechanisms of host responses to IAV infection and provide a basis for discovering potential new mechanistic, diagnostic, and prognostic biomarkers and therapeutic targets for IAV infection.
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Affiliation(s)
- Huda A M Al-Shalan
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology/Virology, College of Veterinary Medicine, Baghdad University, Baghdad, Iraq
| | - Lu Zhou
- Graduate School, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhifan Dong
- Graduate School, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Penghao Wang
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
| | - Philip K Nicholls
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
| | - Berin Boughton
- Australian National Phenome Centre, Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Philip A Stumbles
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
| | - Wayne K Greene
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
| | - Bin Ma
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia.
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Zhou Y, Zhong X, Chen L, Gong L, Luo L, He Q, Zhu L, Tian K. Gut microbiota combined with metabolome dissects long-term nanoplastics exposure-induced disturbed spermatogenesis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115626. [PMID: 37890247 DOI: 10.1016/j.ecoenv.2023.115626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
As the concerned emerging pollutants, several lines of evidence have indicated that nanoplastics (NPs) lead to reproductive toxicity. However, the biological mechanism underlying NPs disturbed spermatogenesis remains largely unknown. Therefore, we aimed to reveal the potential mechanism of impaired spermatogenesis caused by long-term NPs exposure from the perspective of integrated metabolome and microbiome analysis. After 12 weeks of gavage of polystyrene nanoplastics (PS-NPs) and animo-modified polystyrene nanoplastics (Amino-NPs), a well-designed two-exposure stages experimental condition. We found that NPs exposure induced apparent abnormal spermatogenesis, which appeared more severe in the Amino-NPs group. Mechanistically, 14 floras associated with glucose and lipid metabolism were significantly altered, as evidenced by 16 S rRNA sequencing. Testicular metabolome revealed that the Top 50 changed metabolites were also enriched in lipid metabolism. Subsequently, the combined gut microbiome and metabolome analysis uncovered the strong correlations between Klebsiella, Blautia, Parabacteroides, and lipid metabolites (e.g., PC, LysoPC and GPCho). We speculate that the dysbiosis of gut microbiota-related disturbed lipid metabolism may be responsible for long-term NPs-induced damaged spermatogenesis, which provides new insights into NPs-induced dysregulated spermatogenesis.
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Affiliation(s)
- Yan Zhou
- Department of Occupational and Environmental Health, School of Public Health, Zunyi Medical University, Zunyi 563000, PR China
| | - Xiang Zhong
- Department of Gastroenterology, Affiliated Hang Tian Hospital, Zunyi Medical University, Zunyi 563000, PR China
| | - Liangkai Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Liming Gong
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, PR China
| | - Lei Luo
- Department of Occupational and Environmental Health, School of Public Health, Zunyi Medical University, Zunyi 563000, PR China
| | - Qian He
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, PR China
| | - Lin Zhu
- Affiliated Hospital of Shijiazhuang Medical College, Shijiazhuang 050000, PR China
| | - Kunming Tian
- Department of Occupational and Environmental Health, School of Public Health, Zunyi Medical University, Zunyi 563000, PR China; Department of Gynaecology and Obstetrics, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, PR China; Key Laboratory of Maternal& Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi Medical University, Zunyi 563000, PR China.
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Chen J, Liu J, Cao D. Urine metabolomics for assessing fertility-sparing treatment efficacy in endometrial cancer: a non-invasive approach using ultra-performance liquid chromatography mass spectrometry. BMC Womens Health 2023; 23:583. [PMID: 37940929 PMCID: PMC10634093 DOI: 10.1186/s12905-023-02730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
OBJECTIVE This study aimed to reveal the urine metabolic change of endometrial cancer (EC) patients during fertility-sparing treatment and establish non-invasive predictive models to identify patients with complete remission (CR). METHOD This study enrolled 20 EC patients prior to treatment (PT) and 22 patients with CR, aged 25-40 years. Eligibility criteria consisted of stage IA high-grade EC, lesions confined to endometrium, normal hepatic and renal function, normal urine test, no contraindication for fertility-sparing treatment and no prior therapy. Urine samples were analyzed using ultraperformance liquid chromatography mass spectrometry (UPLC-MS), a technique chosen for its high sensitivity and resolution, allows for rapid, accurate identification and quantification of metabolites, providing a comprehensive metabolic profile and facilitating the discovery of potential biomarkers. Analytical techniques were employed to determine distinct metabolites and altered metabolic pathways. The statistical analyses were performed using univariate and multivariate analyses, logistic regression and receiver operating characteristic (ROC) curves to discover and validate the potential biomarker models. RESULTS A total of 108 different urine metabolomes were identified between CR and PT groups. These metabolites were enriched in ascorbate and aldarate metabolism, one carbon pool by folate, and some amino acid metabolisms pathways. A panel consisting of Baicalin, 5beta-1,3,7 (11)-Eudesmatrien-8-one, Indolylacryloylglycine, Edulitine, and Physapubenolide were selected as biomarkers, which demonstrated the best predictive ability with the AUC values of 0.982/0.851 in training/10-fold-cross-validation group, achieving a sensitivity of 0.975 and specificity of 0.967, respectively. CONCLUSION The urine metabolic analysis revealed the metabolic changes in EC patients during the fertility-sparing treatment. The predictive biomarkers present great potential diagnostic value in fertility-sparing treatments for EC patients, offering a less invasive means of monitoring treatment efficacy. Further research should explore the mechanistic underpinnings of these metabolic changes and validate the biomarker panel in larger, diverse populations due to the small sample size and single-institution nature of our study.
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Affiliation(s)
- Junyu Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, National Clinical Research Center for Obstetric & Gynecologic Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jiale Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, National Clinical Research Center for Obstetric & Gynecologic Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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Shan D, Xu D, Hu S, Qi P, Lu J, Wang D. LC-MS/MS based metabolomic analysis of serum from patients with cerebrovascular stenosis. J Pharm Biomed Anal 2023; 235:115608. [PMID: 37527609 DOI: 10.1016/j.jpba.2023.115608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Cerebrovascular stenosis (CVS) is the main cause of ischemic stroke, which greatly threatens human life. Hence, it's important to perform early screenings for CVS. Metabolomics is an emerging omics approach that has great advantages in disease screening and diagnosis. Therefore, we aim to elucidate the correlation between CVS and metabolomics, which can aid in conducting CVS screening at an early stage. Patients with CVS in Beijing Hospital were included in the study. A total of 36 participants, including 18 patients diagnosed with CVS and 18 healthy individuals, were recruited at Beijing Hospital between May 2022 and October 2021. The serum samples were analyzed for liquid chromatography-tandem mass spectrometry (LC-MS/MS). Then, multivariate statistical methods, including principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were performed. Differential metabolites were obtained and demonstrated by volcano plot and heatmap. The study recruited 36 participants, including 18 patients with CVS and 18 healthy participants. A total of 150 metabolites were identified. Multivariate statistical analysis revealed significant differences between patients and healthy participants. Furthermore, 30 serum metabolites levels differed significantly between two groups. Differential metabolites were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis; primary bile acid biosynthesis, and other pathways. This study identified differential metabolites in patients with CVS and elucidated the relevant metabolic pathways. Thus, these findings aid in the study of the pathogenesis of CVS and its early diagnosis. DATA AVAILABILITY STATEMENT: The datasets generated for this study are available on request to the corresponding author.
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Affiliation(s)
- Dezhi Shan
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Beijing, China
| | - Dingkang Xu
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Beijing, China
| | - Shen Hu
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Qi
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jun Lu
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Daming Wang
- Department of Neurosurgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Graduate School of Peking Union Medical College, Beijing, China.
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Dankel SN, Kalleklev TL, Tungland SL, Stafsnes MH, Bruheim P, Aloysius TA, Lindquist C, Skorve J, Nygård OK, Madsen L, Bjørndal B, Sydnes MO, Berge RK. Changes in Plasma Pyruvate and TCA Cycle Metabolites upon Increased Hepatic Fatty Acid Oxidation and Ketogenesis in Male Wistar Rats. Int J Mol Sci 2023; 24:15536. [PMID: 37958519 PMCID: PMC10648824 DOI: 10.3390/ijms242115536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/06/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Altered hepatic mitochondrial fatty acid β-oxidation and associated tricarboxylic acid (TCA) cycle activity contributes to lifestyle-related diseases, and circulating biomarkers reflecting these changes could have disease prognostic value. This study aimed to determine hepatic and systemic changes in TCA-cycle-related metabolites upon the selective pharmacologic enhancement of mitochondrial fatty acid β-oxidation in the liver, and to elucidate the mechanisms and potential markers of hepatic mitochondrial activity. Male Wistar rats were treated with 3-thia fatty acids (e.g., tetradecylthioacetic acid (TTA)), which target mitochondrial biogenesis, mitochondrial fatty acid β-oxidation, and ketogenesis predominantly in the liver. Hepatic and plasma concentrations of TCA cycle intermediates and anaplerotic substrates (LC-MS/MS), plasma ketones (colorimetric assay), and acylcarnitines (HPLC-MS/MS), along with associated TCA-cycle-related gene expression (qPCR) and enzyme activities, were determined. TTA-induced hepatic fatty acid β-oxidation resulted in an increased ratio of plasma ketone bodies/nonesterified fatty acid (NEFA), lower plasma malonyl-CoA levels, and a higher ratio of plasma acetylcarnitine/palmitoylcarnitine (C2/C16). These changes were associated with decreased hepatic and increased plasma pyruvate concentrations, and increased plasma concentrations of succinate, malate, and 2-hydroxyglutarate. Expression of several genes encoding TCA cycle enzymes and the malate-oxoglutarate carrier (Slc25a11), glutamate dehydrogenase (Gdh), and malic enzyme (Mdh1 and Mdh2) were significantly increased. In conclusion, the induction of hepatic mitochondrial fatty acid β-oxidation by 3-thia fatty acids lowered hepatic pyruvate while increasing plasma pyruvate, as well as succinate, malate, and 2-hydroxyglutarate.
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Affiliation(s)
- Simon Nitter Dankel
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Tine-Lise Kalleklev
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Siri Lunde Tungland
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, N-4021 Stavanger, Norway (M.O.S.)
| | - Marit Hallvardsdotter Stafsnes
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway (P.B.)
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway (P.B.)
| | - Thomas Aquinas Aloysius
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Carine Lindquist
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Jon Skorve
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
| | - Ottar Kjell Nygård
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Heart Disease, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Lise Madsen
- Department of Clinical Medicine, University of Bergen, N-5021 Bergen, Norway;
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Sports, Food and Natural Sciences, Western Norway University of Applied Sciences, N-5020 Bergen, Norway
| | - Magne Olav Sydnes
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, N-4021 Stavanger, Norway (M.O.S.)
| | - Rolf Kristian Berge
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway (T.A.A.); (J.S.); (O.K.N.); (B.B.)
- Department of Heart Disease, Haukeland University Hospital, N-5021 Bergen, Norway
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38
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Mayers JR, Varon J, Zhou RR, Daniel-Ivad M, Beaulieu C, Bholse A, Glasser NR, Lichtenauer FM, Ng J, Vera MP, Huttenhower C, Perrella MA, Clish CB, Zhao SD, Baron RM, Balskus EP. Identification and targeting of microbial putrescine acetylation in bloodstream infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558834. [PMID: 37790300 PMCID: PMC10542159 DOI: 10.1101/2023.09.21.558834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The growth of antimicrobial resistance (AMR) has highlighted an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe bacterial infections profoundly alter host metabolism, prior studies have largely ignored alterations in microbial metabolism in this context. Performing metabolomics on patient and mouse plasma samples, we identify elevated levels of bacterially-derived N-acetylputrescine during gram-negative bloodstream infections (BSI), with higher levels associated with worse clinical outcomes. We discover that SpeG is the bacterial enzyme responsible for acetylating putrescine and show that blocking its activity reduces bacterial proliferation and slows pathogenesis. Reduction of SpeG activity enhances bacterial membrane permeability and results in increased intracellular accumulation of antibiotics, allowing us to overcome AMR of clinical isolates both in culture and in vivo. This study highlights how studying pathogen metabolism in the natural context of infection can reveal new therapeutic strategies for addressing challenging infections.
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Affiliation(s)
- Jared R. Mayers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA 02138
| | - Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | - Ruixuan R. Zhou
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, IL, USA 61820
| | - Martin Daniel-Ivad
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA 02138
- Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
| | | | - Amrisha Bholse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA 02115
| | - Nathaniel R. Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA 02138
| | | | - Julie Ng
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | - Mayra Pinilla Vera
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA 02115
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark A. Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
| | - Sihai D. Zhao
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, IL, USA 61820
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Champaign, IL, USA 61820
| | - Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA 02138
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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40
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Karunaratne E, Hill DW, Dührkop K, Böcker S, Grant DF. Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure Identification. Anal Chem 2023; 95:11901-11907. [PMID: 37540774 DOI: 10.1021/acs.analchem.3c00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
The inability to identify the structures of most metabolites detected in environmental or biological samples limits the utility of nontargeted metabolomics. The most widely used analytical approaches combine mass spectrometry and machine learning methods to rank candidate structures contained in large chemical databases. Given the large chemical space typically searched, the use of additional orthogonal data may improve the identification rates and reliability. Here, we present results of combining experimental and computational mass and IR spectral data for high-throughput nontargeted chemical structure identification. Experimental MS/MS and gas-phase IR data for 148 test compounds were obtained from NIST. Candidate structures for each of the test compounds were obtained from PubChem (mean = 4444 candidate structures per test compound). Our workflow used CSI:FingerID to initially score and rank the candidate structures. The top 1000 ranked candidates were subsequently used for IR spectra prediction, scoring, and ranking using density functional theory (DFT-IR). Final ranking of the candidates was based on a composite score calculated as the average of the CSI:FingerID and DFT-IR rankings. This approach resulted in the correct identification of 88 of the 148 test compounds (59%). 129 of the 148 test compounds (87%) were ranked within the top 20 candidates. These identification rates are the highest yet reported when candidate structures are used from PubChem. Combining experimental and computational MS/MS and IR spectral data is a potentially powerful option for prioritizing candidates for final structure verification.
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Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Kai Dührkop
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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41
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Huang Y, Mohanty V, Dede M, Tsai K, Daher M, Li L, Rezvani K, Chen K. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux. Nat Commun 2023; 14:4883. [PMID: 37573313 PMCID: PMC10423258 DOI: 10.1038/s41467-023-40457-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/26/2023] [Indexed: 08/14/2023] Open
Abstract
Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) to infer metabolic fluxes from bulk or single-cell transcriptomic data. Large-scale experiments using cell-lines, the cancer genome atlas (TCGA), and scRNA-seq data obtained from diverse cancer and immunotherapeutic contexts, including CAR-NK cell therapy, have validated METAFlux's capability to characterize metabolic heterogeneity and metabolic interaction amongst cell types.
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Affiliation(s)
- Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Biostatistics & Data Science, School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kyle Tsai
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Li Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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42
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Xiao Y, Yu TJ, Xu Y, Ding R, Wang YP, Jiang YZ, Shao ZM. Emerging therapies in cancer metabolism. Cell Metab 2023; 35:1283-1303. [PMID: 37557070 DOI: 10.1016/j.cmet.2023.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Metabolic reprogramming in cancer is not only a biological hallmark but also reveals treatment vulnerabilities. Numerous metabolic molecules have shown promise as treatment targets to impede tumor progression in preclinical studies, with some advancing to clinical trials. However, the intricacy and adaptability of metabolic networks hinder the effectiveness of metabolic therapies. This review summarizes the metabolic targets for cancer treatment and provides an overview of the current status of clinical trials targeting cancer metabolism. Additionally, we decipher crucial factors that limit the efficacy of metabolism-based therapies and propose future directions. With advances in integrating multi-omics, single-cell, and spatial technologies, as well as the ability to track metabolic adaptation more precisely and dynamically, clinicians can personalize metabolic therapies for improved cancer treatment.
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Affiliation(s)
- Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tian-Jian Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Rui Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Ping Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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43
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Pang H, Hu Z. Metabolomics in drug research and development: The recent advances in technologies and applications. Acta Pharm Sin B 2023; 13:3238-3251. [PMID: 37655318 PMCID: PMC10465962 DOI: 10.1016/j.apsb.2023.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/21/2023] [Accepted: 04/28/2023] [Indexed: 09/02/2023] Open
Abstract
Emerging evidence has demonstrated the vital role of metabolism in various diseases or disorders. Metabolomics provides a comprehensive understanding of metabolism in biological systems. With advanced analytical techniques, metabolomics exhibits unprecedented significant value in basic drug research, including understanding disease mechanisms, identifying drug targets, and elucidating the mode of action of drugs. More importantly, metabolomics greatly accelerates the drug development process by predicting pharmacokinetics, pharmacodynamics, and drug response. In addition, metabolomics facilitates the exploration of drug repurposing and drug-drug interactions, as well as the development of personalized treatment strategies. Here, we briefly review the recent advances in technologies in metabolomics and update our knowledge of the applications of metabolomics in drug research and development.
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Affiliation(s)
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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44
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Zhu H, Wang X, Lu S, Ou K. Metabolic reprogramming of clear cell renal cell carcinoma. Front Endocrinol (Lausanne) 2023; 14:1195500. [PMID: 37347113 PMCID: PMC10280292 DOI: 10.3389/fendo.2023.1195500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a malignancy that exhibits metabolic reprogramming as a result of genetic mutations. This reprogramming accommodates the energy and anabolic needs of the cancer cells, leading to changes in glucose, lipid, and bio-oxidative metabolism, and in some cases, the amino acid metabolism. Recent evidence suggests that ccRCC may be classified as a metabolic disease. The metabolic alterations provide potential targets for novel therapeutic interventions or biomarkers for monitoring tumor growth and prognosis. This literature review summarized recent discoveries of metabolic alterations in ccRCC, including changes in glucose, lipid, and amino acid metabolism. The development of metabolic drugs targeting these metabolic pathways was also discussed, such as HIF-2α inhibitors, fatty acid synthase (FAS) inhibitors, glutaminase (GLS) inhibitors, indoleamine 2,3-dioxygenase (IDO) inhibitors, and arginine depletion. Future trends in drug development are proposed, including the use of combination therapies and personalized medicine approaches. In conclusion, this review provides a comprehensive overview of the metabolic alterations in ccRCC and highlights the potential for developing new treatments for this disease.
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Affiliation(s)
- Haiyan Zhu
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xin Wang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shihao Lu
- Orthopaedics, Changzheng Hospital Affiliated to Second Military Medical University, Shanghai, China
| | - Kongbo Ou
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, China
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45
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Yu Y, Li J, Ren K. Phosphoenolpyruvate carboxykinases as emerging targets in cancer therapy. Front Cell Dev Biol 2023; 11:1196226. [PMID: 37250903 PMCID: PMC10217351 DOI: 10.3389/fcell.2023.1196226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Metabolic reprogramming is commonly accompanied by alterations in the expression of metabolic enzymes. These metabolic enzymes not only catalyze the intracellular metabolic reaction, but also participate in a series of molecular events to regulate tumor initiation and development. Thus, these enzymes may act as promising therapeutic targets for tumor management. Phosphoenolpyruvate carboxykinases (PCKs) are the key enzymes involved in gluconeogenesis, which mediates the conversion of oxaloacetate into phosphoenolpyruvate. Two isoforms of PCK, namely cytosolic PCK1 and mitochondrial PCK2, has been found. PCK not only participates in the metabolic adaptation, but also regulates immune response and signaling pathways for tumor progression. In this review, we discussed the regulatory mechanisms of PCKs expression including transcription and post-translational modification. We also summarized the function of PCKs in tumor progression in different cellular contexts and explores its role in developing promising therapeutic opportunities.
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Affiliation(s)
- Yong Yu
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jingying Li
- Department of Health Management, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Kaiming Ren
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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46
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Jeon YG, Kim YY, Lee G, Kim JB. Physiological and pathological roles of lipogenesis. Nat Metab 2023; 5:735-759. [PMID: 37142787 DOI: 10.1038/s42255-023-00786-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Lipids are essential metabolites, which function as energy sources, structural components and signalling mediators. Most cells are able to convert carbohydrates into fatty acids, which are often converted into neutral lipids for storage in the form of lipid droplets. Accumulating evidence suggests that lipogenesis plays a crucial role not only in metabolic tissues for systemic energy homoeostasis but also in immune and nervous systems for their proliferation, differentiation and even pathophysiological roles. Thus, excessive or insufficient lipogenesis is closely associated with aberrations in lipid homoeostasis, potentially leading to pathological consequences, such as dyslipidaemia, diabetes, fatty liver, autoimmune diseases, neurodegenerative diseases and cancers. For systemic energy homoeostasis, multiple enzymes involved in lipogenesis are tightly controlled by transcriptional and post-translational modifications. In this Review, we discuss recent findings regarding the regulatory mechanisms, physiological roles and pathological importance of lipogenesis in multiple tissues such as adipose tissue and the liver, as well as the immune and nervous systems. Furthermore, we briefly introduce the therapeutic implications of lipogenesis modulation.
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Affiliation(s)
- Yong Geun Jeon
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ye Young Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Gung Lee
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jae Bum Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea.
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47
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Neef SK, Hofmann U, Mürdter TE, Schwab M, Haag M. Performance comparison of narrow-bore and capillary liquid-chromatography for non-targeted metabolomics profiling by HILIC-QTOF-MS. Talanta 2023; 260:124578. [PMID: 37119797 DOI: 10.1016/j.talanta.2023.124578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/13/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Clinical metabolomics studies often have to cope with limited sample amounts, thus miniaturized liquid chromatography (LC) systems are a promising alternative. Their applicability has already been demonstrated in various fields, including a few metabolomics studies that mainly used reversed-phase chromatography. However, hydrophilic interaction chromatography (HILIC), which is widely used in metabolomics due to its particular suitability for the analysis of polar molecules, has rarely been tested for miniaturized LC-MS analysis of small molecules. In the present work, the suitability of a capillary HILIC (CapHILIC)-QTOF-MS system for non-targeted metabolomics was evaluated based on extracts of porcine formalin-fixed, paraffin-embedded (FFPE) tissue samples. The performance was assessed with respect to the number and retention time span of metabolic features as well as the analytical repeatability, the signal-to-noise ratio and the signal intensity of 16 annotated metabolites from different compound classes. The results were compared with a well established narrow-bore HILIC-QTOF-MS system. Both platforms have detected a similar number of features and performed excellent with respect to retention time stability (median RT span <0.05 min) and analytical repeatability (>75% of features with CV < 20%). The signal areas of all metabolites assessed were increased up to 18-fold by the use of CapHILIC, although the signal-to-noise ratio was only improved for 50% of the metabolites. An even better reproducibility (median CV = 5.2%) and up to 80-fold increase in signal intensity were observed after optimization of CapHILIC conditions for analysis of bile acid standard solutions. Even though the observed improvement for specific bile acids (e.g. taurocholic acid) in biological matrix needs to be evaluated, the platform comparison indicates, that the tested CapHILIC system is particularly suitable for analyses of a less broad metabolite spectrum, and specifically optimized chromatography.
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Affiliation(s)
- Sylvia K Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany; Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany.
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48
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Du K, Zhai C, Li X, Gang H, Gao X. Feature-Based Molecular Networking Facilitates the Comprehensive Identification of Differential Metabolites in Diabetic Cognitive Dysfunction Rats. Metabolites 2023; 13:metabo13040538. [PMID: 37110195 PMCID: PMC10142102 DOI: 10.3390/metabo13040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/18/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Cognitive dysfunction is a frequent complication of type 2 diabetes mellitus (T2DM), usually accompanied by metabolic disorders. However, the metabolic changes in diabetic cognitive dysfunction (DCD) patients, especially compared to T2DM groups, are not fully understood. Due to the subtle differences in metabolic alterations between DCD groups and T2DM groups, the comprehensive detection of the untargeted metabolic profiles of hippocampus and urine samples of rats was conducted by LC-MS, considering the different ionization modes and polarities of the examined compounds, and feature-based molecular networking (FBMN) was performed to help identify differential metabolites from a comprehensive perspective in this study. In addition, an association analysis of the differential metabolites in hippocampus and urine was conducted by the O2PLS model. Finally, a total of 71 hippocampal tissue differential metabolites and 179 urine differential metabolites were identified. The pathway enrichment results showed that glutamine and glutamate metabolism, alanine, aspartate, and glutamate metabolism, glycerol phospholipid metabolism, TCA cycle, and arginine biosynthesis in the hippocampus of DCD animals were changed. Seven metabolites (AUC > 0.9) in urine appeared as key differential metabolites that might reflect metabolic changes in the target tissue of DCD rats. This study showed that FBMN facilitated the comprehensive identification of differential metabolites in DCD rats. The differential metabolites may suggest an underlying DCD and be considered as potential biomarkers for DCD. Large samples and clinical experiments are needed for the subsequent elucidation of the possible mechanisms leading to these alterations and the verification of potential biomarkers.
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Affiliation(s)
- Ke Du
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing102488, China
| | - Chuanjia Zhai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing102488, China
| | - Xuejiao Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing102488, China
| | - Hongchuan Gang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing102488, China
| | - Xiaoyan Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing102488, China
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49
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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50
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Maiti KS. Non-Invasive Disease Specific Biomarker Detection Using Infrared Spectroscopy: A Review. Molecules 2023; 28:2320. [PMID: 36903576 PMCID: PMC10005715 DOI: 10.3390/molecules28052320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Many life-threatening diseases remain obscure in their early disease stages. Symptoms appear only at the advanced stage when the survival rate is poor. A non-invasive diagnostic tool may be able to identify disease even at the asymptotic stage and save lives. Volatile metabolites-based diagnostics hold a lot of promise to fulfil this demand. Many experimental techniques are being developed to establish a reliable non-invasive diagnostic tool; however, none of them are yet able to fulfil clinicians' demands. Infrared spectroscopy-based gaseous biofluid analysis demonstrated promising results to fulfil clinicians' expectations. The recent development of the standard operating procedure (SOP), sample measurement, and data analysis techniques for infrared spectroscopy are summarized in this review article. It has also outlined the applicability of infrared spectroscopy to identify the specific biomarkers for diseases such as diabetes, acute gastritis caused by bacterial infection, cerebral palsy, and prostate cancer.
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Affiliation(s)
- Kiran Sankar Maiti
- Max–Planck–Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-289-14054
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
- Laser-Forschungslabor, Klinikum der Universität München, Fraunhoferstrasse 20, 82152 Planegg, Germany
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