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Rockel JS, Potla P, Kapoor M. Transcriptomics and metabolomics: Challenges of studying obesity in osteoarthritis. OSTEOARTHRITIS AND CARTILAGE OPEN 2024; 6:100479. [PMID: 38774038 PMCID: PMC11103424 DOI: 10.1016/j.ocarto.2024.100479] [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: 03/11/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024] Open
Abstract
Objective Obesity is a leading risk factor for both the incidence and progression of osteoarthritis (OA). Omic technologies, including transcriptomics and metabolomics are capable of identifying RNA and metabolite profiles in tissues and biofluids of OA patients. The objective of this review is to highlight studies using transcriptomics and metabolomics that contribute to our understanding of OA pathology in relation to obesity. Design We conducted a targeted search of PUBMED for articles, and GEO for datasets, published up to February 13, 2024, screening for those using high-throughput transcriptomic and metabolomic techniques to study human or pre-clinical animal model tissues or biofluids related to obesity-associated OA. We describe relevant studies and discuss challenges studying obesity as a disease-related factor in OA. Results Of the 107 publications identified by our search criteria, only 15 specifically used transcriptomics or metabolomics to study joint tissues or biofluids in obesity-related OA. Specific transcriptomic and metabolomic signatures associated with obesity-related OA have been defined in select local joint tissues, biofluids and other biological material. However, considerable challenges exist in understanding contributions of obesity-associated modifications of transcriptomes and metabolomes related to OA, including sociodemographic, anthropometric, dietary and molecular redundancy-related factors. Conclusions A number of additional transcriptomic and metabolomic studies are needed to comprehensively understand how obesity affects OA incidence, progression and outcomes. Integration of transcriptome and metabolome signatures from multiple tissues and biofluids, using network-based approaches will likely help to better define putative therapeutic targets that could enable precision medicine approaches to obese OA patients.
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Affiliation(s)
- Jason S. Rockel
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Pratibha Potla
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Mohit Kapoor
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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2
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Tran DH, Kim D, Kesavan R, Brown H, Dey T, Soflaee MH, Vu HS, Tasdogan A, Guo J, Bezwada D, Al Saad H, Cai F, Solmonson A, Rion H, Chabatya R, Merchant S, Manales NJ, Tcheuyap VT, Mulkey M, Mathews TP, Brugarolas J, Morrison SJ, Zhu H, DeBerardinis RJ, Hoxhaj G. De novo and salvage purine synthesis pathways across tissues and tumors. Cell 2024; 187:3602-3618.e20. [PMID: 38823389 PMCID: PMC11246224 DOI: 10.1016/j.cell.2024.05.011] [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: 04/05/2023] [Revised: 03/16/2024] [Accepted: 05/03/2024] [Indexed: 06/03/2024]
Abstract
Purine nucleotides are vital for RNA and DNA synthesis, signaling, metabolism, and energy homeostasis. To synthesize purines, cells use two principal routes: the de novo and salvage pathways. Traditionally, it is believed that proliferating cells predominantly rely on de novo synthesis, whereas differentiated tissues favor the salvage pathway. Unexpectedly, we find that adenine and inosine are the most effective circulating precursors for supplying purine nucleotides to tissues and tumors, while hypoxanthine is rapidly catabolized and poorly salvaged in vivo. Quantitative metabolic analysis demonstrates comparative contribution from de novo synthesis and salvage pathways in maintaining purine nucleotide pools in tumors. Notably, feeding mice nucleotides accelerates tumor growth, while inhibiting purine salvage slows down tumor progression, revealing a crucial role of the salvage pathway in tumor metabolism. These findings provide fundamental insights into how normal tissues and tumors maintain purine nucleotides and highlight the significance of purine salvage in cancer.
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Affiliation(s)
- Diem H Tran
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Dohun Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rushendhiran Kesavan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Harrison Brown
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Trishna Dey
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Mona Hoseini Soflaee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium, Partner Site, Essen, Germany
| | - Jason Guo
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Divya Bezwada
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Houssam Al Saad
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ashley Solmonson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Halie Rion
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rawand Chabatya
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Salma Merchant
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Nathan J Manales
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Vanina T Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Megan Mulkey
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean J Morrison
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Gerta Hoxhaj
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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Wang C, Li Y, Feng J, Liu H, Wang Y, Wan Y, Zheng M, Li X, Chen T, Xiao X. Plasmalogens and Octanoylcarnitine Serve as Early Warnings for Central Retinal Artery Occlusion. Mol Neurobiol 2024:10.1007/s12035-024-04093-9. [PMID: 38459364 DOI: 10.1007/s12035-024-04093-9] [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: 10/19/2023] [Accepted: 03/03/2024] [Indexed: 03/10/2024]
Abstract
Central retinal artery occlusion (CRAO) is a kind of ophthalmic emergency which may cause loss of functional visual acuity. However, the limited treatment options emphasize the significance of early disease prevention. Metabolomics has the potential to be a powerful tool for early identification of individuals at risk of CRAO. The aim of the study was to identify potential biomarkers for CRAO through a comprehensive analysis. We employed metabolomics analysis to compare venous blood samples from CRAO patients with cataract patients for the venous difference, as well as arterial and venous blood from CRAO patients for the arteriovenous difference. The analysis of metabolites showed that PC(P-18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), PC(P-18:0/20:4(5Z,8Z,11Z,14Z)) and octanoylcarnitine were strongly correlated with CRAO. We also used univariate logistic regression, random forest (RF), and support vector machine (SVM) to screen clinical parameters of patients and found that HDL-C and ApoA1 showed significant predictive efficacy in CRAO patients. We compared the predictive performance of the clinical parameter model with combined model. The prediction efficiency of the combined model was significantly better with area under the receiver operating characteristic curve (AUROC) of 0.815. Decision curve analysis (DCA) also exhibited a notably higher net benefit rate. These results underscored the potency of these three substances as robust predictors of CRAO occurrence.
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Affiliation(s)
- Chuansen Wang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Ying Li
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Jiaqing Feng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Hang Liu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuedan Wang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Yuwei Wan
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Mengxue Zheng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Xuejie Li
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China
| | - Ting Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China.
| | - Xuan Xiao
- Department of Ophthalmology, Renmin Hospital of Wuhan University, No. 238 Jie Fang Road, Wuhan, 430060, Hubei, China.
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan, China.
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Bonhomme MM, Patarin F, Kruse CJ, François AC, Renaud B, Couroucé A, Leleu C, Boemer F, Toquet MP, Richard EA, Seignot J, Wouters CP, Votion DM. Untargeted Metabolomics Profiling Reveals Exercise Intensity-Dependent Alterations in Thoroughbred Racehorses' Plasma after Routine Conditioning Sessions. ACS OMEGA 2023; 8:48557-48571. [PMID: 38144146 PMCID: PMC10733985 DOI: 10.1021/acsomega.3c08583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023]
Abstract
Thoroughbred (TB) racehorses undergo rigorous conditioning programs to optimize their physical and mental capabilities through varied exercise sessions. While conventional investigations focus on limited hematological and biochemical parameters, this field study employed untargeted metabolomics to comprehensively assess metabolic responses triggered by exercise sessions routinely used in TB conditioning. Blood samples were collected pre- and post-exercise from ten racehorses, divided into two groups based on exercise intensity: high intensity (n = 6, gallop at ± 13.38 m/s, 1400 m) and moderate intensity (n = 4, soft canter at ± 7.63 m/s, 2500 m). Intensity was evaluated through monitoring of the speed, heart rate, and lactatemia. Resting and 30 min post-exercise plasma samples were analyzed using ultraperformance liquid chromatography coupled with high-resolution mass spectrometry. Unsupervised principal component analysis revealed exercise-induced metabolome changes, with high-intensity exercise inducing greater alterations. Following high-intensity exercise, 54 metabolites related to amino acid, fatty acid, nucleic acid, and vitamin metabolism were altered versus 23 metabolites, primarily linked to fatty acid and amino acid metabolism, following moderate-intensity exercise. Metabolomics confirmed energy metabolism changes reported by traditional biochemistry studies and highlighted the involvement of lipid and amino acid metabolism during routine exercise and recovery, aspects that had previously been overlooked in TB racehorses.
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Affiliation(s)
- Maëlle M. Bonhomme
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Florence Patarin
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Caroline-J. Kruse
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Anne-Christine François
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Benoît Renaud
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Anne Couroucé
- Equine
Department, Oniris, National Vet School
of Nantes, 101 Route
de Gachet, 44300 Nantes, France
- UR 7450
Biotargen, University of Caen Normandie, 3 Rue Nelson Mandela, 14280 Saint-Contest, France
| | - Claire Leleu
- Equi-Test, La Lande, 53290 Grez-en-Bouère, France
| | - François Boemer
- Biochemical
Genetics Laboratory, Human Genetics Department, University Hospital
of Liege, University of Liege, Avenue de l’Hôpital
1, 4000 Liège, Belgium
| | - Marie-Pierre Toquet
- UR 7450
Biotargen, University of Caen Normandie, 3 Rue Nelson Mandela, 14280 Saint-Contest, France
- LABÉO
(Frank Duncombe), 1 Route
de Rosel, 14280 Saint-Contest, France
| | - Eric A. Richard
- UR 7450
Biotargen, University of Caen Normandie, 3 Rue Nelson Mandela, 14280 Saint-Contest, France
- LABÉO
(Frank Duncombe), 1 Route
de Rosel, 14280 Saint-Contest, France
| | - Jérôme Seignot
- Clinique
Vétérinaire du Parc, 1 Avenue Malesherbes, 78600 Maisons-Laffitte, France
| | - Clovis P. Wouters
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
| | - Dominique-Marie Votion
- Department
of Functional Sciences, Comparative Veterinary Medicine, Fundamental
and Applied Research for Animals & Health (FARAH), Faculty of
Veterinary Medicine, University of Liege, Boulevard de Colonster 20, 4000 Liège, Belgium
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Kim JW, Lee JY, Oh M, Lee EW. An integrated view of lipid metabolism in ferroptosis revisited via lipidomic analysis. Exp Mol Med 2023; 55:1620-1631. [PMID: 37612411 PMCID: PMC10474074 DOI: 10.1038/s12276-023-01077-y] [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: 04/10/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
Ferroptosis is a form of regulated cell death characterized by iron-dependent lipid peroxidation. This process contributes to cellular and tissue damage in various human diseases, such as cardiovascular diseases, neurodegeneration, liver disease, and cancer. Although polyunsaturated fatty acids (PUFAs) in membrane phospholipids are preferentially oxidized, saturated/monounsaturated fatty acids (SFAs/MUFAs) also influence lipid peroxidation and ferroptosis. In this review, we first explain how cells differentially synthesize SFA/MUFAs and PUFAs and how they control fatty acid pools via fatty acid uptake and β-oxidation, impacting ferroptosis. Furthermore, we discuss how fatty acids are stored in different lipids, such as diacyl or ether phospholipids with different head groups; triglycerides; and cholesterols. Moreover, we explain how these fatty acids are released from these molecules. In summary, we provide an integrated view of the diverse and dynamic metabolic processes in the context of ferroptosis by revisiting lipidomic studies. Thus, this review contributes to the development of therapeutic strategies for ferroptosis-related diseases.
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Affiliation(s)
- Jong Woo Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Ji-Yoon Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Mihee Oh
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34141, Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea.
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Tracing metabolic flux in vivo: motion pictures differ from snapshots. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1309-1310. [PMID: 36075946 PMCID: PMC9534848 DOI: 10.1038/s12276-022-00842-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022]
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