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Bhardwaj JK, Siwach A, Sachdeva SN. Metabolomics and cellular altered pathways in cancer biology: A review. J Biochem Mol Toxicol 2024; 38:e23807. [PMID: 39148273 DOI: 10.1002/jbt.23807] [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: 03/05/2024] [Revised: 07/16/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024]
Abstract
Cancer is a deadly disease that affects a cell's metabolism and surrounding tissues. Understanding the fundamental mechanisms of metabolic alterations in cancer cells would assist in developing cancer treatment targets and approaches. From this perspective, metabolomics is a great analytical tool to clarify the mechanisms of cancer therapy as well as a useful tool to investigate cancer from a distinct viewpoint. It is a powerful emerging technology that detects up to thousands of molecules in tissues and biofluids. Like other "-omics" technologies, metabolomics involves the comprehensive investigation of micromolecule metabolites and can reveal important details about the cancer state that is otherwise not apparent. Recent developments in metabolomics technologies have made it possible to investigate cancer metabolism in greater depth and comprehend how cancer cells utilize metabolic pathways to make the amino acids, nucleotides, and lipids required for tumorigenesis. These new technologies have made it possible to learn more about cancer metabolism. Here, we review the cellular and systemic effects of cancer and cancer treatments on metabolism. The current study provides an overview of metabolomics, emphasizing the current technologies and their use in clinical and translational research settings.
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Affiliation(s)
- Jitender Kumar Bhardwaj
- Reproductive Physiology Laboratory, Department of Zoology, Kurukshetra University, Kurukshetra, Haryana, India
| | - Anshu Siwach
- Reproductive Physiology Laboratory, Department of Zoology, Kurukshetra University, Kurukshetra, Haryana, India
| | - Som Nath Sachdeva
- Department of Civil Engineering, National Institute of Technology, Kurukshetra and Kurukshetra University, Kurukshetra, Haryana, India
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Shu Z, Ji Y, Liu F, Jing Y, Jiao C, Li Y, Zhao Y, Wang G, Zhang J. Proteomics Analysis of the Protective Effect of Polydeoxyribonucleotide Extracted from Sea Cucumber ( Apostichopus japonicus) Sperm in a Hydrogen Peroxide-Induced RAW264.7 Cell Injury Model. Mar Drugs 2024; 22:325. [PMID: 39057434 PMCID: PMC11277713 DOI: 10.3390/md22070325] [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: 06/13/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Sea cucumber viscera contain various naturally occurring active substances, but they are often underutilized during sea cucumber processing. Polydeoxyribonucleotide (PDRN) is an adenosine A2A receptor agonist that activates the A2A receptor to produce various biological effects. Currently, most studies on the activity of PDRN have focused on its anti-inflammatory, anti-apoptotic, and tissue repair properties, yet relatively few studies have investigated its antioxidant activity. In this study, we reported for the first time that PDRN was extracted from the sperm of Apostichopus japonicus (AJS-PDRN), and we evaluated its antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS), and hydroxyl radical scavenging assays. An in vitro injury model was established using H2O2-induced oxidative damage in RAW264.7 cells, and we investigated the protective effect of AJS-PDRN on these cells. Additionally, we explored the potential mechanism by which AJS-PDRN protects RAW264.7 cells from damage using iTRAQ proteomics analysis. The results showed that AJS-PDRN possessed excellent antioxidant activity and could significantly scavenge DPPH, ABTS, and hydroxyl radicals. In vitro antioxidant assays demonstrated that AJS-PDRN was cytoprotective and significantly enhanced the antioxidant capacity of RAW264.7 cells. The results of GO enrichment and KEGG pathway analysis indicate that the protective effects of AJS-PDRN pretreatment on RAW264.7 cells are primarily achieved through the regulation of immune and inflammatory responses, modulation of the extracellular matrix and signal transduction pathways, promotion of membrane repair, and enhancement of cellular antioxidant capacity. The results of a protein-protein interaction (PPI) network analysis indicate that AJS-PDRN reduces cellular oxidative damage by upregulating the expression of intracellular selenoprotein family members. In summary, our findings reveal that AJS-PDRN mitigates H2O2-induced oxidative damage through multiple pathways, underscoring its significant potential in the prevention and treatment of diseases caused by oxidative stress.
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Affiliation(s)
- Zhiqiang Shu
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yizhi Ji
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Fang Liu
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Yuexin Jing
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Chunna Jiao
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Yue Li
- Department of Food Science and Technology, Shanghai Ocean University, Shanghai 200120, China; (Z.S.)
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
| | - Yunping Zhao
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Gongming Wang
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
| | - Jian Zhang
- Shandong Marine Resource and Environment Research Institute, Yantai 264006, China
- Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food, Yantai 264006, China
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Dai X, Wang H, Zhong R, Li J, Hou Y. Causality of genetically determined metabolites on susceptibility to prevalent urological cancers: a two-sample Mendelian randomization study and meta-analysis. Front Genet 2024; 15:1398165. [PMID: 39011400 PMCID: PMC11246892 DOI: 10.3389/fgene.2024.1398165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024] Open
Abstract
Background Prevalent urological cancers, including kidney, prostate, bladder, and testicular cancers, contribute significantly to global cancer incidence and mortality. Metabolomics, focusing on small-molecule intermediates, has emerged as a tool to understand cancer etiology. Given the knowledge gap in this field, we employ a two-sample Mendelian randomization (MR) analysis to investigate the causal relationships between genetically determined metabolites (GDMs) and the susceptibility to four common urological cancers. Methods The study employs genome-wide association studies (GWAS) data from European populations, featuring the most extensive case count available for both blood metabolites and four prevalent urological cancers. Preliminary and secondary MR analyses were separately conducted, employing inverse variance weighted (IVW) as the primary method. Multiple statistical analyses, including the MR-Steiger test, Cochran's Q test, leave-one-out analysis, MR-Egger intercept analysis, and MR-PRESSO analysis, were executed to ensure robustness. Additionally, a meta-analysis was carried out to consolidate findings. The weighted median (WM) method was utilized for a relatively lenient correction (PWM < 0.05). Results After rigorous genetic variation filtering, 645 out of 1,400 metabolites were included in both preliminary and secondary MR analyses. Preliminary MR analysis identified 96 potential causal associations between 94 distinct metabolites and four urological cancers. Secondary analysis based on Finnish outcome data revealed 93 potential causal associations. Cross-database meta-analysis identified 68 blood metabolites associated with four urological cancers. Notably, 31 metabolites remained significant after using WM for correction, with additional 37 suggestive causal relationships. Reverse MR analysis revealed a significant causal association between genetically predicted prostate cancer and elevated 4-hydroxychlorothalonil levels (IVW, combined OR: 1.039, 95% CI 1.014-1.064, p = 0.002; WM, combined OR: 1.052, 95% CI 1.010-1.095, p = 0.014). Conclusion This comprehensive MR study provides insights into the causal relationships between blood metabolites and urological cancers, revealing potential biomarkers and therapeutic targets, thereby addressing gaps in understanding and laying the foundation for targeted interventions in urological cancer research and treatment.
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Affiliation(s)
- Xianyu Dai
- Urology Department, First Hospital of Jilin University, Changchun, China
| | - Hongjie Wang
- Urology Department, First Hospital of Jilin University, Changchun, China
| | - Rong Zhong
- Urology Department, First Hospital of Jilin University, Changchun, China
| | - Jiajun Li
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuchuan Hou
- Urology Department, First Hospital of Jilin University, Changchun, China
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López-López Á, López-Gonzálvez Á, Barbas C. Metabolomics for searching validated biomarkers in cancer studies: a decade in review. Expert Rev Mol Diagn 2024; 24:601-626. [PMID: 38904089 DOI: 10.1080/14737159.2024.2368603] [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: 12/27/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
INTRODUCTION In the dynamic landscape of modern healthcare, the ability to anticipate and diagnose diseases, particularly in cases where early treatment significantly impacts outcomes, is paramount. Cancer, a complex and heterogeneous disease, underscores the critical importance of early diagnosis for patient survival. The integration of metabolomics information has emerged as a crucial tool, complementing the genotype-phenotype landscape and providing insights into active metabolic mechanisms and disease-induced dysregulated pathways. AREAS COVERED This review explores a decade of developments in the search for biomarkers validated within the realm of cancer studies. By critically assessing a diverse array of research articles, clinical trials, and studies, this review aims to present an overview of the methodologies employed and the progress achieved in identifying and validating biomarkers in metabolomics results for various cancer types. EXPERT OPINION Through an exploration of more than 800 studies, this review has allowed to establish a general idea about state-of-art in the search of biomarkers in metabolomics studies involving cancer which include certain level of results validation. The potential for metabolites as diagnostic markers to reach the clinic and make a real difference in patient health is substantial, but challenges remain to be explored.
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Affiliation(s)
- Ángeles López-López
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
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Gerhardtova I, Cizmarova I, Jankech T, Olesova D, Jampilek J, Parrak V, Nemergutova K, Sopko L, Piestansky J, Kovac A. Implementation of Modern Therapeutic Drug Monitoring and Lipidomics Approaches in Clinical Practice: A Case Study with Colistin Treatment. Pharmaceuticals (Basel) 2024; 17:753. [PMID: 38931420 PMCID: PMC11206893 DOI: 10.3390/ph17060753] [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: 05/09/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Nowadays, lipidomics plays a crucial role in the investigation of novel biomarkers of various diseases. Its implementation into the field of clinical analysis led to the identification of specific lipids and/or significant changes in their plasma levels in patients suffering from cancer, Alzheimer's disease, sepsis, and many other diseases and pathological conditions. Profiling of lipids and determination of their plasma concentrations could also be helpful in the case of drug therapy management, especially in combination with therapeutic drug monitoring (TDM). Here, for the first time, a combined approach based on the TDM of colistin, a last-resort antibiotic, and lipidomic profiling is presented in a case study of a critically ill male patient suffering from Pseudomonas aeruginosa-induced pneumonia. Implementation of innovative analytical approaches for TDM (online combination of capillary electrophoresis with tandem mass spectrometry, CZE-MS/MS) and lipidomics (liquid chromatography-tandem mass spectrometry, LC-MS/MS) was demonstrated. The CZE-MS/MS strategy confirmed the chosen colistin drug dosing regimen, leading to stable colistin concentrations in plasma samples. The determined colistin concentrations in plasma samples reached the required minimal inhibitory concentration of 1 μg/mL. The complex lipidomics approach led to monitoring 545 lipids in collected patient plasma samples during and after the therapy. Some changes in specific individual lipids were in good agreement with previous lipidomics studies dealing with sepsis. The presented case study represents a good starting point for identifying particular individual lipids that could correlate with antimicrobial and inflammation therapeutic management.
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Affiliation(s)
- Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Ivana Cizmarova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University Bratislava, Odbojarov 10, 832 32 Bratislava, Slovakia;
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University Bratislava, Odbojarov 10, 832 32 Bratislava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Institute of Experimental Endocrinology, Biomedical Research Center SAS, Dubravska cesta 9, 845 10 Bratislava, Slovakia
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Vojtech Parrak
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Clinic of Hematology and Transfusiology, St. Cyril and Methodius Hospital, Antolska 11, 851 07 Bratislava, Slovakia; (K.N.); (L.S.)
| | - Kristina Nemergutova
- Clinic of Hematology and Transfusiology, St. Cyril and Methodius Hospital, Antolska 11, 851 07 Bratislava, Slovakia; (K.N.); (L.S.)
| | - Ladislav Sopko
- Clinic of Hematology and Transfusiology, St. Cyril and Methodius Hospital, Antolska 11, 851 07 Bratislava, Slovakia; (K.N.); (L.S.)
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University Bratislava, Odbojarov 10, 832 32 Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University Bratislava, Odbojarov 10, 832 32 Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia; (I.G.); (T.J.); (D.O.); (J.J.); (V.P.)
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy in Kosice, Komenského 68/73, 041 81 Kosice, Slovakia
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Kim YH, Chung JS, Lee HH, Park JH, Kim MK. Influence of Dietary Polyunsaturated Fatty Acid Intake on Potential Lipid Metabolite Diagnostic Markers in Renal Cell Carcinoma: A Case-Control Study. Nutrients 2024; 16:1265. [PMID: 38732512 PMCID: PMC11085891 DOI: 10.3390/nu16091265] [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: 03/29/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Non-invasive diagnostics are crucial for the timely detection of renal cell carcinoma (RCC), significantly improving survival rates. Despite advancements, specific lipid markers for RCC remain unidentified. We aimed to discover and validate potent plasma markers and their association with dietary fats. Using lipid metabolite quantification, machine-learning algorithms, and marker validation, we identified RCC diagnostic markers in studies involving 60 RCC and 167 healthy controls (HC), as well as 27 RCC and 74 HC, by analyzing their correlation with dietary fats. RCC was associated with altered metabolism in amino acids, glycerophospholipids, and glutathione. We validated seven markers (l-tryptophan, various lysophosphatidylcholines [LysoPCs], decanoylcarnitine, and l-glutamic acid), achieving a 96.9% AUC, effectively distinguishing RCC from HC. Decreased decanoylcarnitine, due to reduced carnitine palmitoyltransferase 1 (CPT1) activity, was identified as affecting RCC risk. High intake of polyunsaturated fatty acids (PUFAs) was negatively correlated with LysoPC (18:1) and LysoPC (18:2), influencing RCC risk. We validated seven potential markers for RCC diagnosis, highlighting the influence of high PUFA intake on LysoPC levels and its impact on RCC occurrence via CPT1 downregulation. These insights support the efficient and accurate diagnosis of RCC, thereby facilitating risk mitigation and improving patient outcomes.
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Affiliation(s)
- Yeon-Hee Kim
- Cancer Epidemiology Branch, Division of Cancer Epidemiology and Prevention, National Cancer Center, 323 Ilsandong-gu, Goyang-si 10408, Republic of Korea; (Y.-H.K.); (J.-H.P.)
| | - Jin-Soo Chung
- Department of Urology, Center for Urologic Cancer, Research Institute, Hospital of National Cancer Center, 323 Ilsandong-gu, Goyang-si 10408, Republic of Korea; (J.-S.C.); (H.-H.L.)
| | - Hyung-Ho Lee
- Department of Urology, Center for Urologic Cancer, Research Institute, Hospital of National Cancer Center, 323 Ilsandong-gu, Goyang-si 10408, Republic of Korea; (J.-S.C.); (H.-H.L.)
| | - Jin-Hee Park
- Cancer Epidemiology Branch, Division of Cancer Epidemiology and Prevention, National Cancer Center, 323 Ilsandong-gu, Goyang-si 10408, Republic of Korea; (Y.-H.K.); (J.-H.P.)
| | - Mi-Kyung Kim
- Cancer Epidemiology Branch, Division of Cancer Epidemiology and Prevention, National Cancer Center, 323 Ilsandong-gu, Goyang-si 10408, Republic of Korea; (Y.-H.K.); (J.-H.P.)
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Alves Costa Silva C, Piccinno G, Suissa D, Bourgin M, Schreibelt G, Durand S, Birebent R, Fidelle M, Sow C, Aprahamian F, Manghi P, Punčochář M, Asnicar F, Pinto F, Armanini F, Terrisse S, Routy B, Drubay D, Eggermont AMM, Kroemer G, Segata N, Zitvogel L, Derosa L, Bol KF, de Vries IJM. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial. Nat Commun 2024; 15:1633. [PMID: 38395948 PMCID: PMC10891084 DOI: 10.1038/s41467-024-45357-1] [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: 05/09/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.
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Grants
- The MIND-DC trial was funded by ZonMw, Ministry of Health, Welfare and Sport (VWS), Stichting ATK, Miltenyi Biotec (in-kind). This work was supported by SEERAVE Foundation, European Union Horizon 2020:Project Number: 825410 and Project Acronym: ONCOBIOME, Institut National du Cancer (INCa), ANR Ileobiome - 19-CE15-0029-01, ANR RHU5 “ANR-21-RHUS-0017” IMMUNOLIFE&#x201D;, MAdCAM INCA_ 16698, Ligue contre le cancer, LABEX OncoImmunology, la direction generale de l&#x2019;offre de soins (DGOS), Universite Paris-Sud, SIRIC SOCRATE (INCa/DGOS/INSERM 6043), and PACRI network. G.K. is supported by the Ligue contre le Cancer (équipe labellis&#x00E9;e); Agence National de la Recherche (ANR) – Projets blancs; AMMICa US23/CNRS UMS3655; Association pour la recherche sur le cancer (ARC); Canc&#x00E9;rop&#x00F4;le Ile-de-France; Fondation pour la Recherche M&#x00E9;dicale (FRM); a donation by Elior; Equipex Onco-Pheno-Screen; European Joint Programme on Rare Diseases (EJPRD); European Research Council Advanced Investigator Award (ERC-2021-ADG, ICD-Cancer, Grant No. 101052444), European Union Horizon 2020 Projects Oncobiome, Prevalung (grant No. 101095604) and Crimson; Fondation Carrefour; Institut National du Cancer (INCa); Institut Universitaire de France; LabEx Immuno-Oncology (ANR-18-IDEX-0001); a Cancer Research ASPIRE Award from the Mark Foundation; the RHU Immunolife; Seerave Foundation; SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); and SIRIC Cancer Research and Personalized Medicine (CARPEM). This study contributes to the IdEx Universit&#x00E9; de Paris ANR-18-IDEX-0001. This work is supported by the Prism project funded by the Agence Nationale de la Recherche under grant number ANR-18-IBHU-0002. CACS was funded by MSD Avenir. MF is funded by SEERAVE Foundation and MERCK Foundation. LD and BR were supported by Philantropia at Gustave Roussy Foundation.
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Affiliation(s)
- Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Gianmarco Piccinno
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Déborah Suissa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Mélanie Bourgin
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Gerty Schreibelt
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Marine Fidelle
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Cissé Sow
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Safae Terrisse
- Oncology Department, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Paris, France
| | - Bertrand Routy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, QC, Canada
| | - Damien Drubay
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Office of Biostatistics and Epidemiology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Alexander M M Eggermont
- Princess Máxima Center and University Medical Center Utrecht, 3584 CS Utrecht, The Netherlands
- Comprehensive Cancer Center Munich, Technical University Munich & Ludwig Maximiliaan University, Munich, Germany
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France.
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France.
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France.
- Center of Clinical Investigations BIOTHERIS, INSERM CIC1428, Villejuif, France.
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Kalijn F Bol
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands
| | - I Jolanda M de Vries
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
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8
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Gerhardtova I, Jankech T, Majerova P, Piestansky J, Olesova D, Kovac A, Jampilek J. Recent Analytical Methodologies in Lipid Analysis. Int J Mol Sci 2024; 25:2249. [PMID: 38396926 PMCID: PMC10889185 DOI: 10.3390/ijms25042249] [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: 01/19/2024] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.
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Affiliation(s)
- Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 05 Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 68/73, SK-041 81 Kosice, Slovakia
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
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9
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Cai Y, Wang Z, Guo S, Lin C, Yao H, Yang Q, Wang Y, Yu X, He X, Sun W, Qiu S, Guo Y, Tang S, Xie Y, Zhang A. Detection, mechanisms, and therapeutic implications of oncometabolites. Trends Endocrinol Metab 2023; 34:849-861. [PMID: 37739878 DOI: 10.1016/j.tem.2023.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/10/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023]
Abstract
Metabolic abnormalities are a hallmark of cancer cells and are essential to tumor progression. Oncometabolites have pleiotropic effects on cancer biology and affect a plethora of processes, from oncogenesis and metabolism to therapeutic resistance. Targeting oncometabolites, therefore, could offer promising therapeutic avenues against tumor growth and resistance to treatments. Recent advances in characterizing the metabolic profiles of cancer cells are shedding light on the underlying mechanisms and associated metabolic networks. This review summarizes the diverse detection methods, molecular mechanisms, and therapeutic targets of oncometabolites, which may lead to targeting oncometabolism for cancer therapy.
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Affiliation(s)
- Ying Cai
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Zhibo Wang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Sifan Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Qiang Yang
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Yan Wang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China
| | - Xiaodan Yu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China
| | - Xiaowen He
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China
| | - Wanying Sun
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China.
| | - Yu Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China.
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital, Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Medical University, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China.
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10
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Chen CJ, Lee DY, Yu J, Lin YN, Lin TM. Recent advances in LC-MS-based metabolomics for clinical biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:2349-2378. [PMID: 35645144 DOI: 10.1002/mas.21785] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 06/15/2023]
Abstract
The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
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Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ning Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Min Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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11
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Nizioł J, Ossoliński K, Płaza-Altamer A, Kołodziej A, Ossolińska A, Ossoliński T, Nieczaj A, Ruman T. Untargeted urinary metabolomics for bladder cancer biomarker screening with ultrahigh-resolution mass spectrometry. Sci Rep 2023; 13:9802. [PMID: 37328580 PMCID: PMC10275937 DOI: 10.1038/s41598-023-36874-y] [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: 03/24/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023] Open
Abstract
Bladder cancer (BC) is a common urological malignancy with a high probability of death and recurrence. Cystoscopy is used as a routine examination for diagnosis and following patient monitoring for recurrence. Repeated costly and intrusive treatments may discourage patients from having frequent follow-up screenings. Hence, exploring novel non-invasive ways to help identify recurrent and/or primary BC is critical. In this work, 200 human urine samples were profiled using ultra-high-performance liquid chromatography and ultra-high-resolution mass spectrometry (UHPLC-UHRMS) to uncover molecular markers differentiating BC from non-cancer controls (NCs). Univariate and multivariate statistical analyses with external validation identified metabolites that distinguish BC patients from NCs disease. More detailed divisions for the stage, grade, age, and gender are also discussed. Findings indicate that monitoring urine metabolites may provide a non-invasive and more straightforward diagnostic method for identifying BC and treating recurrent diseases.
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Affiliation(s)
- Joanna Nizioł
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland.
| | - Krzysztof Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Aneta Płaza-Altamer
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
| | - Artur Kołodziej
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
| | - Anna Ossolińska
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Tadeusz Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Anna Nieczaj
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
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12
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Xu H, Xu J, Liu X, Song W, Lyu X, Guo X, Hu W, Yang H, Wang L, Pan H, Chen J, Xing X, Zhu H, Sun W, Gong F. Serum metabolomics profiling of improved metabolic syndrome is characterized by decreased pro-inflammatory biomarkers: A longitudinal study in Chinese male adults. Nutr Res 2023; 115:13-25. [PMID: 37216838 DOI: 10.1016/j.nutres.2023.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Metabolic syndrome (MetS) is a serious global health concern. The objective of this study is to dynamically investigate the changes of metabolic profiles and metabolites in Chinese male MetS subjects after an 18 months diet and exercise intervention. Fifty male MetS patients defined according to International Diabetes Federation 2005 guidelines were subjected to diet and exercise counseling for 18 months. Serum samples were taken at baseline, 12 months, and 18 months, respectively, for clinical evaluation and metabolomics analyses. Diet and exercise intervention for 18 months achieved significant improvements in the metabolic profiles of all participants. Nineteen subjects (38.0%) exhibited MetS remission at the end of the study. A total of 812 relative features were characterized and 61 were successfully identified. Furthermore, 17 differential metabolites were of significance at both time points (baseline-12 months, baseline-18 months) and presented nonlinear trends through time. Eight metabolites (47.1%) were predominantly converged to inflammation and oxidative stress. Pro-inflammatory biomarkers were remarkably decreased after 18 months of intervention, and prostaglandin E2, neuroprotectin D1, and taxiphyllin in combination were firstly found to demonstrate a fair discriminative power (area under curve = 0.911) to predict the improvement of MetS undergone diet and exercise intervention. The significant shift of metabolomic profiling after 18 months of lifestyle counseling provide a novel insight and reveal that earlier inflammation control may be of potential benefit in MetS management.
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Affiliation(s)
- Hanyuan Xu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Department of Clinical Nutrition, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiyu Xu
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Song
- Medical Science Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Xiaorui Lyu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaonan Guo
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Wenjing Hu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jichun Chen
- Nutrition Department, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, China
| | - Xiaoping Xing
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Wei Sun
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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13
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Zhu Y, Zhou H, Chen H, Zhang J, Liang Y, Yang S, Wang X, Chen G, Zhang Q. Global Serum Metabolomic and Lipidomic Analyses Reveal Lipid Perturbations and Potential Biomarkers of the Colorectal Cancer by Adenoma–Carcinoma Sequence. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2023. [DOI: 10.1016/j.cjac.2023.100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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14
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Manzi M, Zabalegui N, Monge ME. Postoperative Metabolic Phenoreversion in Clear Cell Renal Cell Carcinoma. J Proteome Res 2023; 22:1-15. [PMID: 36484409 DOI: 10.1021/acs.jproteome.2c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ultimate goal of surgical treatment in cancer is to remove the tumor mass for restoring a healthy state. A 16-lipid panel that discriminated healthy controls from clear cell renal cell carcinoma (ccRCC) patients in a prior study was evaluated in the present work in paired-serum samples collected from patients (n = 41) before and after nephrectomy. Changes in the lipid and metabolite fingerprints from ccRCC patients were investigated and compared with fingerprints from healthy individuals obtained by means of ultra-performance liquid chromatography-high-resolution mass spectrometry. The lipid panel differentiated phenotypes associated with metabolic restoration after surgery, representing a serum signature of phenoreversion to a healthy metabolic state. In particular, PC 16:0/0:0, PC 18:2/18:2, and linoleic acid allowed discriminating serum samples from ccRCC patients with poor prognosis from those with an improved outcome during the follow-up period. Ratios of PC 16:0/0:0 and PC 18:2/18:2 with linoleic acid levels may contribute as prognostic tools to support decision-making during the patient follow-up care. The preliminary character of these results should be validated with larger cohorts, including subjects with different ethnicities, life style, and diets. MetaboLights study references: MTBLS1839, MTBLS3838, and MTBLS4629.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.,Departamento de Fisiología, Biología molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina
| | - Nicolás Zabalegui
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
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15
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Wang P, Yuan Y, Qiu M. Identification of Plasma Metabolites Associated with Lung Cancer Survival. Methods Mol Biol 2023; 2695:181-193. [PMID: 37450119 DOI: 10.1007/978-1-0716-3346-5_12] [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: 07/18/2023]
Abstract
Limited knowledge has been reported regarding the performance of plasma metabolomics for predicting lung cancer prognosis. In this chapter, we compared the plasma metabolomics of lung cancer patients with differential disease-free survival (DFS, <3 years vs. >4 years) using liquid chromatography-mass spectrometry. We identified 29 survival-related aqueous metabolites but no lipid metabolites. Amino acids and organic acids constitute the majority of these metabolites. The metabolic pathways of these metabolites were cysteine and methionine metabolism and arginine biosynthesis. The Cox proportional hazards regression models confirmed the predictive values of 18 metabolites for DFS, while the phosphocholine and xanthine showed independent predictive values. Regarding cancer phenotypes, thelephoric acid, phosphocholine, inosine, 3-hydroxyanthranilic acid, hypoxanthine, xanthine, and 4-hydroxybenzoic acid showed good correction with lymph node metastasis. Taken together, plasma metabolomics is a powerful tool for identifying prognostic metabolites of lung cancer.
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Affiliation(s)
- Peiyu Wang
- Thoracic Oncology Institute/Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Yuyao Yuan
- Department of Pathology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, China
| | - Mantang Qiu
- Thoracic Oncology Institute/Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
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16
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Blood Plasma Metabolome Profiling at Different Stages of Renal Cell Carcinoma. Cancers (Basel) 2022; 15:cancers15010140. [PMID: 36612136 PMCID: PMC9818272 DOI: 10.3390/cancers15010140] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Early diagnostics significantly improves the survival of patients with renal cell carcinoma (RCC), which is the prevailing type of adult kidney cancer. However, the absence of clinically obvious symptoms and effective screening strategies at the early stages result to disease progression and survival rate reducing. The study was focused on revealing of potential low molecular biomarkers for early-stage RCC. The untargeted direct injection mass spectrometry-based metabolite profiling of blood plasma samples from 51 non-cancer volunteers (control) and 78 patients with different RCC subtypes and stages (early stages of clear cell RCC (ccRCC), papillary RCC (pRCC), chromophobe RCC (chrRCC) and advanced stages of ccRCC) was performed. Comparative analysis of the blood plasma metabolites between the control and cancer groups provided the detection of metabolites associated with different tumor stages. The designed model based on the revealed metabolites demonstrated high diagnostic power and accuracy. Overall, using the metabolomics approach the study revealed the metabolites demonstrating a high value for design of plasma-based test to improve early ccRCC diagnosis.
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17
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Metabolomic and elemental profiling of blood serum in bladder cancer. J Pharm Anal 2022; 12:889-900. [PMID: 36605581 PMCID: PMC9805945 DOI: 10.1016/j.jpha.2022.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 01/09/2023] Open
Abstract
Bladder cancer (BC) is one of the most frequently diagnosed types of urinary cancer. Despite advances in treatment methods, no specific biomarkers are currently in use. Targeted and untargeted profiling of metabolites and elements of human blood serum from 100 BC patients and the same number of normal controls (NCs), with external validation, was attempted using three analytical methods, i.e., nuclear magnetic resonance, gold and silver-109 nanoparticle-based laser desorption/ionization mass spectrometry (LDI-MS), and inductively coupled plasma optical emission spectrometry (ICP-OES). All results were subjected to multivariate statistical analysis. Four potential serum biomarkers of BC, namely, isobutyrate, pyroglutamate, choline, and acetate, were quantified with proton nuclear magnetic resonance, which had excellent predictive ability as judged by the area under the curve (AUC) value of 0.999. Two elements, Li and Fe, were also found to distinguish between cancer and control samples, as judged from ICP-OES data and AUC of 0.807 (in validation set). Twenty-five putatively identified compounds, mostly related to glycans and lipids, differentiated BC from NCs, as detected using LDI-MS. Five serum metabolites were found to discriminate between tumor grades and nine metabolites between tumor stages. The results from three different analytical platforms demonstrate that the identified distinct serum metabolites and metal elements have potential to be used for noninvasive detection, staging, and grading of BC.
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18
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Nascentes Melo LM, Lesner NP, Sabatier M, Ubellacker JM, Tasdogan A. Emerging metabolomic tools to study cancer metastasis. Trends Cancer 2022; 8:988-1001. [PMID: 35909026 DOI: 10.1016/j.trecan.2022.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]
Abstract
Metastasis is responsible for 90% of deaths in patients with cancer. Understanding the role of metabolism during metastasis has been limited by the development of robust and sensitive technologies that capture metabolic processes in metastasizing cancer cells. We discuss the current technologies available to study (i) metabolism in primary and metastatic cancer cells and (ii) metabolic interactions between cancer cells and the tumor microenvironment (TME) at different stages of the metastatic cascade. We identify advantages and disadvantages of each method and discuss how these tools and technologies will further improve our understanding of metastasis. Studies investigating the complex metabolic rewiring of different cells using state-of-the-art metabolomic technologies have the potential to reveal novel biological processes and therapeutic interventions for human cancers.
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Affiliation(s)
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Sabatier
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessalyn M Ubellacker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany.
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19
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Shi H, Peng J, Hao J, Wang X, Xu M, Li S. Growth performance, digestibility, and plasma metabolomic profiles of Saanen goats exposed to different doses of aflatoxin B1. J Dairy Sci 2022; 105:9552-9563. [DOI: 10.3168/jds.2022-22129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
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20
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Hu X, Wang Z, Chen H, Zhao A, Sun N, Deng C. Diagnosing, Typing, and Staging of Renal Cell Carcinoma by Designer Matrix-Based Urinary Metabolic Analysis. Anal Chem 2022; 94:14846-14853. [PMID: 36260912 DOI: 10.1021/acs.analchem.2c01563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular diagnosing, typing, and staging have been considered to be the ideal alternatives of imaging-based detection methods in clinics. Designer matrix-based analytical tools, with high speed, throughout, efficiency and low/noninvasiveness, have attracted much attention recently for in vitro metabolite detection. Herein, we develop an advanced metabolic analysis tool based on highly porous metal oxides derived from available metal-organic frameworks (MOFs), which elaborately inherit the morphology and porosity of MOFs and newly incorporate laser adsorption capacity of metal oxides. Through optimized conditions, direct high-quality fingerprinting spectra in 0.5 μL of urine are acquired. Using these fingerprinting spectra, we can discriminate the renal cell carcinoma (RCC) from healthy controls with higher than 0.99 of area under the curve (AUC) values (R2Y(cum) = 0.744, Q2 (cum) = 0.880), as well, from patients with other tumors (R2Y(cum) = 0.748, Q2(cum) = 0.871). We also realize the typing of three RCC subtypes, including clear cell RCC, chromophobe RCC (R2Y(cum) = 0.620, Q2(cum) = 0.656), and the staging of RCC (R2Y(cum) = 0.755, Q2(cum) = 0.857). Moreover, the tumor sizes (threshold value is 3 cm) can be remarkably recognized by this advanced metabolic analysis tool (R2Y(cum) = 0.710, Q2(cum) = 0.787). Our work brings a bright prospect for designer matrix-based analytical tools in disease diagnosis, typing and staging.
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Affiliation(s)
- Xufang Hu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Zongping Wang
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310000, China
| | - Haolin Chen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - An Zhao
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310000, China.,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Chunhui Deng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, and Department of Chemistry, Fudan University, Shanghai 200032, China
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21
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Nizioł J, Ossoliński K, Płaza-Altamer A, Kołodziej A, Ossolińska A, Ossoliński T, Ruman T. Untargeted ultra-high-resolution mass spectrometry metabolomic profiling of blood serum in bladder cancer. Sci Rep 2022; 12:15156. [PMID: 36071106 PMCID: PMC9452537 DOI: 10.1038/s41598-022-19576-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Bladder cancer (BC) is a common urological cancer of high mortality and recurrence rates. Currently, cystoscopy is performed as standard examination for the diagnosis and subsequent monitoring for recurrence of the patients. Frequent expensive and invasive procedures may deterrent patients from regular follow-up screening, therefore it is important to look for new non-invasive methods to aid in the detection of recurrent and/or primary BC. In this study, ultra-high-performance liquid chromatography coupled with ultra-high-resolution mass spectrometry was employed for non-targeted metabolomic profiling of 200 human serum samples to identify biochemical signatures that differentiate BC from non-cancer controls (NCs). Univariate and multivariate statistical analyses with external validation revealed twenty-seven metabolites that differentiate between BC patients from NCs. Abundances of these metabolites displayed statistically significant differences in two independent training and validation sets. Twenty-three serum metabolites were also found to be distinguishing between low- and high-grade of BC patients and controls. Thirty-seven serum metabolites were found to differentiate between different stages of BC. The results suggest that measurement of serum metabolites may provide more facile and less invasive diagnostic methodology for detection of bladder cancer and recurrent disease management.
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Affiliation(s)
- Joanna Nizioł
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszow, Poland.
| | - Krzysztof Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Aneta Płaza-Altamer
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstańców Warszawy Ave., 35-959, Rzeszow, Poland
| | - Artur Kołodziej
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstańców Warszawy Ave., 35-959, Rzeszow, Poland
| | - Anna Ossolińska
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Tadeusz Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszow, Poland
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22
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Epidemiology and Prevention of Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14164059. [PMID: 36011051 PMCID: PMC9406474 DOI: 10.3390/cancers14164059] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
With 400,000 diagnosed and 180,000 deaths in 2020, renal cell carcinoma (RCC) accounts for 2.4% of all cancer diagnoses worldwide. The highest disease burden developed countries, primarily in Europe and North America. Incidence is projected to increase in the future as more countries shift to Western lifestyles. Risk factors for RCC include fixed factors such as gender, age, and hereditary diseases, as well as intervening factors such as smoking, obesity, hypertension, diabetes, diet and alcohol, and occupational exposure. Intervening factors in primary prevention, understanding of congenital risk factors and the establishment of early diagnostic tools are important for RCC. This review will discuss RCC epidemiology, risk factors, and biomarkers involved in reducing incidence and improving survival.
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23
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Zhao M, Liu X, Bu X, Li Y, Wang M, Zhang B, Sun W, Li C. Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation. PeerJ 2022; 10:e13853. [PMID: 35966924 PMCID: PMC9373988 DOI: 10.7717/peerj.13853] [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: 03/29/2022] [Accepted: 07/16/2022] [Indexed: 01/18/2023] Open
Abstract
Rivaroxaban, an oral factor Xa inhibitor, has been used to treating a series of thromboembolic disorders in clinical practice. Measurement of the anticoagulant effect of rivaroxaban is important to avoid serious bleeding events, thus ensuring the safety and efficacy of drug administration. Metabolomics could help to predict differences in the responses among patients by profiling metabolites in biosamples. In this study, plasma metabolomes before and 3 hours after rivaroxaban intake in 150 nonvalvular atrial fibrillation (NVAF) patients and 100 age/gender-matched controls were analyzed by liquid chromatography coupled with mass spectrometry (LC-MS/MS). When compared with controls, a total of thirteen plasma metabolites were differentially expressed in the NVAF patients. Pathway analysis revealed that purine and lipid metabolism were dysregulated. A panel of three metabolites (17a-ethynylestradiol, tryptophyl-glutamate and adenosine) showed good predictive ability to distinguish nonvalvular atrial fibrillation with an area under the receiver operating characteristic curve (AUC) of 1 for the discovery phase and 1 for validation. Under rivaroxaban treatment, a total of seven metabolites changed, the lipid and glycosylphosphatidylinositol biosynthesis pathways were altered and the panel consisting of avocadene, prenyl glucoside and phosphatidylethanolamine showed predictive ability with an AUC of 0.86 for the discovery dataset and 0.82 for the validation. The study showed that plasma metabolomic analyses hold the potential to differentiate nonvalvular atrial fibrillation and can help to monitor the effect of rivaroxaban anticoagulation.
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Affiliation(s)
- Mindi Zhao
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaoxiao Bu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yao Li
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng Wang
- Department of Clinical Laboratory, Baoding First Central Hospital, Baoding, Hebei, China
| | - Bo Zhang
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Chuanbao Li
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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24
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Fan Y, Xu C, Xie L, Wang Y, Zhu S, An J, Li Y, Tian Z, Yan Y, Yu S, Liu H, Jia B, Wang Y, Wang L, Yang L, Bian Y. Abnormal bile acid metabolism is an important feature of gut microbiota and fecal metabolites in patients with slow transit constipation. Front Cell Infect Microbiol 2022; 12:956528. [PMID: 35967856 PMCID: PMC9366892 DOI: 10.3389/fcimb.2022.956528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/04/2022] [Indexed: 12/12/2022] Open
Abstract
Destructions in the intestinal ecosystem are implicated with changes in slow transit constipation (STC), which is a kind of intractable constipation characterized by colonic motility disorder. In order to deepen the understanding of the structure of the STC gut microbiota and the relationship between the gut microbiota and fecal metabolites, we first used 16S rRNA amplicon sequencing to evaluate the gut microbiota in 30 STC patients and 30 healthy subjects. The α-diversity of the STC group was changed to a certain degree, and the β-diversity was significantly different, which indicated that the composition of the gut microbiota of STC patients was inconsistent with healthy subjects. Among them, Bacteroides, Parabacteroides, Desulfovibrionaceae, and Ruminiclostridium were significantly upregulated, while Subdoligranulum was significantly downregulated. The metabolomics showed that different metabolites between the STC and the control group were involved in the process of bile acids and lipid metabolism, including taurocholate, taurochenodeoxycholate, taurine, deoxycholic acid, cyclohexylsulfamate, cholic acid, chenodeoxycholate, arachidonic acid, and 4-pyridoxic acid. We found that the colon histomorphology of STC patients was significantly disrupted, and TGR5 and FXR were significantly downregulated. The differences in metabolites were related to changes in the abundance of specific bacteria and patients’ intestinal dysfunction. Analysis of the fecal genomics and metabolomics enabled separation of the STC from controls based on random forest model prediction [STC vs. control (14 gut microbiota and metabolite biomarkers)—Sensitivity: 1, Specificity: 0.877]. This study provided a perspective for the diagnosis and intervention of STC related with abnormal bile acid metabolism.
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Affiliation(s)
- Yadong Fan
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chen Xu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Lulu Xie
- School of Medicine, Nankai University, Tianjin, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shan Zhu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jiren An
- The First Clinical College, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Yuwei Li
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Zhikui Tian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yiqi Yan
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shuang Yu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Haizhao Liu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Beitian Jia
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yiyang Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Li Wang
- The Pharmacy Department, Tianjin Second People's Hospital, Tianjin, China
| | - Long Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Long Yang, ; Yuhong Bian,
| | - Yuhong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Long Yang, ; Yuhong Bian,
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25
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di Meo NA, Loizzo D, Pandolfo SD, Autorino R, Ferro M, Porta C, Stella A, Bizzoca C, Vincenti L, Crocetto F, Tataru OS, Rutigliano M, Battaglia M, Ditonno P, Lucarelli G. Metabolomic Approaches for Detection and Identification of Biomarkers and Altered Pathways in Bladder Cancer. Int J Mol Sci 2022; 23:ijms23084173. [PMID: 35456991 PMCID: PMC9030452 DOI: 10.3390/ijms23084173] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
Metabolomic analysis has proven to be a useful tool in biomarker discovery and the molecular classification of cancers. In order to find new biomarkers, and to better understand its pathological behavior, bladder cancer also has been studied using a metabolomics approach. In this article, we review the literature on metabolomic studies of bladder cancer, focusing on the different available samples (urine, blood, tissue samples) used to perform the studies and their relative findings. Moreover, the multi-omic approach in bladder cancer research has found novel insights into its metabolic behavior, providing excellent start-points for new diagnostic and therapeutic strategies. Metabolomics data analysis can lead to the discovery of a “signature pathway” associated with the progression of bladder cancer; this aspect could be potentially valuable in predictions of clinical outcomes and the introduction of new treatments. However, further studies are needed to give stronger evidence and to make these tools feasible for use in clinical practice.
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Affiliation(s)
- Nicola Antonio di Meo
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Davide Loizzo
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
| | - Savio Domenico Pandolfo
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
- Division of Urology, University of Naples “Federico II”, 80100 Naples, Italy
| | - Riccardo Autorino
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology (IEO), IRCCS, 20141 Milan, Italy;
| | - Camillo Porta
- Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (C.P.); (A.S.)
| | - Alessandro Stella
- Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (C.P.); (A.S.)
| | - Cinzia Bizzoca
- Department of General Surgery “Ospedaliera”, Polyclinic Hospital of Bari, 70124 Bari, Italy; (C.B.); (L.V.)
| | - Leonardo Vincenti
- Department of General Surgery “Ospedaliera”, Polyclinic Hospital of Bari, 70124 Bari, Italy; (C.B.); (L.V.)
| | - Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Octavian Sabin Tataru
- I.O.S.U.D., George Emil Palade University of Medicine and Pharmacy, Science and Technology, 540142 Targu Mures, Romania;
| | - Monica Rutigliano
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Michele Battaglia
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Pasquale Ditonno
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
- Correspondence:
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26
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Wang PP, Song X, Zhao XK, Wei MX, Gao SG, Zhou FY, Han XN, Xu RH, Wang R, Fan ZM, Ren JL, Li XM, Wang XZ, Yang MM, Hu JF, Zhong K, Lei LL, Li LY, Chen Y, Chen YJ, Ji JJ, Yang YZ, Li J, Wang LD. Serum Metabolomic Profiling Reveals Biomarkers for Early Detection and Prognosis of Esophageal Squamous Cell Carcinoma. Front Oncol 2022; 12:790933. [PMID: 35155234 PMCID: PMC8832491 DOI: 10.3389/fonc.2022.790933] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/04/2022] [Indexed: 11/15/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common aggressive malignancies worldwide, particularly in northern China. The absence of specific early symptoms and biomarkers leads to late-stage diagnosis, while early diagnosis and risk stratification are crucial for improving overall prognosis. We performed UPLC-MS/MS on 450 ESCC patients and 588 controls consisting of a discovery group and two validation groups to identify biomarkers for early detection and prognosis. Bioinformatics and clinical statistical methods were used for profiling metabolites and evaluating potential biomarkers. A total of 105 differential metabolites were identified as reliable biomarker candidates for ESCC with the same tendency in three cohorts, mainly including amino acids and fatty acyls. A predictive model of 15 metabolites [all-trans-13,14-dihydroretinol, (±)-myristylcarnitine, (2S,3S)-3-methylphenylalanine, 3-(pyrazol-1-yl)-L-alanine, carnitine C10:1, carnitine C10:1 isomer1, carnitine C14-OH, carnitine C16:2-OH, carnitine C9:1, formononetin, hyodeoxycholic acid, indole-3-carboxylic acid, PysoPE 20:3, PysoPE 20:3(2n isomer1), and resolvin E1] was developed by logistic regression after LASSO and random forest analysis. This model held high predictive accuracies on distinguishing ESCC from controls in the discovery and validation groups (accuracies > 89%). In addition, the levels of four downregulated metabolites [hyodeoxycholic acid, (2S,3S)-3-methylphenylalanine, carnitine C9:1, and indole-3-carboxylic acid] were significantly higher in early cancer than advanced cancer. Furthermore, three independent prognostic markers were identified by multivariate Cox regression analyses with and without clinical indicators: a high level of MG(20:4)isomer and low levels of 9,12-octadecadienoic acid and L-isoleucine correlated with an unfavorable prognosis; the risk score based on these three metabolites was able to stratify patients into low or high risk. Moreover, pathway analysis indicated that retinol metabolism and linoleic acid metabolism were prominent perturbed pathways in ESCC. In conclusion, metabolic profiling revealed that perturbed amino acids and lipid metabolism were crucial metabolic signatures of ESCC. Both panels of diagnostic and prognostic markers showed excellent predictive performances. Targeting retinol and linoleic acid metabolism pathways may be new promising mechanism-based therapeutic approaches. Thus, this study would provide novel insights for the early detection and risk stratification for the clinical management of ESCC and potentially improve the outcomes of ESCC.
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Affiliation(s)
- Pan Pan Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xue Ke Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Meng Xia Wei
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - She Gan Gao
- Department of Oncology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Fu You Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, China
| | - Xue Na Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Rui Hua Xu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ran Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zong Min Fan
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jing Li Ren
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xue Min Li
- Department of Pathology, Hebei Provincial Cixian People’s Hospital, Cixian, China
| | - Xian Zeng Wang
- Department of Thoracic Surgery, Linzhou People’s Hospital, Linzhou, China
| | - Miao Miao Yang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jing Feng Hu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Kan Zhong
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ling Ling Lei
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Liu Yu Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yao Chen
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ya Jie Chen
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jia Jia Ji
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yuan Ze Yang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Jia Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Li Dong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
- *Correspondence: Li Dong Wang,
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27
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Developing non-invasive bladder cancer screening methodology through potentiometric multisensor urine analysis. Talanta 2021; 234:122696. [PMID: 34364492 DOI: 10.1016/j.talanta.2021.122696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 11/22/2022]
Abstract
We report on the feasibility study exploring the potential of a simple electrochemical multisensor system as a tool for distinguishing between urine samples from patients with confirmed bladder cancer (36 samples) and healthy volunteers (51 samples). The potentiometric sensor responses obtained in urine samples were employed as the input data for various machine learning classification algorithms (logistic regression, random forest, extreme gradient boosting classifier, support vector machine, and voting classifier). The performance metrics of the classifiers were evaluated via Monte-Carlo cross-validation. The best model combining all the acquired data from the people aged 19-88 with different tumor grades and malignancies, including patients with recurrent bladder cancer, yielded 72% accuracy, 71% sensitivity, and 58% specificity. It was found that these metrics can be improved to 76% accuracy, 80% sensitivity, and 75% specificity when only a limited age group (50-88 years of age) is considered. Taking into account the simplicity of the proposed screening method, this technique appears to be a promising tool for further research.
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28
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Plyushchenko IV, Fedorova ES, Potoldykova NV, Polyakovskiy KA, Glukhov AI, Rodin IA. Omics Untargeted Key Script: R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study. J Proteome Res 2021; 21:833-847. [PMID: 34161108 DOI: 10.1021/acs.jproteome.1c00392] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale untargeted LC-MS-based metabolomic profiling is a valuable source for systems biology and biomarker discovery. Data analysis and processing are major tasks due to the high complexity of generated signals and the presence of unwanted variations. In the present study, we introduce an R-based open-source collection of scripts called OUKS (Omics Untargeted Key Script), which provides comprehensive data processing. OUKS is developed by integrating various R packages and metabolomics software tools and can be easily set up and prepared to create a custom pipeline. Novel computational features are related to quality control samples-based signal processing and are implemented by gradient boosting, tree-based, and other nonlinear regression algorithms. Bladder cancer biomarkers discovery study which is based on untargeted LC-MS profiling of urine samples is performed to demonstrate exhaustive functionality of the developed software tool. Unique examination among dozens of metabolomics-specific data curation methods was carried out at each processing step. As a result, potential biomarkers were identified, statistically validated, and described by metabolism disorders. Our study demonstrates that OUKS helps to make untargeted LC-MS metabolomic profiling with the latest computational features readily accessible in a ready-to-use unified manner to a research community.
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Affiliation(s)
- Ivan V Plyushchenko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elizaveta S Fedorova
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Natalia V Potoldykova
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, 119992 Moscow, Russia
| | - Konstantin A Polyakovskiy
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, 119992 Moscow, Russia
| | - Alexander I Glukhov
- Biology Department, Lomonosov Moscow State University, 119991 Moscow, Russia.,Department of Biochemistry, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Igor A Rodin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.,Department of Epidemiology and Evidence-Based Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
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29
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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