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Ban D, Housley SN, Matyunina LV, McDonald LD, Bae-Jump VL, Benigno BB, Skolnick J, McDonald JF. A personalized probabilistic approach to ovarian cancer diagnostics. Gynecol Oncol 2024; 182:168-175. [PMID: 38266403 PMCID: PMC10960662 DOI: 10.1016/j.ygyno.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/18/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE The identification/development of a machine learning-based classifier that utilizes metabolic profiles of serum samples to accurately identify individuals with ovarian cancer. METHODS Serum samples collected from 431 ovarian cancer patients and 133 normal women at four geographic locations were analyzed by mass spectrometry. Reliable metabolites were identified using recursive feature elimination coupled with repeated cross-validation and used to develop a consensus classifier able to distinguish cancer from non-cancer. The probabilities assigned to individuals by the model were used to create a clinical tool that assigns a likelihood that an individual patient sample is cancer or normal. RESULTS Our consensus classification model is able to distinguish cancer from control samples with 93% accuracy. The frequency distribution of individual patient scores was used to develop a clinical tool that assigns a likelihood that an individual patient does or does not have cancer. CONCLUSIONS An integrative approach using metabolomic profiles and machine learning-based classifiers has been employed to develop a clinical tool that assigns a probability that an individual patient does or does not have ovarian cancer. This personalized/probabilistic approach to cancer diagnostics is more clinically informative and accurate than traditional binary (yes/no) tests and represents a promising new direction in the early detection of ovarian cancer.
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Affiliation(s)
- Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - Stephen N Housley
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - Lilya V Matyunina
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - L DeEtte McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - Victoria L Bae-Jump
- Department of Obstetrics and Gynecology, University of North Carolina, 3009 Old Clinic Building, Chapel Hill, NC 27599, USA
| | - Benedict B Benigno
- Ovarian Cancer Institute, 1266 W. Paces Ferry Rd NW #339, Atlanta, GA 30327, USA
| | - Jeffrey Skolnick
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA; Ovarian Cancer Institute, 1266 W. Paces Ferry Rd NW #339, Atlanta, GA 30327, USA; Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA.
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Belenkov YN, Ageev AA, Kozhevnikova MV, Khabarova NV, Krivova AV, Korobkova EO, Popova LV, Emelyanov AV, Appolonova SA, Moskaleva NE, Shestakova KM, Privalova EV. Relationship of Acylcarnitines to Myocardial Ischemic Remodeling and Clinical Manifestations in Chronic Heart Failure. J Cardiovasc Dev Dis 2023; 10:438. [PMID: 37887885 PMCID: PMC10607617 DOI: 10.3390/jcdd10100438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Progressive myocardial remodeling (MR) in chronic heart failure (CHF) leads to aggravation of systolic dysfunction (SD) and clinical manifestations. Identification of metabolomic markers of these processes may help in the search for new therapeutic approaches aimed at achieving reversibility of MR and improving prognosis in patients with CHF. METHODS To determine the relationship between plasma acylcarnitine (ACs) levels, MR parameters and clinical characteristics, in patients with CHF of ischemic etiology (n = 79) and patients with coronary heart disease CHD (n = 19) targeted analysis of 30 ACs was performed by flow injection analysis mass spectrometry. RESULTS Significant differences between cohorts were found for the levels of 11 ACs. Significant positive correlations (r > 0.3) between the medium- and long-chain ACs (MCACs and LCACs) and symptoms (CHF NYHA functional class (FC); r = 0.31-0.39; p < 0.05); negative correlation (r = -0.31-0.34; p < 0.05) between C5-OH and FC was revealed. Positive correlations of MCACs and LCACs (r = 0.31-0.48; p < 0.05) with the left atrium size and volume, the right atrium volume, right ventricle, and the inferior vena cava sizes, as well as the pulmonary artery systolic pressure level were shown. A negative correlation between C18:1 and left ventricular ejection fraction (r = -0.31; p < 0.05) was found. However, a decrease in levels compared to referent values of ACs with medium and long chain lengths was 50% of the CHF-CHD cohort. Carnitine deficiency was found in 6% and acylcarnitine deficiency in 3% of all patients with chronic heart disease. CONCLUSIONS ACs may be used in assessing the severity of the clinical manifestations and MR. ACs are an important locus to study in terms of altered metabolic pathways in patients with CHF of ischemic etiology and SD. Further larger prospective trials are warranted and needed to determine the potential benefits to treat patients with CV diseases with aberrate AC levels.
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Affiliation(s)
- Yuri N. Belenkov
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Anton A. Ageev
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Maria V. Kozhevnikova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Natalia V. Khabarova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Anastasia V. Krivova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Ekaterina O. Korobkova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Ludmila V. Popova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Alexey V. Emelyanov
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
| | - Svetlana A. Appolonova
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (S.A.A.); (N.E.M.); (K.M.S.)
| | - Natalia E. Moskaleva
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (S.A.A.); (N.E.M.); (K.M.S.)
| | - Ksenia M. Shestakova
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (S.A.A.); (N.E.M.); (K.M.S.)
| | - Elena V. Privalova
- Hospital Therapy No. 1 Department, Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia; (A.A.A.); (N.V.K.); (A.V.K.); (E.O.K.); (L.V.P.); (A.V.E.); (E.V.P.)
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Ma Y, Chu M, Fu Z, Liu Q, Liang J, Xu J, Weng Z, Chen X, Xu C, Gu A. The Association of Metabolomic Profiles of a Healthy Lifestyle with Heart Failure Risk in a Prospective Study. Nutrients 2023; 15:2934. [PMID: 37447260 PMCID: PMC10346862 DOI: 10.3390/nu15132934] [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: 05/30/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Lifestyle has been linked to the incidence of heart failure, but the underlying biological mechanisms remain unclear. Using the metabolomic, lifestyle, and heart failure data of the UK Biobank, we identified and validated healthy lifestyle-related metabolites in a matched case-control and cohort study, respectively. We then evaluated the association of healthy lifestyle-related metabolites with heart failure (HF) risk and the added predictivity of these healthy lifestyle-associated metabolites for HF. Of 161 metabolites, 8 were identified to be significantly related to healthy lifestyle. Notably, omega-3 fatty acids and docosahexaenoic acid (DHA) positively associated with a healthy lifestyle score (HLS) and exhibited a negative association with heart failure risk. Conversely, creatinine negatively associated with a HLS, but was positively correlated with the risk of HF. Adding these three metabolites to the classical risk factor prediction model, the prediction accuracy of heart failure incidence can be improved as assessed by the C-statistic (increasing from 0.806 [95% CI, 0.796-0.816] to 0.844 [95% CI, 0.834-0.854], p-value < 0.001). A healthy lifestyle is associated with significant metabolic alterations, among which metabolites related to healthy lifestyle may be critical for the relationship between healthy lifestyle and HF. Healthy lifestyle-related metabolites might enhance HF prediction, but additional validation studies are necessary.
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Affiliation(s)
- Yuanyuan Ma
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Maomao Chu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Zuqiang Fu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- School of Public Health, Southeast University, Nanjing 211189, China
| | - Qian Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jingjia Liang
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jin Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Maternal, Child, and Adolescent Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhenkun Weng
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xiu Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Aihua Gu
- State Key Laboratory of Reproductive Medicine and Offspring Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Toxicology, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
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