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Wang C, Yang J, Li E, Luo S, Sun C, Liao Y, Li M, Ge J, Lei J, Zhou F, Wu L, Liao W. Metabolic signatures of hepatolithiasis using ultra-high performance liquid chromatography-tandem mass spectrometry. Metabolomics 2022; 18:69. [PMID: 35976530 DOI: 10.1007/s11306-022-01927-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS A metabolomic study of hepatolithiasis has yet to be performed. The purpose of the present study was to characterize the metabolite profile and identify potential biomarkers of hepatolithiasis using a metabolomic approach. METHODS We comprehensively analyzed the serum metabolites from 30 patients with hepatolithiasis and 20 healthy individuals using ultra-high performance liquid chromatography-tandem mass spectrometry operated in negative and positive ionization modes. Statistical analyses were performed using univariate (Student's t-test) and multivariate (orthogonal partial least-squares discriminant analysis) statistics and R language. Receiver operator characteristic (ROC) curve analysis was performed to identify potential predictors of hepatolithiasis. RESULTS We identified 277 metabolites that were significantly different between hepatolithiasis serum group and healthy control serum group. These metabolites were principally lipids and lipid-like molecules and amino acid metabolites. The steroid hormone biosynthesis pathway was enriched in hepatolithiasis serum group. In all specific metabolites, 75 metabolites were over-expressed in hepatolithiasis serum group. The AUC values for 60 metabolites exceeded 0.70, 4 metabolites including 18-β-Glycyrrhetinic acid, FMH, Rifampicin and PC (4:0/16:2) exceeded 0.90. CONCLUSIONS We have identified serum metabolites that are associated with hepatolithiasis for the first time. 60 potential metabolic biomarkers were identified, 18-β-Glycyrrhetinic acid, FMH, Rifampicin and PC (4:0/16:2) may have the potential clinical utility in hepatolithiasis.
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Affiliation(s)
- Cong Wang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Jun Yang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Enliang Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Shuaiwu Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Chi Sun
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Yuting Liao
- Department of Nursing, Gannan Medical College, No. 1, Medical Road, Ganzhou, 341000, China
| | - Min Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Jin Ge
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Jun Lei
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China
| | - Fan Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China.
| | - Linquan Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China.
| | - Wenjun Liao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, China.
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Kumar AA, Anusree VR, Satheesh G, Vijayakumar G, Chandran M, Simon L, Lakshmi S, Pillai MR, Jaleel A. Hyperhomocysteinemia-related serum metabolome alterations not normalized by short-term folic acid treatment. Metabolomics 2021; 17:47. [PMID: 33966131 DOI: 10.1007/s11306-021-01798-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/23/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Hyperhomocysteinemia (HHCys) is an independent risk factor for various diseases such as cardiovascular diseases, Alzheimer's, and cancers. Folate deficiency is one of the significant reasons for HHCys. However, it is not known whether folate deficiency with HHCys is associated with any serum metabolites. OBJECTIVES Our objective was to identify the metabolic alterations in people having folate deficiency with HHCys and check whether a short-term folic acid therapy could reverse those metabolic changes. METHODS The study enrolled 34 participants aged between 18 and 40 years having folate deficiency (< 4.6 ng/mL) with HHCys (> 15 μmol/L) and 21 normal healthy individuals. A short-term intervention of oral folic acid (5 mg/day) was done in the HHCys group for 30 days. Untargeted metabolomics analysis of serum was performed in all study subjects before and after the folic acid treatment. Different univariate methods and the multivariable-adjusted linear regression models were employed to determine an association between homocysteine level and metabolite profile. RESULTS Metabolomics analysis data showed that many metabolites involved in the biochemical pathways of lipid metabolisms such as polyunsaturated fatty acids, glycerolipids, and phospholipids were downregulated in the HHCys group. Short-term oral folic acid therapy significantly reduced their serum homocysteine level. However, the metabolic pathway alterations observed in folate-deficient HHCys-condition were unaltered even after the folic acid treatment. CONCLUSIONS Our study revealed that people who have a folic acid deficiency with HHCys have an altered metabolite profile related to lipid metabolism, which cannot be reversed by short-term folic acid therapy.
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Affiliation(s)
- A Aneesh Kumar
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Vanaja R Anusree
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Gopika Satheesh
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Gadadharan Vijayakumar
- Medical Trust Hospital and Diabetes Care Centre, Kulanada, Pathanamthitta, Kerala, India
| | - Mahesh Chandran
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Leena Simon
- Medical Trust Hospital and Diabetes Care Centre, Kulanada, Pathanamthitta, Kerala, India
| | - Subhadra Lakshmi
- Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram, Kerala, India
| | - Madhavan R Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Abdul Jaleel
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, Kerala, 695014, India.
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India.
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Zhong GX, Ye CL, Wei HX, Yang LY, Wei QX, Liu ZJ, Fu LX, Lin XH, Chen JY. Ultrasensitive Detection of RNA with Single-Base Resolution by Coupling Electrochemical Sensing Strategy with Chimeric DNA Probe-Aided Ligase Chain Reaction. Anal Chem 2020; 93:911-919. [PMID: 33284015 DOI: 10.1021/acs.analchem.0c03563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate and sensitive detection of single-base mutations in RNAs is of great value in basic studies of life science and medical diagnostics. However, the current available RNA detection methods are challenged by heterogeneous clinical samples in which trace RNA mutants usually existed in a large pool of normal wild sequences. Thus, there is still great need for developing the highly sensitive and highly specific methods in detecting single-base mutations of RNAs in heterogeneous clinical samples. In the present study, a new chimeric DNA probe-aided ligase chain reaction-based electrochemical method (cmDNA-eLCR) was developed for RNA mutation detection through the BSA-based carrier platform and the horseradish peroxidase-hydrogen peroxide-tetramethylbenzidine (HRP-H2O2-TMB) system. The denaturing polyacrylamide gel electrophoresis and a fluorophore-labeled probe was ingeniously designed to demonstrate the advantage of cmDNA in ligation to normal DNA templated by RNA with the catalysis of T4 RNA ligase 2 as well as its higher selectivity than DNA ligase system. Finally, the proposed cmDNA-eLCR, compared with the traditional eLCR, showed excellent performance in discriminating single base-mismatched sequences, where the signal response for mismatched targets at a high concentration could overlap completely with that for the blank control. Besides, this cmDNA-eLCR assay had a wide linear range crossing six orders of magnitude from 1.0 × 10-15 to1.0 × 10-10 M with a limit of detection as low as 0.6 fM. Furthermore, this assay was applied to detect RNA in real sample with a satisfactory result, thereby demonstrating its great potential in diagnosis of RNA-related diseases.
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Affiliation(s)
- Guang-Xian Zhong
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China
| | - Hong-Xiang Wei
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Leng-Xi Fu
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
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Ouyang D, Li R, Li Y, Zhu X. A 7-lncRNA signature predict prognosis of Uterine corpus endometrial carcinoma. J Cell Biochem 2019; 120:18465-18477. [PMID: 31168849 DOI: 10.1002/jcb.29164] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/16/2022]
Abstract
Current research indicate that long noncoding RNAs (lncRNAs) are associated with the progression of various cancers and can be used as prognostic biomarkers. This study aims to construct a prognostic lncRNA signature for the risk assessment of Uterine corpus endometrial carcinoma (UCEC). The RNA-Seq expression profile and corresponding clinical data of UCEC patients obtained from The Cancer Genome Atlas database. First, some prognosis-related lncRNAs were obtained by univariate Cox analysis. The minimum absolute contraction and selection operator (LASSO) regression and the Cox proportional hazard regression method were used to further identify the lncRNA prognostic model. Finally, seven lncRNAs (AC110491.1, AL451137.1, AC005381.1, AC103563.2, AC007422.2, AC108025.2, and MIR7-3HG) were identified as potential prognostic factors. According to the model constructed by the above analysis, the risk score of each UCEC patient was calculated, and the patients were classified into high and low-risk groups. The low-risk group had significant survival benefits. Moreover, we constructed a nomogram that incorporated independent prognostic factors (age, tumor stage, tumor grade, and risk score). The c-index value for evaluating the predictive nomogram model was 0.801. The area under the curve was 0.797 (3-year survival). The calibration curve also showed that there was a satisfactory agreement between the predicted and observed values in the probability of 1-, 3-, and 5-year overall survival. On the basis of the coexpression relationship, we established a coexpression network of lncRNA-messenger RNA (mRNA) of the 7-lncRNA. The Kyoto Encyclopedia of Genes and Genomes analysis of the coexpressing mRNAs showed that the main pathways related to the 7-lncRNA signature were neuroactive ligand-receptor interaction, serotonergic synapse, and gastric cancer pathway. Therefore, our study revealed that the 7-lncRNA could be used to predict the prognosis of UCEC and for postoperative treatment and follow-up.
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Affiliation(s)
- Dong Ouyang
- Department of Obstetrics and Gynecology, Akesu Hospital of Traditional Chinese Medicine, Akesu, China
| | - Ruyi Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yaxian Li
- Department of Obstetrics and Gynecology, Akesu Hospital of Traditional Chinese Medicine, Akesu, China
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Wren JD, Dozmorov MG, Toby I, Nanduri B, Homayouni R, Manda P, Thakkar S. Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 2017; 18:498. [PMID: 29297277 PMCID: PMC5751547 DOI: 10.1186/s12859-017-1887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jonathan D. Wren
- Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104-5005 USA
- Biochemistry and Molecular Biology Dept, Virginia Commonwealth University, 830 East Main Street, Richmond, Virginia, 23298 USA
- Stephenson Cancer Center, Virginia Commonwealth University, 830 East Main Street, Richmond, Virginia, 23298 USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Virginia Commonwealth University, 830 East Main Street, Richmond, Virginia, 23298 USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, 830 East Main Street, Richmond, Virginia, 23298 USA
| | - Inimary Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9066 USA
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762 USA
| | - Ramin Homayouni
- Department of Biological Sciences, Bioinformatics Program, University of Memphis, Memphis, TN 38152 USA
| | - Prashanti Manda
- Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC USA
| | - Shraddha Thakkar
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079 USA
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