1
|
Jaume G, Peeters T, Song AH, Pettit R, Williamson DFK, Oldenburg L, Vaidya A, de Brot S, Chen RJ, Thiran JP, Le LP, Gerber G, Mahmood F. AI-driven Discovery of Morphomolecular Signatures in Toxicology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604355. [PMID: 39091765 PMCID: PMC11291055 DOI: 10.1101/2024.07.19.604355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Early identification of drug toxicity is essential yet challenging in drug development. At the preclinical stage, toxicity is assessed with histopathological examination of tissue sections from animal models to detect morphological lesions. To complement this analysis, toxicogenomics is increasingly employed to understand the mechanism of action of the compound and ultimately identify lesion-specific safety biomarkers for which in vitro assays can be designed. However, existing works that aim to identify morphological correlates of expression changes rely on qualitative or semi-quantitative morphological characterization and remain limited in scale or morphological diversity. Artificial intelligence (AI) offers a promising approach for quantitatively modeling this relationship at an unprecedented scale. Here, we introduce GEESE, an AI model designed to impute morphomolecular signatures in toxicology data. Our model was trained to predict 1,536 gene targets on a cohort of 8,231 hematoxylin and eosin-stained liver sections from Rattus norvegicus across 127 preclinical toxicity studies. The model, evaluated on 2,002 tissue sections from 29 held-out studies, can yield pseudo-spatially resolved gene expression maps, which we correlate with six key drug-induced liver injuries (DILI). From the resulting 25 million lesion-expression pairs, we established quantitative relations between up and downregulated genes and lesions. Validation of these signatures against toxicogenomic databases, pathway enrichment analyses, and human hepatocyte cell lines asserted their relevance. Overall, our study introduces new methods for characterizing toxicity at an unprecedented scale and granularity, paving the way for AI-driven discovery of toxicity biomarkers.
Collapse
Affiliation(s)
- Guillaume Jaume
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | - Thomas Peeters
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Signal Processing Laboratory, EPFL, Lausanne, Switzerland
| | - Andrew H. Song
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | - Rowland Pettit
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Drew F. K. Williamson
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Lukas Oldenburg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Anurag Vaidya
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA
| | - Simone de Brot
- Institute of Animal Pathology, Vetsuisse, University of Bern, Switzerland
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Switzerland
| | - Richard J. Chen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | | | - Long Phi Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Harvard Data Science Initiative, Harvard University, Cambridge, MA
| | - Georg Gerber
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
- Harvard Data Science Initiative, Harvard University, Cambridge, MA
| |
Collapse
|
2
|
Shrestha RK, Nassar ZD, Hanson AR, Iggo R, Townley SL, Dehairs J, Mah CY, Helm M, Alizadeh-Ghodsi M, Pickering M, Ghesquière B, Watt MJ, Quek LE, Hoy AJ, Tilley WD, Swinnen JV, Butler LM, Selth LA. ACSM1 and ACSM3 Regulate Fatty Acid Metabolism to Support Prostate Cancer Growth and Constrain Ferroptosis. Cancer Res 2024; 84:2313-2332. [PMID: 38657108 DOI: 10.1158/0008-5472.can-23-1489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Solid tumors are highly reliant on lipids for energy, growth, and survival. In prostate cancer, the activity of the androgen receptor (AR) is associated with reprogramming of lipid metabolic processes. Here, we identified acyl-CoA synthetase medium chain family members 1 and 3 (ACSM1 and ACSM3) as AR-regulated mediators of prostate cancer metabolism and growth. ACSM1 and ACSM3 were upregulated in prostate tumors compared with nonmalignant tissues and other cancer types. Both enzymes enhanced proliferation and protected prostate cancer cells from death in vitro, whereas silencing ACSM3 led to reduced tumor growth in an orthotopic xenograft model. ACSM1 and ACSM3 were major regulators of the prostate cancer lipidome and enhanced energy production via fatty acid oxidation. Metabolic dysregulation caused by loss of ACSM1/3 led to mitochondrial oxidative stress, lipid peroxidation, and cell death by ferroptosis. Conversely, elevated ACSM1/3 activity enabled prostate cancer cells to survive toxic levels of medium chain fatty acids and promoted resistance to ferroptosis-inducing drugs and AR antagonists. Collectively, this study reveals a tumor-promoting function of medium chain acyl-CoA synthetases and positions ACSM1 and ACSM3 as key players in prostate cancer progression and therapy resistance. Significance: Androgen receptor-induced ACSM1 and ACSM3 mediate a metabolic pathway in prostate cancer that enables the utilization of medium chain fatty acids for energy production, blocks ferroptosis, and drives resistance to clinically approved antiandrogens.
Collapse
Affiliation(s)
- Raj K Shrestha
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, Australia
| | - Zeyad D Nassar
- South Australian Health and Medical Research Institute, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, Australia
| | - Adrienne R Hanson
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, Australia
| | - Richard Iggo
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Institut Bergonié Unicancer, INSERM, Bordeaux, France
| | - Scott L Townley
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, Australia
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Chui Y Mah
- South Australian Health and Medical Research Institute, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, Australia
| | - Madison Helm
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Mohammadreza Alizadeh-Ghodsi
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Marie Pickering
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Bart Ghesquière
- Metabolomics Core Facility Leuven, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Matthew J Watt
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Lake-Ee Quek
- School of Mathematics and Statistics, Charles Perkins Centre, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Andrew J Hoy
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lisa M Butler
- South Australian Health and Medical Research Institute, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, Australia
| | - Luke A Selth
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, Australia
| |
Collapse
|
3
|
Xu Z, Yu H, Meng X, Yu Z. Lipid metabolizing enzyme ACSM2B is a potential negative regulator of liver cancer progression. Asian J Surg 2024; 47:2517-2519. [PMID: 38278728 DOI: 10.1016/j.asjsur.2024.01.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Affiliation(s)
- Zhengfeng Xu
- Department of General Surgery, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, Heilong jiang Province, China; The Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang Province, China
| | - Hongwei Yu
- Department of General Surgery, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang Province, China
| | - Xingchu Meng
- Department of General Surgery, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, Heilong jiang Province, China.
| | - Ze Yu
- Department of General Surgery, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang Province, China; The Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang Province, China.
| |
Collapse
|
4
|
Parsazad E, Esrafili F, Yazdani B, Ghafarzadeh S, Razmavar N, Sirous H. Integrative bioinformatics analysis of ACS enzymes as candidate prognostic and diagnostic biomarkers in colon adenocarcinoma. Res Pharm Sci 2023; 18:413-429. [PMID: 37614614 PMCID: PMC10443664 DOI: 10.4103/1735-5362.378088] [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: 12/01/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 08/25/2023] Open
Abstract
Background and purpose Acyl-CoA synthetase (ACS) enzymes play an important role in the activation of fatty acids. While many studies have found correlations between the expression levels of ACS enzymes with the progression, growth, and survival of cancer cells, their role and expression patterns in colon adenocarcinoma are still greatly unknown and demand further investigation. Experimental approach The expression data of colon adenocarcinoma samples were downloaded from the Cancer Genome Atlas (TCGA) database. Normalization and differential expression analysis were performed to identify differentially expressed genes (DEGs). Gene set enrichment analysis was applied to identify top enriched genes from ACS enzymes in cancer samples. Gene ontology and protein-protein interaction analyses were performed for the prediction of molecular functions and interactions. Survival analysis and receiver operating characteristic test (ROC) were performed to find potential prognostic and diagnostic biomarkers. Findings/Results ACSL6 and ACSM5 genes demonstrated more significant differential expression and LogFC value compared to other ACS enzymes and also achieved the highest enrichment scores. Gene ontology analysis predicted the involvement of top DEGs in fatty acids metabolism, while protein-protein interaction network analysis presented strong interactions between ACSLs, ACSSs, ACSMs, and ACSBG enzymes with each other. Survival analysis suggested ACSM3 and ACSM5 as potential prognostic biomarkers, while the ROC test predicted stronger diagnostic potential for ACSM5, ACSS2, and ACSF2 genes. Conclusion and implications Our findings revealed the expression patterns, prognostic, and diagnostic biomarker potential of ACS enzymes in colon adenocarcinoma. ACSM3, ACSM5, ACSS2, and ACSF2 genes are suggested as possible prognostic and diagnostic biomarkers.
Collapse
Affiliation(s)
- Ehsan Parsazad
- Department of Bioscience and Biotechnology, Malek Ashtar University, Tehran, I.R. Iran
- Medvac Biopharma Company, Alborz Province, I.R. Iran
| | - Farina Esrafili
- Department of Genetics, Zanjan Branch, Islamic Azad University, Zanjan, I.R. Iran
| | - Behnaz Yazdani
- Department of Tissue Engineering, Najafabad Branch, Islamic Azad University, Najafabad, I.R. Iran
| | - Saghi Ghafarzadeh
- Department of Royan Institute, University of Science and Culture, Tehran, I.R. Iran
| | - Namdar Razmavar
- Department of Biology, University of Guilan, Rasht, I.R. Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| |
Collapse
|
5
|
Li Z, Yao Y, Qi T, Wu Z, Deng D, Liu B. ACSM6 overexpression indicates a non-inflammatory tumor microenvironment and predicts treatment response in bladder cancer: results from multiple real-world cohorts. Front Pharmacol 2023; 14:1222512. [PMID: 37426827 PMCID: PMC10323142 DOI: 10.3389/fphar.2023.1222512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Background: ACSMs play critical roles in lipid metabolism; however, their immunological function within the tumor microenvironment (TME) remains unclear, especially that of ACSM6. In this study, we investigate the latent effect of ACSM6 on bladder cancer (BLCA). Methods: Several real-world cohorts, including the Xiangya (in-house), The Cancer Genome Atlas (TCGA-BLCA), and IMvigor210 cohorts, with TCGA-BLCA cohort serving as the discovery cohort were compared. We investigated the potential immunological effects of ACSM6 in regulating the BLCA tumor microenvironment by analyzing its correlation with immunomodulators, anti-cancer immune cycles, immune checkpoints, tumor-infiltrating immune cells, and the T-cell inflamed score (TIS). Additionally, we assessed the precision of ACSM6 in predicting BLCA molecular subtypes and responses to several treatments using ROC analysis. To ensure the robustness of our findings, all results were confirmed in two independent external cohorts: the IMvigor210 and Xiangya cohorts. Results: ACSM6 expression was markedly upregulated in BLCA. Our analysis suggests that ACSM6 might have significant impact to promote the formation of a non-inflamed tumor microenvironment because of its negative correlation with immunomodulators, anticancer immune cycles, immune checkpoints, tumor-infiltrating immune cells, and the T-cell inflamed score (TIS). Additionally, high ACSM6 expression levels in BLCA may predict the luminal subtype, which is typically associated with resistance to chemotherapy, neoadjuvant chemotherapy, and radiotherapy. These findings were consistent across both the IMvigor210 and Xiangya cohorts. Conclusion: ACSM6 has the potential to serve as a valuable predictor of the tumor microenvironment phenotypes and treatment outcomes in BLCA, thereby contributing to more precise treatment.
Collapse
Affiliation(s)
- Zhiwei Li
- The Second Affiliated Hospital, Department of Urology, Hengyang Medical School, Unversity of South China, Hengyang, Hunan, China
| | - Yiyan Yao
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Tiezheng Qi
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Zuowei Wu
- Department of Interventional Radiology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Dingshan Deng
- Department of Urology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bolong Liu
- Department of Urology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The First Affiliated Hospital, Department of Andrology, Hengyang Medical School, University of South China, Hengyang, China
| |
Collapse
|
6
|
Wen FL, Xu YJ, Xue LE, Fu YF, Cui LL, Wang JZ, Zheng HP, Zhou DH, Lu J. Proteomics analyses of acute kidney injury biomarkers in a rat exertional heat stroke model. Front Physiol 2023; 14:1176998. [PMID: 37378075 PMCID: PMC10291232 DOI: 10.3389/fphys.2023.1176998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The frequency of exertional heat stroke (EHS) increases with the gradual elevation of global temperatures during summer. Acute kidney injury (AKI) is a common complication of EHS, and its occurrence often indicates the worsening of a patient's condition or a poor prognosis. In this study, a rat model of AKI caused by EHS was established, and the reliability of the model was evaluated by HE staining and biochemical assays. The expression of kidney tissue proteins in the EHS rats was analyzed using label-free liquid chromatography-tandem mass spectrometry. A total of 3,129 differentially expressed proteins (DEPs) were obtained, and 10 key proteins were finally identified, which included three upregulated proteins (Ahsg, Bpgm, and Litaf) and seven downregulated proteins (medium-chain acyl-CoA synthetase 2 (Acsm2), Hadha, Keg1, Sh3glb1, Eif3d, Ambp, and Ddah2). The qPCR technique was used to validate these 10 potential biomarkers in rat kidney and urine. In addition, Acsm2 and Ahsg were double-validated by Western blotting. Overall, this study identified 10 reliable biomarkers that may provide potential targets for the treatment of AKI caused by EHS.
Collapse
Affiliation(s)
- Fu-Li Wen
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yong-Jun Xu
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lai-En Xue
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yun-Feng Fu
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lin-Lin Cui
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Jun-Zhu Wang
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - He-Ping Zheng
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Dong-Hui Zhou
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Lu
- Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| |
Collapse
|
7
|
Huang C, Lei H, Liu C, Wang Y. Acute and subchronic exposure of cyadox induced metabolic and transcriptomic disturbances in Wistar rats. Toxicology 2022; 482:153367. [DOI: 10.1016/j.tox.2022.153367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
|
8
|
Yang X, Wu G, Zhang Q, Chen X, Li J, Han Q, Yang L, Wang C, Huang M, Li Y, Chen J, LiLi, Wang H, Liu K. ACSM3 suppresses the pathogenesis of high-grade serous ovarian carcinoma via promoting AMPK activity. Cell Oncol (Dordr) 2022; 45:151-161. [PMID: 35124784 DOI: 10.1007/s13402-021-00658-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 11/03/2022] Open
Abstract
PURPOSE Ovarian carcinoma is the fifth commonest malignancy in females and exhibits a high recurrence rate. High-grade serous ovarian carcinoma (HGSOC) is the main histologic subtype. It displays extensive genetic heterogeneity. Here, we aimed to identify potential therapeutic targets for HGSOC. METHODS Both bioinformatic data from TCGA and 73 pairs of tumor and normal samples from patients were analyzed to reveal the expression level of ACSM3 in HGSOC. Next, cellular and animal experiments, including cell proliferation, colony formation and xenograft assays were performed to explore the suppressive function of ACSM3. Finally, biochemical methods, AMP/ATP ratio measurements and Western blotting were used to elucidate the mechanism underlying the ACSM3-AMPK axis in HGSOC. RESULTS After analyzing transcriptome data of TCGA HGSOC samples, we found that ACSM3 is down-regulated in patient samples compared with normal controls. This observation was validated using data from primary clinical samples. Proliferation, soft agar colony formation and xenograft assays revealed that ACSM3 is able to suppress HGSOC tumor growth both in vitro and in vivo. Moreover, we found that ACSM3 overexpression increased the AMP/ATP ratio and the phosphorylation level of AMPK at threonine 172. In addition, we found that AMPK silencing in EFO21 and SKOV3 cells completely abolished the anti-oncogenic effect of ACSM3. CONCLUSION Our data indicate that the ACSM3-AMPK axis is involved in the pathogenesis of HGSOC and, as such, may act as a therapeutic target for this cancer.
Collapse
Affiliation(s)
- Xu Yang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China.
| | - GuiXia Wu
- Department of Physiology, School of Basic Medicine, Xinjiang Medical University, Urumchi, Xinjiang Uygur Autonomous Region, People's Republic of China
| | - Qin Zhang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Xia Chen
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Juan Li
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Qian Han
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Lei Yang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Chendi Wang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Mei Huang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Yun Li
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Jiao Chen
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - LiLi
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Haiying Wang
- Department of Obstetrics and Gynecology, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, No. 33, Mashi Street, Wenjiang District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Kaijiang Liu
- Department of Gynecological Oncology, Ren Ji Hospital, School of Medicine, Shanghai JiaoTong University, No145 Middle Shandong Road, Huangpu District, Shanghai, 200001, People's Republic of China.
| |
Collapse
|
9
|
Yazdani B, Jazini M, Jabbari N, Karami M, Rahimirad S, Azadeh M, Mahdevar M, Ghaedi K. Altered expression level of ACSM5 in breast cancer: An integrative analysis of tissue biomarkers with diagnostic potential. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
10
|
Gámez-Belmonte R, Tena-Garitaonaindia M, Hernández-Chirlaque C, Córdova S, Ceacero-Heras D, de Medina FS, Martínez-Augustin O. Deficiency in Tissue Non-Specific Alkaline Phosphatase Leads to Steatohepatitis in Mice Fed a High Fat Diet Similar to That Produced by a Methionine and Choline Deficient Diet. Int J Mol Sci 2020; 22:ijms22010051. [PMID: 33374541 PMCID: PMC7793076 DOI: 10.3390/ijms22010051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/15/2023] Open
Abstract
The liver expresses tissue-nonspecific alkaline phosphatase (TNAP), which may participate in the defense against bacterial components, in cell regulation as part of the purinome or in bile secretion, among other roles. We aimed to study the role of TNAP in the development of hepatosteatosis. TNAP+/− haplodeficient and wild type (WT) mice were fed a control diet (containing 10% fat w/w) or the same diet deficient in methionine and choline (MCD diet). The MCD diet induced substantial weight loss together with hepatic steatosis and increased alanine aminotransferase (ALT) plasma levels, but no differences in IL-6, TNF, insulin or resistin. There were no substantial differences between TNAP+/− and WT mice fed the MCD diet. In turn, TNAP+/− mice receiving the control diet presented hepatic steatosis with alterations in metabolic parameters very similar to those induced by the MCD diet. Nevertheless, no weight loss, increased ALT plasma levels or hypoglycemia were observed. These mice also presented increased levels of liver TNF and systemic resistin and glucagon compared to WT mice. The phenotype of TNAP+/− mice fed a standard diet was normal. In conclusion, TNAP haplodeficiency induces steatosis comparable to that produced by a MCD diet when fed a control diet.
Collapse
Affiliation(s)
- Reyes Gámez-Belmonte
- Department of Pharmacology, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain;
| | - Mireia Tena-Garitaonaindia
- Department of Biochemistry and Molecular Biology 2, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, Instituto de Nutrición y Tecnología de los Alimentos José Mataix, University of Granada, 18071 Granada, Spain; (M.T.-G.); (C.H.-C.); (S.C.); (D.C.-H.); (O.M.-A.)
| | - Cristina Hernández-Chirlaque
- Department of Biochemistry and Molecular Biology 2, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, Instituto de Nutrición y Tecnología de los Alimentos José Mataix, University of Granada, 18071 Granada, Spain; (M.T.-G.); (C.H.-C.); (S.C.); (D.C.-H.); (O.M.-A.)
| | - Samir Córdova
- Department of Biochemistry and Molecular Biology 2, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, Instituto de Nutrición y Tecnología de los Alimentos José Mataix, University of Granada, 18071 Granada, Spain; (M.T.-G.); (C.H.-C.); (S.C.); (D.C.-H.); (O.M.-A.)
| | - Diego Ceacero-Heras
- Department of Biochemistry and Molecular Biology 2, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, Instituto de Nutrición y Tecnología de los Alimentos José Mataix, University of Granada, 18071 Granada, Spain; (M.T.-G.); (C.H.-C.); (S.C.); (D.C.-H.); (O.M.-A.)
| | - Fermín Sánchez de Medina
- Department of Pharmacology, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain;
- Correspondence: ; Tel.: +34-958-241747
| | - Olga Martínez-Augustin
- Department of Biochemistry and Molecular Biology 2, CIBERehd, School of Pharmacy, Instituto de Investigación Biosanitaria ibs.GRANADA, Instituto de Nutrición y Tecnología de los Alimentos José Mataix, University of Granada, 18071 Granada, Spain; (M.T.-G.); (C.H.-C.); (S.C.); (D.C.-H.); (O.M.-A.)
| |
Collapse
|
11
|
Fushimi T, Izumi Y, Takahashi M, Hata K, Murano Y, Bamba T. Dynamic Metabolome Analysis Reveals the Metabolic Fate of Medium-Chain Fatty Acids in AML12 Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11997-12010. [PMID: 33073987 DOI: 10.1021/acs.jafc.0c04723] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Several studies in hepatocyte cell lines reported that medium-chain fatty acids (MCFAs) with 6-12 carbons showed different metabolic properties from long-chain fatty acids (LCFAs). However, these studies reported unclear effects of different fatty acid molecules on hepatocyte metabolism. This study is aimed to capture the metabolic kinetics of MCFA assimilation in AML12 cells treated with octanoic acid (FA 8:0), decanoic acid (FA 10:0), or lauric acid (FA12:0) [LCFA; oleic acid (FA 18:1)] via metabolic profiling and dynamic metabolome analysis with 13C-labeling. The concentrations of total ketone bodies in the media of cells treated with FA 8:0 or FA 10:0 were 3.22- or 3.69-fold higher than those obtained with FA 18:1 treatment, respectively. FA 12:0 treatment did not significantly increase ketone body levels compared to DMSO treatment (control), whereas FA 12:0 treatment increased intracellular triacylglycerol (TG) levels 15.4 times compared to the control. Metabolic profiles of FA 12:0-treated samples differed from those of the FA 8:0-treated and FA 10:0-treated samples, suggesting that metabolic assimilation of MCFAs differed significantly depending on the MCFA type. Furthermore, the dynamic metabolome analysis clearly revealed that FA 8:0 was rapidly and quantitatively oxidized to acetyl-CoA and assimilated into ketone bodies, citrate cycle intermediates, and glucogenic amino acids but not readily into TGs.
Collapse
Affiliation(s)
- Tatsuya Fushimi
- Central Research Laboratory, The Nisshin OilliO Group, Ltd., 1 Shinmori-cho, Isogo-ku, Yokohama 235-8558, Japan
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kosuke Hata
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Murano
- Central Research Laboratory, The Nisshin OilliO Group, Ltd., 1 Shinmori-cho, Isogo-ku, Yokohama 235-8558, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
12
|
Watanabe H, Paxton RL, Tolerico MR, Nagalakshmi VK, Tanaka S, Okusa MD, Goto S, Narita I, Watanabe S, Sequeira-Lοpez MLS, Gomez RA. Expression of Acsm2, a kidney-specific gene, parallels the function and maturation of proximal tubular cells. Am J Physiol Renal Physiol 2020; 319:F603-F611. [PMID: 32830538 DOI: 10.1152/ajprenal.00348.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The acyl-CoA synthetase medium-chain family member 2 (Acsm2) gene was first identified and cloned by our group as a kidney-specific "KS" gene. However, its expression pattern and function remain to be clarified. In the present study, we found that the Acsm2 gene was expressed specifically and at a high level in normal adult kidneys. Expression of Acsm2 in kidneys followed a maturational pattern: it was low in newborn mice and increased with kidney development and maturation. In situ hybridization and immunohistochemistry revealed that Acsm2 was expressed specifically in proximal tubular cells of adult kidneys. Data from the Encyclopedia of DNA Elements database revealed that the Acsm2 gene locus in the mouse has specific histone modifications related to the active transcription of the gene exclusively in kidney cells. Following acute kidney injury, partial unilateral ureteral obstruction, and chronic kidney diseases, expression of Acsm2 in the proximal tubules was significantly decreased. In human samples, the expression pattern of ACSM2A, a homolog of mouse Acsm2, was similar to that in mice, and its expression decreased with several types of renal injuries. These results indicate that the expression of Acsm2 parallels the structural and functional maturation of proximal tubular cells. Downregulation of its expression in several models of kidney disease suggests that Acms2 may serve as a novel marker of proximal tubular injury and/or dysfunction.
Collapse
Affiliation(s)
- Hirofumi Watanabe
- Department of Pediatrics, Child Health Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Robert L Paxton
- Department of Pediatrics, Child Health Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Matthew R Tolerico
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Vidya K Nagalakshmi
- Department of Pediatrics, Child Health Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Shinji Tanaka
- Division of Nephrology and Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia, Charlottesville, Virginia
| | - Mark D Okusa
- Division of Nephrology and Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia, Charlottesville, Virginia
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Seiji Watanabe
- Department of Pediatrics, Izu Medical and Welfare Center, Shizuoka, Japan
| | - Maria Luisa S Sequeira-Lοpez
- Department of Pediatrics, Child Health Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - R Ariel Gomez
- Department of Pediatrics, Child Health Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| |
Collapse
|
13
|
Damiano F, De Benedetto GE, Longo S, Giannotti L, Fico D, Siculella L, Giudetti AM. Decanoic Acid and Not Octanoic Acid Stimulates Fatty Acid Synthesis in U87MG Glioblastoma Cells: A Metabolomics Study. Front Neurosci 2020; 14:783. [PMID: 32792906 PMCID: PMC7390945 DOI: 10.3389/fnins.2020.00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Medium-chain fatty acids (MCFA) are dietary components with a chain length ranging from 6 to 12 carbon atoms. MCFA can cross the blood-brain barrier and in the brain can be oxidized through mitochondrial β-oxidation. As components of ketogenic diets, MCFA have demonstrated beneficial effects on different brain diseases, such as traumatic brain injury, Alzheimer’s disease, drug-resistant epilepsy, diabetes, and cancer. Despite the interest in MCFA effects, not much information is available about MCFA metabolism in the brain. In this study, with a gas chromatography-mass spectrometry (GC-MS)-based metabolomics approach, coupled with multivariate data analyses, we followed the metabolic changes of U87MG glioblastoma cells after the addition of octanoic (C8), or decanoic (C10) acids for 24 h. Our analysis highlighted significant differences in the metabolism of U87MG cells after the addition of C8 or C10 and identified several metabolites whose amount changed between the two groups of treated cells. Overall, metabolic pathway analyses suggested the citric acid cycle, Warburg effect, glutamine/glutamate metabolism, and ketone body metabolism as pathways influenced by C8 or C10 addition to U87MG cells. Our data demonstrated that, while C8 affected mitochondrial metabolism resulting in increased ketone body production, C10 mainly influenced cytosolic pathways by stimulating fatty acid synthesis. Moreover, glutamine might be the main substrate to support fatty acids synthesis in C10-treated cells. In conclusion, we identified a metabolic signature associated with C8 or C10 addition to U87MG cells that can be used to decipher metabolic responses of glioblastoma cells to MCFA treatment.
Collapse
Affiliation(s)
- Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Giuseppe E De Benedetto
- Analytical and Isotopic Mass Spectrometry Laboratory, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Serena Longo
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Laura Giannotti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Daniela Fico
- Analytical and Isotopic Mass Spectrometry Laboratory, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Anna M Giudetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| |
Collapse
|
14
|
Nakayama A, Nakatochi M, Kawamura Y, Yamamoto K, Nakaoka H, Shimizu S, Higashino T, Koyama T, Hishida A, Kuriki K, Watanabe M, Shimizu T, Ooyama K, Ooyama H, Nagase M, Hidaka Y, Matsui D, Tamura T, Nishiyama T, Shimanoe C, Katsuura-Kamano S, Takashima N, Shirai Y, Kawaguchi M, Takao M, Sugiyama R, Takada Y, Nakamura T, Nakashima H, Tsunoda M, Danjoh I, Hozawa A, Hosomichi K, Toyoda Y, Kubota Y, Takada T, Suzuki H, Stiburkova B, Major TJ, Merriman TR, Kuriyama N, Mikami H, Takezaki T, Matsuo K, Suzuki S, Hosoya T, Kamatani Y, Kubo M, Ichida K, Wakai K, Inoue I, Okada Y, Shinomiya N, Matsuo H. Subtype-specific gout susceptibility loci and enrichment of selection pressure on ABCG2 and ALDH2 identified by subtype genome-wide meta-analyses of clinically defined gout patients. Ann Rheum Dis 2020; 79:657-665. [PMID: 32238385 PMCID: PMC7213308 DOI: 10.1136/annrheumdis-2019-216644] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/01/2023]
Abstract
Objectives Genome-wide meta-analyses of clinically defined gout were performed to identify subtype-specific susceptibility loci. Evaluation using selection pressure analysis with these loci was also conducted to investigate genetic risks characteristic of the Japanese population over the last 2000–3000 years. Methods Two genome-wide association studies (GWASs) of 3053 clinically defined gout cases and 4554 controls from Japanese males were performed using the Japonica Array and Illumina Array platforms. About 7.2 million single-nucleotide polymorphisms were meta-analysed after imputation. Patients were then divided into four clinical subtypes (the renal underexcretion type, renal overload type, combined type and normal type), and meta-analyses were conducted in the same manner. Selection pressure analyses using singleton density score were also performed on each subtype. Results In addition to the eight loci we reported previously, two novel loci, PIBF1 and ACSM2B, were identified at a genome-wide significance level (p<5.0×10–8) from a GWAS meta-analysis of all gout patients, and other two novel intergenic loci, CD2-PTGFRN and SLC28A3-NTRK2, from normal type gout patients. Subtype-dependent patterns of Manhattan plots were observed with subtype GWASs of gout patients, indicating that these subtype-specific loci suggest differences in pathophysiology along patients’ gout subtypes. Selection pressure analysis revealed significant enrichment of selection pressure on ABCG2 in addition to ALDH2 loci for all subtypes except for normal type gout. Conclusions Our findings on subtype GWAS meta-analyses and selection pressure analysis of gout will assist elucidation of the subtype-dependent molecular targets and evolutionary involvement among genotype, phenotype and subtype-specific tailor-made medicine/prevention of gout and hyperuricaemia.
Collapse
Affiliation(s)
- Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Medical Squadron, Air Base Group, Western Aircraft Control and Warning Wing, Japan Air Self-Defense Force, Kasuga, Japan
| | - Masahiro Nakatochi
- Division of Department of Nursing, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of General Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | | | | | | | | | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Chisato Shimanoe
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Clinical Research Center, Saga University Hospital, Saga, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Naoyuki Takashima
- Department of Health Science, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Urology, National Defense Medical College, Tokorozawa, Japan
| | - Mikiya Takao
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Surgery, National Defense Medical College, Tokorozawa, Japan
| | - Ryo Sugiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yuzo Takada
- Faculty of Medical Science, Teikyo University of Science, Tokyo, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Masashi Tsunoda
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Inaho Danjoh
- Group of Privacy Controls, Tohoku Medical Megabank Organization, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yu Kubota
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Blanka Stiburkova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | - Tanya J Major
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | | |
Collapse
|
15
|
Xiong X, Han L, Liu S, Miao J, Luo M, Xue M, Wang X, Ni L, Yang J, Huang C. Music intervention improves spatial learning and memory and alters serum proteomics profiling in rats. J Neurosci Res 2018; 96:1727-1736. [PMID: 30063070 DOI: 10.1002/jnr.24275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/24/2018] [Accepted: 06/04/2018] [Indexed: 12/29/2022]
Abstract
Music has a long history of healing or mitigating physical and mental illness in the clinical setting. We aimed to test changes in behavioral cognition and serum proteomics in rats undergoing music intervention (MI). The Morris water maze (MWM) was used to evaluate spatial learning and memory in rats. Serum protein expression profiling was examined using magnetic bead-based matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS). MI improved spatial learning and memory in both male and female rats. Peak 1708.61 (m/z values) was significantly increased in MI females vs. female controls. Peak 3925.09 (m/z values) was significantly reduced in MI males versus male controls. The two differential serum peptide peaks (m/z values: 1708.61, 3925.09) were further sequence identified as regions of proteins Desmin and Acsm1. Western blot and immunofluorescence testing of Desmin expression showed consistent results on proteomics analysis. MI plays an important role in behavioral cognition and protein expression in rats. This study provides a foundation in proteomics that suggests that MI might improve spatial learning and memory ability.
Collapse
Affiliation(s)
- Xiaofan Xiong
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Lin Han
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Siyuan Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Jiyu Miao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Mai Luo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Meng Xue
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Lei Ni
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China
| | - Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| |
Collapse
|
16
|
Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B. Mol Genet Genomics 2018; 293:1279-1292. [PMID: 29948332 DOI: 10.1007/s00438-018-1460-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.
Collapse
|
17
|
Steensels S, Ersoy BA. Fatty acid activation in thermogenic adipose tissue. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:79-90. [PMID: 29793055 DOI: 10.1016/j.bbalip.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/10/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023]
Abstract
Channeling carbohydrates and fatty acids to thermogenic tissues, including brown and beige adipocytes, have garnered interest as an approach for the management of obesity-related metabolic disorders. Mitochondrial fatty acid oxidation (β-oxidation) is crucial for the maintenance of thermogenesis. Upon cellular fatty acid uptake or following lipolysis from triglycerides (TG), fatty acids are esterified to coenzyme A (CoA) to form active acyl-CoA molecules. This enzymatic reaction is essential for their utilization in β-oxidation and thermogenesis. The activation and deactivation of fatty acids are regulated by two sets of enzymes called acyl-CoA synthetases (ACS) and acyl-CoA thioesterases (ACOT), respectively. The expression levels of ACS and ACOT family members in thermogenic tissues will determine the substrate availability for β-oxidation, and consequently the thermogenic capacity. Although the role of the majority of ACS and ACOT family members in thermogenesis remains unclear, recent proceedings link the enzymatic activities of ACS and ACOT family members to metabolic disorders and thermogenesis. Elucidating the contributions of specific ACS and ACOT family members to trafficking of fatty acids towards thermogenesis may reveal novel targets for modulating thermogenic capacity and treating metabolic disorders.
Collapse
Affiliation(s)
- Sandra Steensels
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Baran A Ersoy
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
18
|
Mitochondrial β-oxidation of saturated fatty acids in humans. Mitochondrion 2018; 46:73-90. [PMID: 29551309 DOI: 10.1016/j.mito.2018.02.009] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/04/2017] [Accepted: 02/27/2018] [Indexed: 12/30/2022]
Abstract
Mitochondrial β-oxidation of fatty acids generates acetyl-coA, NADH and FADH2. Acyl-coA synthetases catalyze the binding of fatty acids to coenzyme A to form fatty acyl-coA thioesters, the first step in the intracellular metabolism of fatty acids. l-carnitine system facilitates the transport of fatty acyl-coA esters across the mitochondrial membrane. Carnitine palmitoyltransferase-1 transfers acyl groups from coenzyme A to l-carnitine, forming acyl-carnitine esters at the outer mitochondrial membrane. Carnitine acyl-carnitine translocase exchanges acyl-carnitine esters that enter the mitochondria, by free l-carnitine. Carnitine palmitoyltransferase-2 converts acyl-carnitine esters back to acyl-coA esters at the inner mitochondrial membrane. The β-oxidation pathway of fatty acyl-coA esters includes four reactions. Fatty acyl-coA dehydrogenases catalyze the introduction of a double bond at the C2 position, producing 2-enoyl-coA esters and reducing equivalents that are transferred to the respiratory chain via electron transferring flavoprotein. Enoyl-coA hydratase catalyzes the hydration of the double bond to generate a 3-l-hydroxyacyl-coA derivative. 3-l-hydroxyacyl-coA dehydrogenase catalyzes the formation of a 3-ketoacyl-coA intermediate. Finally, 3-ketoacyl-coA thiolase catalyzes the cleavage of the chain, generating acetyl-coA and a fatty acyl-coA ester two carbons shorter. Mitochondrial trifunctional protein catalyzes the three last steps in the β-oxidation of long-chain and medium-chain fatty acyl-coA esters while individual enzymes catalyze the β-oxidation of short-chain fatty acyl-coA esters. Clinical phenotype of fatty acid oxidation disorders usually includes hypoketotic hypoglycemia triggered by fasting or infections, skeletal muscle weakness, cardiomyopathy, hepatopathy, and neurological manifestations. Accumulation of non-oxidized fatty acids promotes their conjugation with glycine and l-carnitine and alternate ways of oxidation, such as ω-oxidation.
Collapse
|
19
|
Long K, Mao K, Che T, Zhang J, Qiu W, Wang Y, Tang Q, Ma J, Li M, Li X. Transcriptome differences in frontal cortex between wild boar and domesticated pig. Anim Sci J 2018. [DOI: 10.1111/asj.12999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Keren Long
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Ke Mao
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Jinwei Zhang
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Wanling Qiu
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding; College of Animal Science and Technology; Sichuan Agricultural University; Chengdu Sichuan China
| |
Collapse
|
20
|
Gopal R, Selvarasu K, Pandian PP, Ganesan K. Integrative transcriptome analysis of liver cancer profiles identifies upstream regulators and clinical significance of ACSM3 gene expression. Cell Oncol (Dordr) 2017; 40:219-233. [PMID: 28390038 DOI: 10.1007/s13402-017-0321-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common human malignancies. It has frequently been associated with metabolic perturbations and liver damages. Various members of the family of acyl-CoA synthetases are known to be involved in the production of bioactive fatty acids, and altered expression of its encoding genes has been found to be involved in metabolic perturbations. For the development of novel diagnostic and therapeutic HCC options, a fundamental understanding of the mechanisms associated with the deregulation of candidate genes involved in metabolic perturbation is required. METHODS A meta-analysis of multiple HCC mRNA profiles was performed to identify consistently deregulated genes. Expression of the acyl-CoA synthetase medium chain family member 3 (ACSM3) gene was subsequently assessed in different HCC tumor stages and correlated with various clinicopathological features. Transcription regulation, survival and pathway-associated features of the ACSM3 gene were investigated using integrative functional genomic and molecular cell biological methods. RESULTS We found that expression of the ACSM3 gene was significantly reduced in HCC tissues and was frequently downregulated in patients exhibiting high alpha-fetoprotein (AFP) levels, high alanine aminotransferase (ALT) levels, multiple nodules and large tumors. Loss of ACSM3 expression was found to correlate with advanced HCC stages and a poor survival. In addition, HNF4α was found to positively regulate the expression of the ACSM3 gene, while PPARγ was found to transcriptionally repress it. Downregulation of ACSM3 expression was perceived upon activation of the TGFβ, WNT, AKT and MYC signalling pathways. In addition, we found that ACSM3 expression correlates with fatty acid oxidation in HCC. CONCLUSION Our data provide evidence for a differential expression and regulation of the ACSM3 gene in HCC, and may lay a foundation for therapeutically targeting fatty acid metabolism in these tumors.
Collapse
Affiliation(s)
- Ramani Gopal
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Karthikeyan Selvarasu
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Ponmathi Panneer Pandian
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India.
| |
Collapse
|
21
|
Wang C, Wang P, Yang LP, Pan J, Yang X, Ma HY. Association of CYP2C9, CYP2A6, ACSM2A, and CPT1A gene polymorphisms with adverse effects of valproic acid in Chinese patients with epilepsy. Epilepsy Res 2017; 132:64-69. [PMID: 28315807 DOI: 10.1016/j.eplepsyres.2017.02.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 12/30/2016] [Accepted: 02/26/2017] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To explore the influence of CYP2C9, CYP2A6, ACSM2A, CPT1A gene polymorphisms on valproic acid (VPA) and its role in metabolism-related liver dysfunction in order to guide the clinical safety and rational use of VPA. METHODS One hundred two patients taking sodium valproate oral solution were genotyped. To assess the genotypes of relevant genes, the CYP2C9 gene was directly sequenced; for polymorphism classification, multiple Long-PCR electrophoresis was conducted for CYP2A6; and imLDR method was used for ACSM2A and CPT1A. GC-MS-SIM was used to determine the levels of VPA and 2-propyl-4-pentenoic acid (4-ene-VPA) in human plasma simultaneously. RESULTS CYP2C9 mutations had a significant impact on 4-ene-VPA concentration, in patients with wild-type CYP2C9 (CYP2C9*1), which has a greater capacity for VPA metabolism than the mutant type (CYP2C9*3), liver dysfunction was substantially higher. Patients with an ACSM2A polymorphism had higher levels of ALT and AST compared with wild-type (p<0.05), but the mutations had no effect on the VPA-related liver dysfunction (p>0.05). Among different CYP2A6 and CPT1A genotype groups, there was no significant correlation in the levels of VPA, 4-ene-VPA, ALT, AST or TB (p>0.05). The content of 4-ene-VPA had no direct correlation with the incidence of liver dysfunction. CONCLUSIONS Early detection of CYP2C9 gene polymorphisms may help to predict or prevent liver dysfunction caused by VPA. While the concentration of 4-ene-VPA was not suitable as an early warning index, the results provide clear theoretical guidance for the rational and safe clinical use of VPA.
Collapse
Affiliation(s)
- Can Wang
- Pharmaceutical Department, Xiangya Hospital, Central South University, Changsha, 410008, China; Pharmaceutical Department, Hunan Cancer Hospital, The Affiliated Cancer Hospital Of Xiangya School Of Medicine, Central South University, Changsha, 410013, China
| | - Ping Wang
- Pharmaceutical Department, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Li-Ping Yang
- Pharmaceutical Department, Hunan Cancer Hospital, The Affiliated Cancer Hospital Of Xiangya School Of Medicine, Central South University, Changsha, 410013, China
| | - Jing Pan
- Clinical Trial Agency of Drugs, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xue Yang
- Pharmaceutical Department, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Hong-Ying Ma
- Pharmaceutical Department, Xiangya Hospital, Central South University, Changsha, 410008, China; Institute Of Hospital Pharmacy, Central South University, Changsha, 410008, China.
| |
Collapse
|
22
|
Detecting multiple variants associated with disease based on sequencing data of case-parent trios. J Hum Genet 2016; 61:851-860. [PMID: 27278787 DOI: 10.1038/jhg.2016.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 01/13/2023]
Abstract
With the advance of next-generation sequencing technology, the rare variants join the common ones in explaining more proportions of heritability. The coexistence of variants of common with rare, causal with neutral and deleterious with protective is a norm and should be appropriately addressed. Some existing methods suffer from low power when one or more forms of coexistence present, impeding their applications in practice. In this paper, for case-parent trios, pseudocontrols are constructed using the nontransmitted alleles of the parents. The Kullback-Leibler divergence is utilized to measure the difference between the distributions of variants in a genetic region for the affected children and pseudocontrols, and two nonparametric test statistics KLTT and cKLTT are proposed. Extensive simulations show that they are robust to the opposite directions of the causal variants and the amount of neutral variants, and have superiority over the existing methods when both rare and common variants are involved. Furthermore, their efficiency is demonstrated in the application to the data from Framingham Heart Study.
Collapse
|
23
|
van der Sluis R, Erasmus E. Xenobiotic/medium chain fatty acid: CoA ligase - a critical review on its role in fatty acid metabolism and the detoxification of benzoic acid and aspirin. Expert Opin Drug Metab Toxicol 2016; 12:1169-79. [PMID: 27351777 DOI: 10.1080/17425255.2016.1206888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Activation of fatty acids by the acyl-CoA synthetases (ACSs) is the vital first step in fatty acid metabolism. The enzymatic and physiological characterization of the human xenobiotic/medium chain fatty acid: CoA ligases (ACSMs) has been severely neglected even though xenobiotics, such as benzoate and salicylate, are detoxified through this pathway. AREAS COVERED This review will focus on the nomenclature and substrate specificity of the human ACSM ligases; the biochemical and enzymatic characterization of ACSM1 and ACSM2B; the high sequence homology of the ACSM2 genes (ACSM2A and ACSM2B) as well as what is currently known regarding disease association studies. EXPERT OPINION Several discrepancies exist in the current literature that should be taken note of. For example, the single nucleotide polymorphisms (SNPs) reported to be associated with aspirin metabolism and multiple risk factors of metabolic syndrome are incorrect. Kinetic data on the substrate specificity of the human ACSM ligases are non-existent and currently no data exist on the influence of SNPs on the enzyme activity of these ligases. One of the biggest obstacles currently in the field is that glycine conjugation is continuously studied as a one-step process, which means that key regulatory factors of the two individual steps remain unknown.
Collapse
Affiliation(s)
- Rencia van der Sluis
- a Centre for Human Metabolomics, Biochemistry Division , North-West University , Potchefstroom , South Africa
| | - Elardus Erasmus
- a Centre for Human Metabolomics, Biochemistry Division , North-West University , Potchefstroom , South Africa
| |
Collapse
|
24
|
Schönfeld P, Wojtczak L. Short- and medium-chain fatty acids in energy metabolism: the cellular perspective. J Lipid Res 2016; 57:943-54. [PMID: 27080715 DOI: 10.1194/jlr.r067629] [Citation(s) in RCA: 574] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 12/12/2022] Open
Abstract
Short- and medium-chain fatty acids (SCFAs and MCFAs), independently of their cellular signaling functions, are important substrates of the energy metabolism and anabolic processes in mammals. SCFAs are mostly generated by colonic bacteria and are predominantly metabolized by enterocytes and liver, whereas MCFAs arise mostly from dietary triglycerides, among them milk and dairy products. A common feature of SCFAs and MCFAs is their carnitine-independent uptake and intramitochondrial activation to acyl-CoA thioesters. Contrary to long-chain fatty acids, the cellular metabolism of SCFAs and MCFAs depends to a lesser extent on fatty acid-binding proteins. SCFAs and MCFAs modulate tissue metabolism of carbohydrates and lipids, as manifested by a mostly inhibitory effect on glycolysis and stimulation of lipogenesis or gluconeogenesis. SCFAs and MCFAs exert no or only weak protonophoric and lytic activities in mitochondria and do not significantly impair the electron transport in the respiratory chain. SCFAs and MCFAs modulate mitochondrial energy production by two mechanisms: they provide reducing equivalents to the respiratory chain and partly decrease efficacy of oxidative ATP synthesis.
Collapse
Affiliation(s)
- Peter Schönfeld
- Institute of Biochemistry and Cell Biology, Otto-von-Guericke University, Magdeburg, 39120 Magdeburg, Germany
| | - Lech Wojtczak
- Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| |
Collapse
|
25
|
Nortje C, van der Sluis R, van Dijk AA, Erasmus E. The Use ofp-Aminobenzoic Acid as a Probe Substance for the Targeted Profiling of Glycine Conjugation. J Biochem Mol Toxicol 2015; 30:136-47. [PMID: 26484797 DOI: 10.1002/jbt.21772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/14/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Carla Nortje
- Focus Area: Human Metabolomics; North-West University; Potchefstroom 2531 North-West South Africa
| | - Rencia van der Sluis
- Focus Area: Human Metabolomics; North-West University; Potchefstroom 2531 North-West South Africa
| | - Alberdina Aike van Dijk
- Focus Area: Human Metabolomics; North-West University; Potchefstroom 2531 North-West South Africa
| | - Elardus Erasmus
- Focus Area: Human Metabolomics; North-West University; Potchefstroom 2531 North-West South Africa
| |
Collapse
|
26
|
Lemarié F, Beauchamp E, Legrand P, Rioux V. Revisiting the metabolism and physiological functions of caprylic acid (C8:0) with special focus on ghrelin octanoylation. Biochimie 2015; 120:40-8. [PMID: 26253695 DOI: 10.1016/j.biochi.2015.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/01/2015] [Indexed: 12/22/2022]
Abstract
Caprylic acid (octanoic acid, C8:0) belongs to the class of medium-chain saturated fatty acids (MCFAs). Dairy products and specific oils like coconut oil are natural sources of dietary C8:0 but higher intakes of this fatty acid can be provided with MCT (Medium-Chain Triglycerides) oil that consists in 75% of C8:0. MCFAs have physical and metabolic properties that are distinct from those of long-chain saturated fatty acids (LCFAs ≥ 12 carbons). Beneficial physiological effects of dietary C8:0 have been studied for a long time and MCT oil has been used as a special energy source for patients suffering from pancreatic insufficiency, impaired lymphatic chylomicron transport and fat malabsorption. More recently, caprylic acid was also shown to acylate ghrelin, the only known peptide hormone with an orexigenic effect. Through its covalent binding to the ghrelin peptide, caprylic acid exhibits an emerging and specific role in modulating physiological functions themselves regulated by octanoylated ghrelin. Dietary caprylic acid is therefore now suspected to provide the ghrelin O-acyltransferase (GOAT) enzyme with octanoyl-CoA co-substrates necessary for the acyl modification of ghrelin. This review tries to highlight the discrepancy between the formerly described beneficial effects of dietary MCFAs on body weight loss and the C8:0 newly reported effect on appetite stimulation via ghrelin octanoylation. The subsequent aim of this review is to demonstrate the relevance of carrying out further studies to better understand the physiological functions of this particular fatty acid.
Collapse
Affiliation(s)
- Fanny Lemarié
- Laboratoire de Biochimie-Nutrition Humaine, Agrocampus Ouest, INRA USC 1378, Rennes, France
| | - Erwan Beauchamp
- Laboratoire de Biochimie-Nutrition Humaine, Agrocampus Ouest, INRA USC 1378, Rennes, France
| | - Philippe Legrand
- Laboratoire de Biochimie-Nutrition Humaine, Agrocampus Ouest, INRA USC 1378, Rennes, France
| | - Vincent Rioux
- Laboratoire de Biochimie-Nutrition Humaine, Agrocampus Ouest, INRA USC 1378, Rennes, France.
| |
Collapse
|
27
|
Badenhorst CPS, Erasmus E, van der Sluis R, Nortje C, van Dijk AA. A new perspective on the importance of glycine conjugation in the metabolism of aromatic acids. Drug Metab Rev 2014; 46:343-61. [PMID: 24754494 DOI: 10.3109/03602532.2014.908903] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A number of endogenous and xenobiotic organic acids are conjugated to glycine, in animals ranging from mosquitoes to humans. Glycine conjugation has generally been assumed to be a detoxification mechanism, increasing the water solubility of organic acids in order to facilitate urinary excretion. However, the recently proposed glycine deportation hypothesis states that the role of the amino acid conjugations, including glycine conjugation, is to regulate systemic levels of amino acids that are also utilized as neurotransmitters in the central nervous systems of animals. This hypothesis is based on the observation that, compared to glucuronidation, glycine conjugation does not significantly increase the water solubility of aromatic acids. In this review it will be argued that the major role of glycine conjugation is to dispose of the end products of phenylpropionate metabolism. Furthermore, glucuronidation, which occurs in the endoplasmic reticulum, would not be ideal for the detoxification of free benzoate, which has been shown to accumulate in the mitochondrial matrix. Glycine conjugation, however, prevents accumulation of benzoic acid in the mitochondrial matrix by forming hippurate, a less lipophilic conjugate that can be more readily transported out of the mitochondria. Finally, it will be explained that the glycine conjugation of benzoate, a commonly used preservative, exacerbates the dietary deficiency of glycine in humans. Because the resulting shortage of glycine can negatively influence brain neurochemistry and the synthesis of collagen, nucleic acids, porphyrins, and other important metabolites, the risks of using benzoate as a preservative should not be underestimated.
Collapse
|
28
|
Jagya N, Varma SPK, Thakral D, Joshi P, Durgapal H, Panda SK. RNA-seq based transcriptome analysis of hepatitis E virus (HEV) and hepatitis B virus (HBV) replicon transfected Huh-7 cells. PLoS One 2014; 9:e87835. [PMID: 24505321 PMCID: PMC3914852 DOI: 10.1371/journal.pone.0087835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 12/30/2013] [Indexed: 12/11/2022] Open
Abstract
Pathogenesis of hepatitis B virus (HBV) and hepatitis E virus (HEV) infection is as varied as they appear similar; while HBV causes an acute and/or chronic liver disease and hepatocellular carcinoma, HEV mostly causes an acute self-limiting disease. In both infections, host responses are crucial in disease establishment and/or virus clearance. In the wake of worsening prognosis described during HEV super-infection over chronic HBV hepatitis, we investigated the host responses by studying alterations in gene expression in liver cells (Huh-7 cell line) by transfection with HEV replicon only (HEV-only), HBV replicon only (HBV-only) and both HBV and HEV replicons (HBV+HEV). Virus replication was validated by strand-specific real-time RT-PCR for HEV and HBsAg ELISA of the culture supernatants for HBV. Indirect immunofluorescence for the respective viral proteins confirmed infection. Transcription profiling was carried out by RNA Sequencing (RNA-Seq) analysis of the poly-A enriched RNA from the transfected cells. Averages of 600 million bases within 5.6 million reads were sequenced in each sample and ∼15,800 genes were mapped with at least one or more reads. A total of 461 genes in HBV+HEV, 408 in HBV-only and 306 in HEV-only groups were differentially expressed as compared to mock transfection control by two folds (p<0.05) or more. Majority of the significant genes with altered expression clustered into immune-associated, signal transduction, and metabolic process categories. Differential gene expression of functionally important genes in these categories was also validated by real-time RT-PCR based relative gene-expression analysis. To our knowledge, this is the first report of in vitro replicon transfected RNA-Seq based transcriptome analysis to understand the host responses against HEV and HBV.
Collapse
Affiliation(s)
- Neetu Jagya
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Satya Pavan Kumar Varma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Deepshi Thakral
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Prashant Joshi
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Hemlata Durgapal
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Subrat Kumar Panda
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- * E-mail:
| |
Collapse
|
29
|
Yoshida M, Watanabe Y, Yamanishi K, Yamashita A, Yamamoto H, Okuzaki D, Shimada K, Nojima H, Yasunaga T, Okamura H, Matsunaga H, Yamanishi H. Analysis of genes causing hypertension and stroke in spontaneously hypertensive rats: gene expression profiles in the brain. Int J Mol Med 2014; 33:887-96. [PMID: 24452243 DOI: 10.3892/ijmm.2014.1631] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/09/2014] [Indexed: 11/06/2022] Open
Abstract
Spontaneously hypertensive rats (SHR) and stroke-prone SHR (SHRSP) are frequently used as rat models not only of essential hypertension and stroke, but also of attention-deficit hyperactivity disorder (ADHD). Normotensive Wistar-Kyoto rats (WKY) are used as the control rats in these cases. An increasing number of studies has demonstrated the critical role of the central nervous system in the development and maintenance of hypertension. In a previous study, we analyzed the gene expression profiles in the adrenal glands of SHR. Thus, in this study, we analyzed gene expression profiles in the brains of SHR in order to identify the genes responsible for causing hypertension and stroke, as well as those involved in ADHD. Using genome-wide microarray technology, we examined the gene expression profiles in the brains of 3 rat strains (SHR, SHRSP and WKY) when the rats were 3 and 6 weeks of age, a period in which the rats are considered to be in a pre-hypertensive state. Gene expression profiles in the brain were compared between SHR and WKY, and between SHRSP and SHR. A total of 179 genes showing a >4- or <-4-fold change in expression were isolated, and candidate genes were selected using two different web tools: the first tool was the Database for Annotation, Visualization and Integrated Discovery (DAVID), which was used to search for significantly enriched genes, and categorized them using Gene Ontology (GO) terms, and the second was the network explorer of Ingenuity Pathway Analysis (IPA), which was used to search for interaction networks among SHR- and SHRSP-specific genes. The IPA of SHR-specific genes revealed that prostaglandin E receptor 4 (Ptger4) is one of the candidate genes responsible for causing hypertension in SHR, and that albumin (Alb) and chymase 1 (Cma1) are also responsible for causing hypertension in SHR in the presence of angiotensinogen (Agt). Similar analyses of SHRSP-specific genes revealed that the angiotensin II receptor-associated gene (Agtrap) interacts with the FBJ osteosarcoma oncogene (Fos), and with the angiotensin II receptor type-1b (Agtr1b). As Agtrap and Agtr1b not only participate in the 'uptake of norepinephrine' and 'blood pressure', but also in the 'behavior' of SHRSP at 6 weeks of age, our data demonstrate a close association between hypertension and ADHD.
Collapse
Affiliation(s)
- Momoko Yoshida
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| | - Yuko Watanabe
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| | - Kyosuke Yamanishi
- Department of Neuropsychiatry, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Akifumi Yamashita
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideyuki Yamamoto
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Daisuke Okuzaki
- DNA-Chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazunori Shimada
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| | - Hiroshi Nojima
- DNA-Chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Teruo Yasunaga
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Haruki Okamura
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Hisato Matsunaga
- Department of Neuropsychiatry, Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Hiromichi Yamanishi
- Hirakata General Hospital for Developmental Disorders, Hirakata, Osaka 573-0122, Japan
| |
Collapse
|
30
|
Darnell M, Weidolf L. Metabolism of xenobiotic carboxylic acids: focus on coenzyme A conjugation, reactivity, and interference with lipid metabolism. Chem Res Toxicol 2013; 26:1139-55. [PMID: 23790050 DOI: 10.1021/tx400183y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While xenobiotic carboxylic acids (XCAs) have been studied extensively with respect to their enzymatic conversion to potentially reactive acyl glucuronides with implications to drug induced hepatotoxicity, the formation of xenobiotic-S-acyl-CoA thioesters (xenobiotic-CoAs) have been much less studied in spite of data indicating that such conjugates may be equally or more reactive than the corresponding acyl glucuronides. This review addresses enzymes and cell organelles involved in the formation of xenobiotic-CoAs, the reactivity of such conjugates toward biological macromolecules, and in vitro and in vivo methodology to assess consequences of such reactivity. Further, the propensity of xenobiotic-CoAs to interfere with endogenous lipid metabolism, e.g., inhibition of β-oxidation or depletion of the CoA or carnitine pools, adds to the complexity of the potential contribution of XCAs to hepatotoxicity by a number of mechanisms in addition to those in common with the corresponding acyl glucuronides. On the basis of our review of the literature on xenobiotic-CoA conjugates, there appear to be a number of gaps in our understanding of the bioactivation of XCA both with respect to the mechanisms involved and the experimental approaches to distinguish between the role of acyl glucuronides and xenobiotic-CoA conjugates. These aspects are focused upon and described in detail in this review.
Collapse
Affiliation(s)
- Malin Darnell
- CVMD iMed DMPK, AstraZeneca R&D Mölnda l, 431 83 Mölndal, Sweden
| | | |
Collapse
|
31
|
The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 2013; 495:360-4. [PMID: 23354050 DOI: 10.1038/nature11837] [Citation(s) in RCA: 581] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 12/11/2012] [Indexed: 12/11/2022]
Abstract
The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.
Collapse
|
32
|
Teng S, Yang JY, Wang L. Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data. BMC Med Genomics 2013; 6 Suppl 1:S10. [PMID: 23369200 PMCID: PMC3552705 DOI: 10.1186/1755-8794-6-s1-s10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene targets could provide useful information for biomarker development and drug target identification. Results In this study, we have developed a machine learning approach for predicting the human tissue-specific genes using microarray expression data. The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding. Random Forests (RFs) and Support Vector Machines (SVMs) were used to construct accurate classifiers. The RF classifiers were found to outperform SVM models for tissue-specific gene prediction. The results suggest that the candidate genes for brain or liver specific expression can provide valuable information for further experimental studies. Our approach was also applied for identifying tissue-selective gene targets for different types of tissues. Conclusions A machine learning approach has been developed for accurately identifying the candidate genes for tissue specific/selective expression. The approach provides an efficient way to select some interesting genes for developing new biomedical markers and improve our knowledge of tissue-specific expression.
Collapse
Affiliation(s)
- Shaolei Teng
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | | |
Collapse
|
33
|
Kasuya F, Kazuhiro M, Tatsuya H, Nakamoto K, Tokuyama S, Masuyama T. Effect of the non-steroidal anti-inflammatory drugs on the acyl-CoA synthetase activity toward medium-chain, long-chain and polyunsaturated fatty acids in mitochondria of mouse liver and brain. J Enzyme Inhib Med Chem 2012; 28:223-7. [DOI: 10.3109/14756366.2011.636742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Fumiyo Kasuya
- Biochemical Toxicology Laboratory, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| | - Misumi Kazuhiro
- Biochemical Toxicology Laboratory, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| | - Hasegawa Tatsuya
- Biochemical Toxicology Laboratory, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| | - Kazuo Nakamoto
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| | - Shogo Tokuyama
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| | - Teiichi Masuyama
- Biochemical Toxicology Laboratory, Faculty of Pharmaceutical Sciences, Kobegakuin University,
Kobe, Japan
| |
Collapse
|
34
|
Gonzalez M, Sealls W, Jesch ED, Brosnan MJ, Ladunga I, Ding X, Black PN, DiRusso CC. Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease. Physiol Genomics 2010; 43:121-35. [PMID: 21098682 DOI: 10.1152/physiolgenomics.00209.2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Liver-specific ablation of cytochrome P450 reductase in mice (LCN) results in hepatic steatosis that can progress to steatohepatitis characterized by inflammation and fibrosis. The specific cause of the fatty liver phenotype is poorly understood but is hypothesized to result from elevated expression of genes encoding fatty acid synthetic genes. Since expression of these genes is known to be suppressed by polyunsaturated fatty acids, we performed physiological and genomics studies to evaluate the effects of dietary linoleic and linolenic fatty acids (PUFA) or arachidonic and decosahexaenoic acids (HUFA) on the hepatic phenotypes of control and LCN mice by comparison with a diet enriched in saturated fatty acids. The dietary interventions with HUFA reduced the fatty liver phenotype in livers of LCN mice and altered the gene expression patterns in these livers to more closely resemble those of control mice. Importantly, the expression of genes encoding lipid pathway enzymes were not different between controls and LCN livers, indicating a strong influence of diet over POR genotype. These analyses highlighted the impact of POR ablation on expression of genes encoding P450 enzymes and proteins involved in stress and inflammation. We also found that livers from animals of both genotypes fed diets enriched in PUFA had gene expression patterns more closely resembling those fed diets enriched in saturated fatty acids. These results strongly suggest only HUFA supplied from an exogenous source can suppress hepatic lipogenesis.
Collapse
Affiliation(s)
- Monika Gonzalez
- Center for Metabolic Disease, Ordway Research Institute and Center for Cardiovascular Science, Albany Medical College, Albany, New York, USA
| | | | | | | | | | | | | | | |
Collapse
|