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Punchai S, Chaiyagot N, Artkaew N, Jusakul A, Cha’on U, Thanan R, Vaeteewoottacharn K, Lert-Itthiporn W. Iron-induced kidney cell damage: insights into molecular mechanisms and potential diagnostic significance of urinary FTL. Front Mol Biosci 2024; 11:1352032. [PMID: 38449697 PMCID: PMC10916690 DOI: 10.3389/fmolb.2024.1352032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
Background: Iron overload can lead to organ and cell injuries. Although the mechanisms of iron-induced cell damage have been extensively studied using various cells, little is known about these processes in kidney cells. Methods: In this study, we first examined the correlation between serum iron levels and kidney function. Subsequently, we investigated the molecular impact of excess iron on kidney cell lines, HEK293T and HK-2. The presence of the upregulated protein was further validated in urine. Results: The results revealed that excess iron caused significant cell death accompanied by morphological changes. Transcriptomic analysis revealed an up-regulation of the ferroptosis pathway during iron treatment. This was confirmed by up-regulation of ferroptosis markers, ferritin light chain (FTL), and prostaglandin-endoperoxide synthase 2 (PTGS2), and down-regulation of acyl-CoA synthetase long-chain family member 4 (ACSL4) and glutathione peroxidase 4 (GPX4) using real-time PCR and Western blotting. In addition, excess iron treatment enhanced protein and lipid oxidation. Supportively, an inverse correlation between urinary FTL protein level and kidney function was observed. Conclusion: These findings suggest that excess iron disrupts cellular homeostasis and affects key proteins involved in kidney cell death. Our study demonstrated that high iron levels caused kidney cell damage. Additionally, urinary FTL might be a useful biomarker to detect kidney damage caused by iron toxicity. Our study also provided insights into the molecular mechanisms of iron-induced kidney injury, discussing several potential targets for future interventions.
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Affiliation(s)
- Soraya Punchai
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nachayada Chaiyagot
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nadthanicha Artkaew
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
| | - Apinya Jusakul
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ubon Cha’on
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
| | - Kulthida Vaeteewoottacharn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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2
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Mon AM, Intuyod K, Klungsaeng S, Jusakul A, Pongking T, Lert-Itthiporn W, Luvira V, Pairojkul C, Plengsuriyakarn T, Na-Bangchang K, Pinlaor S, Pinlaor P. Overexpression of microRNA-205-5p promotes cholangiocarcinoma growth by reducing expression of homeodomain-interacting protein kinase 3. Sci Rep 2023; 13:22444. [PMID: 38105269 PMCID: PMC10725890 DOI: 10.1038/s41598-023-49694-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023] Open
Abstract
The microRNA miR-205-5p has diverse effects in different malignancies, including cholangiocarcinoma (CCA), but its effects on CCA progression is unclear. Here we investigated the role and function of miR-205-5p in CCA. Three CCA cell lines and human serum samples were found to have much higher expression levels of miR-205-5p than seen in typical cholangiocyte cell lines and healthy controls. Inhibition of miR-205-5p suppressed CCA cell motility, invasion and proliferation of KKU-213B whereby overexpression of miR-205-5p promoted cell proliferation and motility of KKU-100 cells. Bioinformatics tools (miRDB, TargetScan, miRWalk, and GEPIA) all predicted various miR-205-5p targets. Experiments using miR-205-5p inhibitor and mimic indicated that homeodomain-interacting protein kinase 3 (HIPK3) was a potential direct target of miR-205-5p. Overexpression of HIPK3 using HIPK3 plasmid cloning DNA suppressed migration and proliferation of KKU-100 cells. Notably, HIPK3 expression was lower in human CCA tissues than in normal adjacent tissues. High HIPK3 expression was significantly associated with longer survival time of CCA patients. Multivariate regression analysis indicated tissue HIPK3 levels as an independent prognostic factor for CCA patients. These findings indicate that overexpression of miR-205-5p promotes CCA cells proliferation and migration partly via HIPK3-dependent way. Therefore, targeting miR-205-5p may be a potential treatment approach for CCA.
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Affiliation(s)
- Aye Myat Mon
- Medical Technology Program, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kitti Intuyod
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sirinapha Klungsaeng
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Apinya Jusakul
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Thatsanapong Pongking
- Biomedical Sciences Program, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Vor Luvira
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Tullayakorn Plengsuriyakarn
- Graduate Program in Bioclinical Sciences, Center of Excellence in Pharmacology and Molecular Biology of Malaria and Cholangiocarcinoma, Chulabhorn International College of Medicine, Thammasat University (Rangsit Campus), Pathum Thani, 12120, Thailand
| | - Kesara Na-Bangchang
- Graduate Program in Bioclinical Sciences, Center of Excellence in Pharmacology and Molecular Biology of Malaria and Cholangiocarcinoma, Chulabhorn International College of Medicine, Thammasat University (Rangsit Campus), Pathum Thani, 12120, Thailand
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Porntip Pinlaor
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
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3
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Kyaw TS, Sukmak M, Nahok K, Sharma A, Silsirivanit A, Lert-Itthiporn W, Sansurin N, Senthong V, Anutrakulchai S, Sangkhamanon S, Pinlaor S, Selmi C, Hammock BD, Cha'on U. Monosodium glutamate consumption reduces the renal excretion of trimethylamine N-oxide and the abundance of Akkermansia muciniphila in the gut. Biochem Biophys Res Commun 2022; 630:158-166. [PMID: 36155062 PMCID: PMC9851609 DOI: 10.1016/j.bbrc.2022.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/09/2022] [Indexed: 01/21/2023]
Abstract
We previously demonstrated that monosodium glutamate (MSG) consumption increases trimethylamine (TMA) level in the renal tissue as well as dimethylamine and methylamine levels in urine of rats, suggesting the effects of MSG on humans. To better define the findings, we investigated whether MSG consumption alters serum trimethylamine N-oxide (TMAO) level, and as a consequence, induces kidney injury in the rat model. Adult male Wistar rats (n = 40) were randomized to be fed with a standard diet (control group) or a standard diet with 0.5, 1.5 or 3.0 g% MSG corresponding to 7, 21, or 42 g/day in 60 kg man, respectively in drinking water (MSG-treated groups), or a standard diet with 3.0 g% MSG in drinking water which was withdrawn after 4 weeks (MSG-withdrawal group). Blood and urine samples were collected to analyze the TMAO levels using 1H NMR and markers of kidney injury. Fecal samples were also collected for gut microbiota analysis. We found serum TMAO levels increased and urinary TMAO excretion decreased during MSG consumption, in parallel with the increase of the neutrophil gelatinase-associated lipocalin (NGAL) excretion which subsided with the withdrawal of MSG. The fecal 16 S rRNA analysis during MSG consumption showed gut microbiota changes with a consistent suppression of Akkermansia muciniphila, a mucin producing bacteria, but not of TMA-producing bacteria. In conclusions, our findings suggested that prolonged high dose MSG consumption may cause TMAO accumulation in the blood via reduction of renal excretion associated with acute kidney injury. The mechanisms by which MSG reduced TMAO excretion require further investigation.
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Affiliation(s)
- Thin Su Kyaw
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Manatsaphon Sukmak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Kanokwan Nahok
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Amod Sharma
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Nichapa Sansurin
- Northeast Laboratory Animal Center, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Vichai Senthong
- Department of Internal Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Sirirat Anutrakulchai
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand; Department of Internal Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Sakkarn Sangkhamanon
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Carlo Selmi
- Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center IRCCS, Rozzano, 20089, Milan, Italy; Department of Clinical Biosciences, Humanitas University, Pieve Emanuele, 20090, Milan, Italy.
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Research Center, University of California, Davis, CA, 95616, USA
| | - Ubon Cha'on
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, 40002, Thailand.
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4
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Detarya M, Lert-Itthiporn W, Mahalapbutr P, Klaewkla M, Sorin S, Sawanyawisuth K, Silsirivanit A, Seubwai W, Wongkham C, Araki N, Wongkham S. Emerging roles of GALNT5 on promoting EGFR activation in cholangiocarcinoma: a mechanistic insight. Am J Cancer Res 2022; 12:4140-4159. [PMID: 36225633 PMCID: PMC9548001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a lethal cancer in that the incidence is now increasing worldwide. N-acetylgalactosaminyltransferase 5 (GALNT5), an enzyme that initiates the first step of mucin type-O glycosylation, has been reported to promote aggressiveness of CCA cells via the epithelial to the mesenchymal transition (EMT) process, and Akt/Erk activation. In this study, the clinical and biological relevance of GALNT5 and the molecular mechanisms by which GALNT5 modulated EGFR in promoting CCA progression were examined. Using publicly available datasets, upregulation of GALNT5 in patient CCA tissues and its correlation with EGFR expression was noted. High levels of GALNT5 were significantly associated with the short survival of patients, suggesting a prognostic marker of GALNT5 for CCA. GALNT5 modulated EGFR expression as shown in CCA cell lines. Upregulation of GALNT5 significantly increased EGFR mRNA and protein in GALNT5 overexpressing cells, whereas suppression of GALNT5 expression gave the opposite results. The molecular dynamics simulations and MM/PB(GB)SA-based free energy calculations showed that O-glycosylation on the EGFR extracellular domain enhanced the structural stability, compactness, and H-bond formation of the EGF/GalNAc-EGFR complex compared with those of EGF/EGFR. This stabilized the growth factor binding site and fostered stronger interactions between EGF and EGFR. Using the EGF-induced EGFR activation model, GALNT5 was shown to mediate EGFR stability via a decreased rate of EGFR degradation and enhanced EGFR activity by increasing the binding affinity of EGF/EGFR that consequently increasing the activation of EGFR and its downstream effectors Akt and Erk. In summary, GALNT5 was upregulated in CCA tissues and associated with a worse prognosis. The study identified for the first time the impacts of GALNT5 on EGFR activity by increasing: 1) EGFR expression via a transcriptional-dependent mechanism, 2) EGFR stability by reducing EGFR degradation, and 3) EGFR activation through an increased binding affinity of EGF/EGFR which all together fostered the activation of EGFR. These results expanded the understanding of the molecular mechanism of how GALNT5 impacted CCA progression and suggested GALNT5 as a new target for therapeutic intervention against metastatic CCA.
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Affiliation(s)
- Marutpong Detarya
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Methus Klaewkla
- Future Health Innovation Technology Co., Ltd.Bangkok 10170, Thailand
| | - Supannika Sorin
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Kanlayanee Sawanyawisuth
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Wunchana Seubwai
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Chaisiri Wongkham
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto UniversityKumamoto 860-8556, Japan
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
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5
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Aung TM, Ciin MN, Silsirivanit A, Jusakul A, Lert-Itthiporn W, Proungvitaya T, Roytrakul S, Proungvitaya S. Serum Angiopoietin-Like Protein 4: A Potential Prognostic Biomarker for Prediction of Vascular Invasion and Lymph Node Metastasis in Cholangiocarcinoma Patients. Front Public Health 2022; 10:836985. [PMID: 35392474 PMCID: PMC8980351 DOI: 10.3389/fpubh.2022.836985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 11/26/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a tumor arising from cholangiocytes lining the bile ducts. Vascular invasion and lymph node metastasis are important prognostic factors for disease staging as well as clinical therapeutic decisions for CCA patients. In the present study, we applied CCA sera proteomic analysis to identify a potential biomarker for prognosis of CCA patients. Then, using bioinformatics tools, we identified angiopoietin-like protein 4 (ANGPTL4) which expressed highest signal intensity among candidate proteins in proteomic analysis of CCA sera. Expression of ANGPTL4 in CCA tissues was determined using immunohistochemistry. The results showed that ANGPTL4 was stained at higher level in CCA cells when compared with normal cholangiocytes. The high expression of ANGPTL4 was associated with lymph node metastasis and advanced tumor stage (p = 0.013 and p = 0.031, respectively). Furthermore, serum ANGPTL4 levels in CCA and healthy control (HC) were analyzed using a dot blot assay. And it was found that ANGPTL4 level was significantly higher in CCA than HC group (p < 0.0001). ROC curve analysis revealed that serum ANGPTL4 level was effectively distinguished CCA from healthy patients (cutoff = 0.2697 arbitrary unit (AU), 80.0% sensitivity, 72.7% specificity, AUC = 0.825, p < 0.0001). Serum ANGPTL4 level was associated with vascular invasion and lymph node metastasis (p = 0.0004 and p = 0.006), so that it differentiated CCA with vascular invasion from CCA without vascular invasion (cutoff = 0.5526 AU, 64.9% sensitivity, 92.9% specificity, AUC = 0.751, p = 0.006) and it corresponded to CCA with/without lymph node metastasis (cutoff = 0.5399 AU, 71.4% sensitivity, 70.8% specificity, AUC = 0.691, p = 0.01) by ROC analysis. Serum ANGPTL4 levels showed superior predictive efficiency compared with CA 19-9 and CEA for vascular invasion and lymph node metastasis. In addition, serum ANGPTL4 level was an independent predictive indicator by multivariate regression analysis. In conclusion, serum ANGPTL4 could be a novel prognostic biomarker for prediction of vascular invasion and lymph node metastasis of CCA patients.
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Affiliation(s)
- Tin May Aung
- Faculty of Associated Medical Sciences, Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Khon Kaen University, Khon Kaen, Thailand
| | - Mang Ngaih Ciin
- Faculty of Associated Medical Sciences, Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Khon Kaen University, Khon Kaen, Thailand
| | - Atit Silsirivanit
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Apinya Jusakul
- Faculty of Associated Medical Sciences, Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Worachart Lert-Itthiporn
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tanakorn Proungvitaya
- Faculty of Associated Medical Sciences, Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Siriporn Proungvitaya
- Faculty of Associated Medical Sciences, Centre of Research and Development of Medical Diagnostic Laboratories (CMDL), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
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6
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Klinhom-On N, Seubwai W, Sawanyawisuth K, Lert-Itthiporn W, Waraasawapati S, Detarya M, Wongkham S. FOXM1c is the predominant FOXM1 isoform expressed in cholangiocarcinoma that associated with metastatic potential and poor prognosis of patients. Heliyon 2021; 7:e06846. [PMID: 33997388 PMCID: PMC8093466 DOI: 10.1016/j.heliyon.2021.e06846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/16/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
Forkhead box M1 (FOXM1) is a transcriptional factor which plays an important role in oncogenesis. Four FOXM1 isoforms, FOXM1a, FOXM1b, FOXM1c and FOXM1d, are known so far. Different FOXM1 isoforms influence progression of cancer in different cancer types. In this study, the FOXM1c isoform and its impact in cholangiocarcinoma (CCA) was identified. FOXM1c was found to be the predominant isoform in patient-CCA tissues and cell lines. Detection of FOXM1c expression in CCA tissues reflected the worse prognosis of the patients, namely the advanced stage and shorter survival. Suppression of FOXM1 expression using siRNA considerably reduced migration and invasion abilities of CCA cell lines. RNA sequencing analysis revealed claudin-1 as a target of FOXM1. FOXM1 exhibited a negative correlation with claudin-1 expression which was demonstrated in patient CCA tissues and cell lines. FOXM1 may be a potential target for therapeutic treatment of the metastatic CCA.
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Affiliation(s)
- Nathakan Klinhom-On
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 40002, Thailand
| | - Wunchana Seubwai
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, 40002, Thailand
| | - Kanlayanee Sawanyawisuth
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, 40002, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, 40002, Thailand
| | - Sakda Waraasawapati
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, 40002, Thailand
| | - Marutpong Detarya
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 40002, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, 40002, Thailand
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7
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Saengboonmee C, Seubwai W, Lert-Itthiporn W, Sanlung T, Wongkham S. Association of Diabetes Mellitus and Cholangiocarcinoma: Update of Evidence and the Effects of Antidiabetic Medication. Can J Diabetes 2020; 45:282-290. [PMID: 33218924 DOI: 10.1016/j.jcjd.2020.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022]
Abstract
Diabetes mellitus (DM) is a risk factor for cancer in many organs and associated with an increased risk of cholangiocarcinoma (CCA). The molecular linkage between these diseases has been demonstrated in preclinical studies, which have highlighted the role of hyperinsulinemia and hyperglycemia in the carcinogenesis and progression of CCA. Recent studies on the emerging role of antidiabetic medication in the development and progression of CCA showed a subclass of antidiabetic drug with a therapeutic effect on CCA. Although associations between CCA, insulin analogues and sulfonylureas are unclear, incretin-based therapy is likely associated with an increased risk for CCA, and may lead to CCA progression, as demonstrated by in vitro and in vivo experiments. In contrast, biguanides, especially metformin, exert an opposite effect, associated with a reduced risk of CCA and inhibited in vitro and in vivo CCA progression. The association between incretin-based therapy and the risk of CCA needs further clarification, as metformin is being studied in an ongoing clinical trial. Understanding the association between DM and CCA is critical for preventing the development of CCA in patients with DM, and for establishing the appropriateness of antidiabetic medication to treat CCA. Determining how metformin affects CCA can lead to repurposing this safe and well-known drug for improving CCA treatment, regardless of the diabetes status of patients.
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Affiliation(s)
- Charupong Saengboonmee
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States.
| | - Wunchana Seubwai
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanachai Sanlung
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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8
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Cha'on U, Wongtrangan K, Thinkhamrop B, Tatiyanupanwong S, Limwattananon C, Pongskul C, Panaput T, Chalermwat C, Lert-Itthiporn W, Sharma A, Anutrakulchai S. CKDNET, a quality improvement project for prevention and reduction of chronic kidney disease in the Northeast Thailand. BMC Public Health 2020; 20:1299. [PMID: 32854662 PMCID: PMC7450931 DOI: 10.1186/s12889-020-09387-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of chronic kidney disease (CKD) is high in the Northeast Thailand compared to other parts of the country. Therefore, a broad program applying all levels of care is inevitable. This paper describes the results of the first year trial of the Chronic Kidney Disease Prevention in the Northeast Thailand (CKDNET), a quality improvement project collaboratively established to curb CKD. METHODS We have covered general population, high risk persons and all stages of CKD patients with expansive strategies such as early screening, effective CKD registry, prevention and CKD comprehensive care models including cost effectiveness analysis. RESULTS The preliminary results from CKD screening in general population of two rural sub-districts show that 26.8% of the screened population has CKD and 28.9% of CKD patients are of unknown etiology. We have established the CKD registry that has enlisted a total of 10.4 million individuals till date, of which 0.13 million are confirmed to have CKD. Pamphlets, posters, brochures and other media of 94 different types in the total number of 478,450 has been distributed for CKD education and awareness at the community level. A CKD guideline that suits for local situation has been formulated to deal the problem effectively and improve care. Moreover, our multidisciplinary intervention and self-management supports were effective in improving glomerular filtration rate (49.57 versus 46.23 ml/min/1.73 m2; p < 0.05), blood pressure (129.6/76.1 versus 135.8/83.6 mmHg) and quality of life of CKD patients included in the program compared to those of the patients under conventional care. The cost effectiveness analysis revealed that lifetime cost for the comprehensive health services under the CKDNET program was 486,898 Baht compared to that of the usual care of 479,386 Baht, resulting in an incremental-cost effectiveness ratio of 18,702 Baht per quality-adjusted life years gained. CONCLUSION CKDNET, a quality improvement project of the holistic approach is currently applying to the population in the Northeast Thailand which will facilitate curtailing of CKD burden in the region.
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Affiliation(s)
- Ubon Cha'on
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
| | - Kanok Wongtrangan
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
| | - Bandit Thinkhamrop
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
- Data Management and Statistical Analysis Center, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Sajja Tatiyanupanwong
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
- Chaiyaphum Hospital, Chaiyaphum, Thailand
| | - Chulaporn Limwattananon
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
- Faculty of Pharmaceutical Science, Khon Kaen University, Khon Kaen, Thailand
| | - Cholatip Pongskul
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
- Department of Internal Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanachai Panaput
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
- Khon Kaen Hospital, Khon Kaen, Thailand
| | - Chalongchai Chalermwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
| | - Amod Sharma
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand
| | - Sirirat Anutrakulchai
- Chronic Kidney Disease Prevention in the Northeast of Thailand (CKDNET), Khon Kaen University, Khon Kaen, Thailand.
- Department of Internal Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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9
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Sripa B, Seubwai W, Vaeteewoottacharn K, Sawanyawisuth K, Silsirivanit A, Kaewkong W, Muisuk K, Dana P, Phoomak C, Lert-Itthiporn W, Luvira V, Pairojkul C, Teh BT, Wongkham S, Okada S, Chamgramol Y. Functional and genetic characterization of three cell lines derived from a single tumor of an Opisthorchis viverrini-associated cholangiocarcinoma patient. Hum Cell 2020; 33:695-708. [PMID: 32207095 DOI: 10.1007/s13577-020-00334-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 02/14/2020] [Indexed: 12/21/2022]
Abstract
Three cholangiocarcinoma (CCA) cell line-formerly named, M156, M213 and M214 have been intensively used with discrepancy of their tumor origins. They were assumed to be originated from three different donors without authentication. To verify the origins of these cell lines, the short tandem repeat (STR) analysis of the currently used cell lines, the cell stocks from the establisher and the primary tumor of a CCA patient were performed. Their phenotypic and genotypic originality were compared. The currently used 3 CCA cell lines exhibited similar STR as CCA patient ID-M213 indicating the same origin of these cells. The cell stocks from the establisher, however, revealed the same STR of M213 and M214 cells, but not M156. The misidentification of M214 and M156 is probably due to the mislabeling and cross-contamination of M213 cells during culture. These currently used cell lines were renamed as KKU-213A, -213B and -213C, for the formerly M213, M214 and M156 cells, respectively. These cell lines were established from a male with an intrahepatic mass-forming CCA stage-4B. The tumor was an adenosquamous carcinoma with the liver fluke ova granuloma in evidence. All cell lines had positive CK19 with differential CA19-9 expression. They exhibited aneuploidy karyotypes, distinct cell morphology, cell growth, cytogenetic characteristic and progressive phenotypes. KKU-213C formed a adenosquamous carcinoma, whereas KKU-213A and KKU-213B formed poorly- and well-differentiated squamous cell carcinomas in xenografted mice. mRNA microarray revealed different expression profiles among these three cell lines. The three cell lines have unique characteristics and may resemble the heterogeneity of tumor origin.
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Affiliation(s)
- Banchob Sripa
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wunchana Seubwai
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kulthida Vaeteewoottacharn
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kanlayanee Sawanyawisuth
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Worasak Kaewkong
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Biochemistry, Faculty of Medical Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Kanha Muisuk
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Paweena Dana
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chatchai Phoomak
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Vor Luvira
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Bin T Teh
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Sopit Wongkham
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Seiji Okada
- Division of Hematopoeisis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Yaovalux Chamgramol
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand.
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10
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Lert-Itthiporn W, Suktitipat B, Grove H, Sakuntabhai A, Malasit P, Tangthawornchaikul N, Matsuda F, Suriyaphol P. Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome. BMC Med Genet 2018; 19:23. [PMID: 29439659 PMCID: PMC5812212 DOI: 10.1186/s12881-018-0534-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/24/2018] [Indexed: 11/24/2022]
Abstract
Background Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined. Methods This study was divided into two parts. In the first part, we applied imputation to genotyped SNPs from Southeast Asian populations from the Pan-Asian SNP database. Five percent of the total SNPs were removed. The remaining SNPs were applied to imputation with IMPUTE2. The imputed outcomes were verified with the removed SNPs. We compared imputation references from Chinese and Japanese haplotypes from the HapMap phase II (HMII) and the complete set of haplotypes from the 1000 Genomes Project (1000G). The second part was imputation accuracy and yield in Thai patient dataset. Half of the autosomal SNPs was removed to create Set 1. Another dataset, Set 2, was then created where we switched which half of the SNPs were removed. Both Set 1 and Set 2 were imputed with HMII to create a complete imputed SNPs dataset. The dataset was used to validate association testing, SNPs annotation and imputation outcome. Results The accuracy was highest for all populations when using the HMII reference, but at the cost of a lower yield. Thai genotypes showed the highest accuracy over other populations in both HMII and 1000G panels, although accuracy and yield varied across chromosomes. Imputation was tested in a clinical dataset to compare accuracy in gene-related regions, and coding regions were found to have a higher accuracy and yield. Conclusions This work provides the first evidence of imputation reference selection for Southeast Asian studies and highlights the effects of SNP locations respective to genes on imputation outcome. Researchers will need to consider the trade-off between accuracy and yield in future imputation studies. Electronic supplementary material The online version of this article (10.1186/s12881-018-0534-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Worachart Lert-Itthiporn
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Bhoom Suktitipat
- Integrative Computational BioScience Center, Department of Biochemistry, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center of Excellence in Bioinformatics and Clinical Data Management, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Harald Grove
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center of Excellence in Bioinformatics and Clinical Data Management, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Anavaj Sakuntabhai
- Unité de Génétique Fonctionnelle des Maladies Infectieuses, Department Genome and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France.,Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Prida Malasit
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand.,Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nattaya Tangthawornchaikul
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand.,Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand. .,Center of Excellence in Bioinformatics and Clinical Data Management, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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11
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Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TNB, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY. Characterising private and shared signatures of positive selection in 37 Asian populations. Eur J Hum Genet 2017; 25:499-508. [PMID: 28098149 DOI: 10.1038/ejhg.2016.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Philip J Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Worachart Lert-Itthiporn
- Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanrutai Chin-Inmanu
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tran Nguyen Bich Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Katie Anders
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina
| | - Yeun-Jun Chung
- Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | | | - RickTwee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sarah J Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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