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Hsieh CR, Wu RC, Kuo CJ, Yeh PJ, Yeh YM, Chen CL, Chiu CT, Chiu CH, Pan YB, Tsou YK, Le PH. Adequate antiviral treatment lowers overall complications of cytomegalovirus colitis among inpatients with inflammatory bowel diseases. BMC Infect Dis 2024; 24:443. [PMID: 38671346 DOI: 10.1186/s12879-024-09317-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) colitis significantly complicates the course of inflammatory bowel disease (IBD), frequently leading to severe flare-ups and poor outcomes. The role of antiviral therapy in hospitalized IBD patients with CMV colitis is currently under debate. This retrospective analysis seeks to clarify the influence of antiviral treatment on these patients. METHODS We retrospectively reviewed IBD patients diagnosed with CMV colitis via immunohistochemistry staining from colonic biopsies at a major tertiary center from January 2000 to May 2021. The study focused on patient demographics, clinical features, risk factors, prognostic indicators, and antiviral treatment outcomes. RESULTS Among 118 inpatients, 42 had CMV colitis. Risk factors included hypoalbuminemia and antibiotic use. IBD patients with CMV colitis receiving < 14 days of antiviral therapy had higher complication (72% vs. 43%, p = 0.028) and surgery rates (56% vs. 26%, p = 0.017) compared to those without CMV. Adequate antiviral therapy (≥ 14 days) significantly reduced complications in the CMV group (29% vs. 72%, p = 0.006), especially in Crohn's disease (20% vs. 100%, p = 0.015). Independent predictors of IBD-related complications were CMV colitis (Odds Ratio [OR] 3.532, 90% Confidence Interval [CI] 1.012-12.331, p = 0.048), biological treatment failure (OR 4.953, 95% CI 1.91-12.842, p = 0.001), and adequate antiviral therapy (OR 0.108, 95% CI 0.023-0.512, p = 0.005). CONCLUSION CMV colitis and a history of biological treatment failure increase complication risks in IBD patients. Adequate antiviral therapy significantly mitigates these risks, highlighting its importance in managing IBD patients with CMV colitis.
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Affiliation(s)
- Ching-Reigh Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Ren-Chin Wu
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- Chang Gung Inflammatory Bowel Disease Center, Taoyuan, Taiwan
| | - Chia-Jung Kuo
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan
- Chang Gung Inflammatory Bowel Disease Center, Taoyuan, Taiwan
| | - Pai-Jui Yeh
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- Chang Gung Inflammatory Bowel Disease Center, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan
- Chang Gung Inflammatory Bowel Disease Center, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Yu-Bin Pan
- Biostatistical Section, Clinical Trial Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Yung-Kuan Tsou
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Puo-Hsien Le
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan.
- Chang Gung Microbiota Therapy Center, Taoyuan, Taiwan.
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.
- Chang Gung Inflammatory Bowel Disease Center, Taoyuan, Taiwan.
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Ong SC, Luo HW, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH, Tang P. The core exosome proteome of Trichomonas vaginalis. J Microbiol Immunol Infect 2024; 57:246-256. [PMID: 38383245 DOI: 10.1016/j.jmii.2024.02.003] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/15/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Trichomonas vaginalis is parasitic protozoan that causes human urogenital infections. Accumulated reports indicated that exosomes released by this parasite play a crucial role in transmitting information and substances between cells during host-parasite interactions. Current knowledge on the protein contents in T. vaginalis exosome is mainly generated from three previous studies that used different T. vaginalis isolates as an experimental model. Whether T. vaginalis exosomes comprise a common set of proteins (core exosome proteome) is still unclear. METHODS To explore the core exosome proteome in T. vaginalis, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the contents of sucrose ultracentrifugation-enriched exosome and supernatant fractions isolated from six isolates. RESULTS Transmission electron microscopy (TEM) confirmed the presence of exosomes in the enriched fraction. Proteomic analysis identified a total of 1870 proteins from exosomal extracts. There were 1207 exosomal-specific proteins after excluding 436 'non-core exosomal proteins'. Among these, 72 common exosomal-specific proteins were expressed in all six isolates. Compared with three published T. vaginalis exosome proteome datasets, we identified 16 core exosomal-specific proteins. These core exosomal-specific proteins included tetraspanin (TvTSP1), the classical exosome marker, and proteins mainly involved in catalytic activity and binding such as ribosomal proteins, ras-associated binding (Rab) proteins, and heterotrimeric G proteins. CONCLUSIONS Our study highlighted the importance of using supernatant fraction from exosomal extract as a control to eliminate 'non-core exosomal proteins'. We compiled a reference core exosome proteome of T. vaginalis, which is essential for developing a fundamental understanding of exosome-mediated cell communication and host-parasite interaction.
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Affiliation(s)
- Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Hong-Wei Luo
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Chih-Yu Tsai
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Huang PJ, Weng YC, Huang KY, Lee CC, Yeh YM, Chen YT, Chiu CH, Tang P. ProFun: A web server for functional enrichment analysis of parasitic protozoan genes. J Microbiol Immunol Infect 2024:S1684-1182(24)00008-2. [PMID: 38311498 DOI: 10.1016/j.jmii.2024.01.007] [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] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/05/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024]
Abstract
BACKGROUND The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts from a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the most important pathogen in the tropics, no FEA package is available for protozoan functional (ProFun) enrichment analysis. To speed up comparative multi-omics research on parasitic protozoans, we constructed ProFun, a web-based, user-friendly platform for the research community. METHODS ProFun utilizes the Docker container, ShinyProxy, and R Shiny to construct a scalable web service with load-balancing infrastructure. We have integrated a series of visual analytic functions, in-house scripts, and custom-made annotation packages to create three analytical modules for 40 protozoan species: (1) Gene Overlaps; (2) Over-representation Analysis (ORA); (3) Gene Set Enrichment Analysis (GSEA). RESULTS We have established ProFun, a web server for functional enrichment analysis of differentially expressed genes. FEA becomes as simple as pasting a list of gene IDs into the textbox of our website. Users can customize enrichment parameters and results with just one click. The intuitive web interface and publication-ready charts enable users to reveal meaningful biological events and pinpoint potential targets for further studies. CONCLUSION ProFun is the first web application that enables gene functional enrichment analysis of parasitic protozoans. In addition to supporting FEA analysis, ProFun also allows the comparison of FEA results across complicated experimental designs. ProFun is freely available at http://dalek.cgu.edu.tw:8080/app/profun.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Yi-Chen Weng
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan.
| | - Chi-Ching Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Yu-Tong Chen
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Petrus Tang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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4
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Hung SY, Yeh YM, Chiu CH, Armstrong DG, Lin CW, Yang HM, Huang SY, Huang YY, Huang CH. Microbiome of limb-threatening diabetic foot ulcers indicates the association of fastidious Stenotrophomonas and major amputation. J Microbiol Immunol Infect 2024; 57:156-163. [PMID: 37919171 DOI: 10.1016/j.jmii.2023.10.007] [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] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/05/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Proper identification of the polymicrobial microorganisms in patients with limb-threatening diabetic foot ulcers (LTDFUs) using conventional culture is insufficient. This prospective study evaluates the potential value of adjuvant molecular testing assisting in identify fastidious micro-organisms in LTDFUs compared to standard treatment alone. METHODS Ninety patients with LTDFUs received interdisciplinary and standard antibiotic treatment in a referral diabetic foot center. A simultaneous 16S amplicon sequencing (16S AS) specimen along with conventional culture collected at admission was used to retrospectively evaluate the microbiological findings and its association with amputation outcomes. RESULTS The microorganism count revealed by 16S AS overwhelmed that of conventional culturing (17 vs. 3 bacteria/ulcer respectively). The Stenotrophomonas spp. revealed in 29 patients were highly correlated with major (above ankle) amputation (OR: 4.76, 95% CI 1.01-22.56), while only one had been concomitantly identified by conventional culturing. Thus, there were 27 cases without proper antibiotics coverage during treatment. CONCLUSIONS Adjuvant molecular testing assisted identification of fastidious pathogens such as Stenotrophomonas infection and might be associated with major amputation in patients with LTDFUs.
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Affiliation(s)
- Shih-Yuan Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - David G Armstrong
- Southwestern Academic Limb Salvage Alliance (SALSA), Department of Surgery, Keck School of Medicine of University of Southern California (USC), Los Angeles, USA (D.G.A.)
| | - Cheng-Wei Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Hui-Mei Yang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Shu-Yu Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Yu-Yao Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan; College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Chung-Huei Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan City, Taiwan.
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5
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Chang JWC, Hsieh JJ, Tsai CY, Chiu HY, Lin YF, Wu CE, Shen YC, Hou MM, Chang CY, Chen JA, Chen CL, Chiu CT, Yeh YM, Chiu CH. Gut microbiota and clinical response to immune checkpoint inhibitor therapy in patients with advanced cancer. Biomed J 2024:100698. [PMID: 38280521 DOI: 10.1016/j.bj.2024.100698] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND There is currently no well-accepted consensus on the association between gut microbiota and the response to treatment of immune checkpoint inhibitors (ICIs) in patients with advanced cancer. METHODS Fecal samples were collected before ICI treatment. Gut microbiota was analyzed using 16 S ribosomal RNA sequencing. We investigated the relationship between the α-diversity of fecal microbiota and patients' clinical outcomes. Microbiota profiles from patients and healthy controls were determined. Pre-treatment serum was examined by cytokine array. RESULTS We analyzed 74 patients, including 42 with melanoma, 8 with kidney cancer, 13 with lung cancer, and 11 with other cancers. Combination therapy of anti-PD1 and anti-CTLA-4 was used in 14 patients, and monotherapy in the rest. Clinical benefit was observed in 35 (47.3 %) cases, including 2 complete responses, 16 partial responses, and 17 stable diseases according to RECIST criteria. No significant difference in α-diversity was found between the benefiter and non-benefiter groups. However, patients with α-diversity within the range of our healthy control had a significantly longer median overall survival (18.9 months), compared to the abnormal group (8.2 months) (p = 0.041, hazard ratio = 0.546) for all patients. The microbiota composition of the benefiters was similar to that of healthy individuals. Furthermore, specific bacteria, such as Prevotella copri and Faecalibacterium prausnitzii, were associated with a favorable outcome. We also observed that serum IL-18 before treatment was significantly lower in the benefiters, compared to non-benefiters. CONCLUSIONS The α-diversity of gut microbiota is positively correlated with more prolonged overall survival in cancer patients following ICI therapy.
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Affiliation(s)
- John Wen-Cheng Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Immuno-Oncology Center of Excellence, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jia-Juan Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chih-Yu Tsai
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Horng-Yih Chiu
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yu-Feng Lin
- Immuno-Oncology Center of Excellence, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nursing, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chiao-En Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Immuno-Oncology Center of Excellence, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yung-Chi Shen
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ming-Mo Hou
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Immuno-Oncology Center of Excellence, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chieh-Ying Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Jian-An Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Microbiology and Immunology, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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Chen CC, Huang JL, Chen KJ, Kong MS, Hua MC, Yeh YM, Chang HJ. Comparison of 16S rRNA gene sequencing microbiota among children with serological IgE-mediated food hypersensitivity. Pediatr Res 2024; 95:241-250. [PMID: 37648747 DOI: 10.1038/s41390-023-02735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND We hypothesized that specific food hypersensitivity (FH) in children is linked to specific gut microbiota. The aim of our study was to quantify and evaluate differences in gut microbial composition among children with different IgE-mediated FH. METHODS Children (n = 81) aged 18 to 36 months were enrolled, fecal samples of 57 children with FH and 24 healthy children were evaluated using next-generation sequencing. Individual microbial diversity and composition were analyzed via targeting the 16 S rRNA gene hypervariable V3-V5 regions. RESULTS Children with IgE-mediated FH (in milk, egg white, soy) had significantly lower gut microbiota diversity and richness than healthy children. Children with IgE-mediated FH exhibited relatively high abundances of Firmicutes and relative underrepresentation of the phylum Bacteroidetes. We observed significant increases in relative abundances of Ruminococcaceae, Clostridiaceae, and Erysipelotrichaceae (p < 0.01, compared to control) in children with milk hypersensitivity and of Clostridiaceae and Erysipelotrichaceae (p < 0.01) in children with peanut hypersensitivity. We also found significant increases in the numbers of Clostridiaceae, Lachnospiraceae and Pasteurellaceae (p < 0.01) in children with egg white hypersensitivity. CONCLUSIONS These findings identify early evidence of different gut microbiota development/ differentiation in children with food hypersensitivity. Specific food hypersensitivities may be associated with compositional changes in intestinal microbiota. IMPACT These findings identify early evidence of different gut microbiota development/differentiation in children with food hypersensitivity. We built a gut microbial profile that could identify toddlers at risk for food hypersensitivity. Children with enriched Firmicutes (phylum) with partial different families may be associated with food hypersensitivity. Enriched family Clostridiaceae, Ruminococcaceae, Lachnospiraceae, or Erysipelotrichaceae in gut microbiota may be associated with specific food hypersensitivities (such as milk, egg white, peanut) in children.
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Affiliation(s)
- Chien-Chang Chen
- Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
- Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Jing-Long Huang
- Chang Gung University College of Medicine, Taoyuan, Taiwan
- Division of Allergy, Asthma and Rheumatology, Department of Pediatrics, New Taipei Municipal Tu Cheng Hospital, Chang Gung Memorial Hospital, New Taipei, Taiwan
| | - Kun-Jei Chen
- Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Man-Shan Kong
- Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Man-Chin Hua
- Chang Gung University College of Medicine, Taoyuan, Taiwan
- Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hung-Ju Chang
- Division of Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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7
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Lee CC, Lin YC, Pan TY, Yang CH, Li PH, Chen SY, Gao JJ, Yang C, Chu LJ, Huang PJ, Yeh YM, Tang P, Chang YS, Yu JS, Hsiao YC. HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks. Anal Chem 2023; 95:15486-15496. [PMID: 37820297 PMCID: PMC10603604 DOI: 10.1021/acs.analchem.3c01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.
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Affiliation(s)
- Chi-Ching Lee
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Yu-Chieh Lin
- Graduate
Institute of Artificial Intelligence, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Teng Yu Pan
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Cheng Hann Yang
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Pei-Hsuan Li
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Sin You Chen
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Jhih Jie Gao
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Chi Yang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
| | - Po-Jung Huang
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Department
of Biomedical Sciences, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
| | - Petrus Tang
- Molecular
Infectious Disease Research Center, Chang
Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Department
of Parasitology, College of Medicine, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Research
Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 33302 Taoyuan, Taiwan
| | - Yung-Chin Hsiao
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
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Lan KY, Le PH, Chiu CT, Chen CC, Yeh YM, Cheng HT, Kuo CJ, Chen CL, Chen YC, Yeh PJ, Chiu CH, Chang CJ. Fecal microbiota transplantation for treatment of refractory or recurrent Clostridioides difficile infection in Taiwan: a cost-effectiveness analysis. Front Med (Lausanne) 2023; 10:1229148. [PMID: 37849493 PMCID: PMC10577297 DOI: 10.3389/fmed.2023.1229148] [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: 06/01/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Background Compared to antibiotic treatment, fecal microbiota transplantation (FMT) is a more effective treatment for refractory or recurrent CDI (rCDI). Patients with inflammatory bowel disease (IBD) have a higher incidence of CDI and worse outcomes. There has been no study from Asia to evaluate the cost-effectiveness of FMT for overall rCDI patients and rCDI patients with IBD. Methods We applied a Markov model with deterministic and probabilistic sensitivity analyses to evaluate the cost and effectiveness of different treatments for rCDI patients with a time horizon of 1 year from the payer's perspective. We compared the cost and clinical outcomes of FMT through colonoscopy to two antibiotics (vancomycin and fidaxomicin) using data from Chang Gung Memorial Hospital, Taoyuan, Taiwan. Results Compared to vancomycin, FMT was cost-effective in overall rCDI patients as well as IBD patients with rCDI [USD 39356 (NT$1,101,971.98)/quality-adjusted life year (QALY) gained in overall patients; USD65490 (NT$1,833,719.14)/QALY gained in IBD patients]. Compared to fidaxomicin, FMT was only cost-effective in overall rCDI patients [USD20255 (NT$567,133.45)/QALY gained] but slightly increased QALY (0.0018 QALY gained) in IBD patients with rCDI. Conclusion FMT is cost-effective, compared to vancomycin or fidaxomicin, for the treatment of rCDI in most scenarios from the payers' perspective in Taiwan.
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Affiliation(s)
- Kai-Yen Lan
- Department of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Puo-Hsien Le
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Chien-Chang Chen
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Department of Pediatric Gastroenterology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Hao-Tsai Cheng
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
| | - Chia-Jung Kuo
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Yi-Ching Chen
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Pai-Jui Yeh
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Department of Pediatric Gastroenterology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Chee-Jen Chang
- Department of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Graduate Institute of Clinical Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memory Hospital, Linko Branch, Taoyuan, Taiwan
- Research Service Center for Health Informatics, Chang Gung University, Taoyuan, Taiwan
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9
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Huang LS, Yeh YM, Chiu SF, Huang PJ, Chu LJ, Huang CY, Cheng FW, Chen LC, Lin HC, Shih YW, Lin WN, Huang KY. Intestinal microbiota analysis of different Blastocystis subtypes and Blastocystis-negative individuals in Taiwan. Biomed J 2023:100661. [PMID: 37774792 DOI: 10.1016/j.bj.2023.100661] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/13/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Intestinal parasitic infections are the most common infectious diseases among Southeast Asian migrant workers in Taiwan, especially for infections with Blastocystis hominis. However, little is known about the impact of Blastocystis subtypes (STs) on the gut microbiota. MATERIAL AND METHODS We retrospectively evaluated the prevalence of intestinal parasites in a teaching hospital in Northern Taiwan in the period of 2015 to 2019. Blastocystis-positive stool specimens were collected for ST analysis by polymerase chain reaction in 2020. Intestinal microbiota analyses of different Blastocystis STs and Blastocystis-free individuals were conducted by 16S rRNA sequencing. RESULTS A total of 13,859 subjects were analyzed, of which 1,802 cases (13%) were diagnosed with intestinal parasitic infections. B. hominis infections were the most prevalent (n = 1546, 85.7%). ST analysis of Blastocystis-positive samples (n=150) indicated that ST1 was the most common type, followed by ST3, ST4, ST2, ST7, and ST5. Different Blastocystis STs (ST1, ST3, and ST4) were associated with distinct richness and diversity of the microbiota. Taxonomic profiles revealed that Akkermansia muciniphila was significantly enriched for all analyzed Blastocystis STs, whereas Holdemanella biformis was more abundant in the Blastocystis-free group. Additionally, Succinivibrio dextrinosolvens and Coprococcus eutactus were specifically more abundant in ST3 carriers than in non-infected individuals. CONCLUSIONS This study demonstrates that A. muciniphila is positively associated with all Blastocystis STs, while H. biformis was negatively associated with them. Several bacteria were enriched in specific STs, highlighting the need for further microbiota analysis at the ST level to elucidate the pathogenicity of Blastocystis.
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Affiliation(s)
- Li-San Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan; Department of Inspection, Taipei City Hospital, Renai Branch, Taipei City 114, Taiwan; Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei city 114, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan city 333, Taiwan; Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan city 333, Taiwan
| | - Shu-Fang Chiu
- Department of Inspection, Taipei City Hospital, Renai Branch, Taipei City 114, Taiwan; Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei city 114, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei city 114, Taiwan
| | - Po-Jung Huang
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan city 333, Taiwan; Department of Biomedical Sciences, Chang Gung University, Taoyuan city 333, Taiwan
| | - Lichieh Julie Chu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan city 333, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan city 333, Taiwan; Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan city 333, Taiwan
| | - Ching-Yun Huang
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei city 114, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei city 114, Taiwan
| | - Fang-Wen Cheng
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan; Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei city 114, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan
| | - Hsin-Chung Lin
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan; Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan
| | - Ya-Wen Shih
- School of nursing, National Taipei University of Nursing and Health Sciences, Taipei City 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan; Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei city 114, Taiwan.
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Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P. Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasit Vectors 2023; 16:226. [PMID: 37415204 DOI: 10.1186/s13071-023-05842-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial. METHODS In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions. RESULTS First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release. CONCLUSION These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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11
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Wang LJ, Li SC, Yeh YM, Lee SY, Kuo HC, Yang CY. Gut mycobiome dysbiosis and its impact on intestinal permeability in attention-deficit/hyperactivity disorder. J Child Psychol Psychiatry 2023. [PMID: 37016804 DOI: 10.1111/jcpp.13779] [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] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Dysbiosis in the gut microbial community might be involved in the pathophysiology of attention-deficit/hyperactivity disorder (ADHD). The fungal component of the gut microbiome, namely the mycobiota, is a hyperdiverse group of multicellular eukaryotes that can influence host intestinal permeability. This study therefore aimed to investigate the impact of fungal mycobiome dysbiosis and intestinal permeability on ADHD. METHODS Faecal samples were collected from 35 children with ADHD and from 35 healthy controls. Total DNA was extracted from the faecal samples and the internal transcribed spacer regions were sequenced using high-throughput next-generation sequencing (NGS). The fungal taxonomic classification was analysed using bioinformatics tools and the differentially expressed fungal species between the ADHD and healthy control groups were identified. An in vitro permeability assay (Caco-2 cell layer) was used to evaluate the biological effects of fungal dysbiosis on intestinal epithelial barrier function. RESULTS The β-diversity (the species diversity between two communities), but not α-diversity (the species diversity within a community), reflected the differences in fungal community composition between ADHD and control groups. At the phylum level, the ADHD group displayed a significantly higher abundance of Ascomycota and a significantly lower abundance of Basidiomycota than the healthy control group. At the genus level, the abundance of Candida (especially Candida albicans) was significantly increased in ADHD patients compared to the healthy controls. In addition, the in vitro cell assay revealed that C. albicans secretions significantly enhanced the permeability of Caco-2 cells. CONCLUSIONS The current study is the first to explore altered gut mycobiome dysbiosis using the NGS platform in ADHD. The findings from this study indicated that dysbiosis of the fungal mycobiome and intestinal permeability might be associated with susceptibility to ADHD.
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Affiliation(s)
- Liang-Jen Wang
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sheng-Yu Lee
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Department of Psychiatry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chia-Yu Yang
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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12
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Janapatla RP, Dudek A, Chen CL, Chuang CH, Chien KY, Feng Y, Yeh YM, Wang YH, Chang HJ, Lee YC, Chiu CH. Marine prebiotics mediate decolonization of Pseudomonas aeruginosa from gut by inhibiting secreted virulence factor interactions with mucins and enriching Bacteroides population. J Biomed Sci 2023; 30:9. [PMID: 36732731 PMCID: PMC9896862 DOI: 10.1186/s12929-023-00902-w] [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: 09/29/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa intestinal carriage rates are significantly higher in immunosuppressed individuals and hospitalized patients who therefore have increased risk of infections and antibiotic-associated diarrhea. To combat intestinal dysbiosis and decolonize P. aeruginosa from gastrointestinal tract, we investigated the anti-adherence and gut microbiota modulation properties of marine prebiotic fucoidans. METHODS Proteomic analysis of culture supernatant was performed by LC-MS/MS. Using lectin-based enzyme-linked immunosorbent assay, hemagglutinin domain interaction and inhibition with biomolecules were studied. We investigated the role of nutritional grade fucoidans in a mouse model and used 16S ribosomal RNA sequencing to examine fecal microbiota composition. RESULTS Analysis of culture supernatant proteins indicated the secretion of two-partner secretion (TPS) family proteins, including TpsA1/CdiA2 and TpsA2/CdiA1. Lectin like activity at the N-terminal of TpsA due to a conserved hemagglutinin domain (Pfam identifier [ID] PF05860) mediates binding to mucins that carry multiple fucosylated glycans. Fucose-rich sulfated polysaccharides (fucoidans) and sulfated dextrans were found to be potent inhibitors of the recombinant N-terminal hemagglutinin domain of TpsA (TpsA-NT-HAD) binding to mucins. In a mouse model, antibiotic-induced dysbiosis was essential for P. aeruginosa gastrointestinal colonization. After prophylactic oral fucoidans supplementation, a higher proportion (60%) of the mice were decolonized over time and resisted re-colonization, this was associated with remarkable expansion of Bacteroides (post-infection day-3 abundance, 29-50%) and consequential reductions in bloom of Enterobacteriaceae and Enterococcaceae populations. In the non-supplemented group, Parabacteroides mediated recovery from dysbiosis but failed to decolonize P. aeruginosa. CONCLUSIONS Supplementing diet with marine prebiotic fucoidans can mediate earlier recovery from dysbiosis and decolonization of P. aeruginosa from gut by inhibiting secreted virulence factor (TpsA/CdiA) interaction with mucins and promoting the growth of beneficial Bacteroides population. We suggest the prophylactic use of nutritional grade fucoidans to decolonize P. aeruginosa from gastrointestinal tract of at-risk individuals to prevent infection and transmission of colonizing P. aeruginosa.
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Affiliation(s)
- Rajendra Prasad Janapatla
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Anna Dudek
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | | | - Kun-Yi Chien
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ye Feng
- grid.13402.340000 0004 1759 700XInstitute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan-Ming Yeh
- grid.413801.f0000 0001 0711 0593Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Ju Chang
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Chuan Lee
- grid.21107.350000 0001 2171 9311Department of Biology, Johns Hopkins University, Baltimore, MD USA
| | - Cheng-Hsun Chiu
- grid.413801.f0000 0001 0711 0593Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.413801.f0000 0001 0711 0593Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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13
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Chen YC, Le PH, Wang YH, Chuang TC, Yeh YM, Chiu CT, Chiu CH. Gut Colonization and Antibiotic-Associated Diarrhea by Clostridium innocuum in Children and Adults. Clin Infect Dis 2023; 76:369-371. [PMID: 36029096 DOI: 10.1093/cid/ciac696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yi-Ching Chen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Puo-Hsien Le
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tzu-Chun Chuang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Chao A, Chao AS, Lin CY, Weng C, Wu RC, Yeh YM, Huang SS, Lee YS, Lai CH, Huang HJ, Tang YH, Lin YS, Wang CJ, Wu KY. Analysis of endometrial lavage microbiota reveals an increased relative abundance of the plastic-degrading bacteria Bacillus pseudofirmus and Stenotrophomonas rhizophila in women with endometrial cancer/endometrial hyperplasia. Front Cell Infect Microbiol 2022; 12:1031967. [PMID: 36439209 PMCID: PMC9682088 DOI: 10.3389/fcimb.2022.1031967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
The pathogenic influences of uterine bacteria on endometrial carcinogenesis remain unclear. The aim of this pilot study was to compare the microbiota composition of endometrial lavage samples obtained from women with either endometrial hyperplasia (EH) or endometrial cancer (EC) versus those with benign uterine conditions. We hypothesized that specific microbiota signatures would distinguish between the two groups, possibly leading to the identification of bacterial species associated with endometrial tumorigenesis. A total of 35 endometrial lavage specimens (EH, n = 18; EC, n = 7; metastatic EC, n = 2; benign endometrial lesions, n = 8) were collected from 32 women who had undergone office hysteroscopy. Microbiota composition was determined by sequencing the V3−V4 region of 16S rRNA genes and results were validated by real-time qPCR in 46 patients with EC/EH and 13 control women. Surprisingly, we found that Bacillus pseudofirmus and Stenotrophomonas rhizophila – two plastic-degrading bacterial species – were over-represented in endometrial lavage specimens collected from patients with EC/EH. Using computational analysis, we found that the functional profile of endometrial microbiota in EC/EH was associated with fatty acid and amino acid metabolism. In summary, our hypothesis-generating data indicate that the plastic-degrading bacteria Bacillus pseudofirmus and Stenotrophomonas rhizophila are over-represented within the endometrial lavage microbiota of women with EC/EH living in Taiwan. Whether this may be related to plastic pollution deserves further investigation.
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Affiliation(s)
- Angel Chao
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - An-Shine Chao
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cindy Hsuan Weng
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ren-Chin Wu
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
| | - Yuan-Ming Yeh
- Department of Pathology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Shih-Sin Huang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yun-Shien Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Biotechnology, Ming-Chuan University, Taoyuan, Taiwan
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huei-Jean Huang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yun-Hsin Tang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Shan Lin
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
| | - Chin-Jung Wang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kai-Yun Wu
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- *Correspondence: Kai-Yun Wu,
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Huang YH, Wu YH, Tang HY, Chen ST, Wang CC, Ho WJ, Lin YH, Liu GH, Lin PY, Lo CJ, Yeh YM, Cheng ML. Gut Microbiota and Bile Acids Mediate the Clinical Benefits of YH1 in Male Patients with Type 2 Diabetes Mellitus: A Pilot Observational Study. Pharmaceutics 2022; 14:pharmaceutics14091857. [PMID: 36145605 PMCID: PMC9505101 DOI: 10.3390/pharmaceutics14091857] [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: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Our previous clinical trial showed that a novel concentrated herbal extract formula, YH1 (Rhizoma coptidis and Shen-Ling-Bai-Zhu-San), improved blood glucose and lipid control. This pilot observational study investigated whether YH1 affects microbiota, plasma, and fecal bile acid (BA) compositions in ten untreated male patients with type 2 diabetes (T2D), hyperlipidemia, and a body mass index ≥ 23 kg/m2. Stool and plasma samples were collected for microbiome, BA, and biochemical analyses before and after 4 weeks of YH1 therapy. As previous studies found, the glycated albumin, 2-h postprandial glucose, triglycerides, total cholesterol, and low-density lipoprotein cholesterol levels were significantly improved after YH1 treatment. Gut microbiota revealed an increased abundance of the short-chain fatty acid-producing bacteria Anaerostipes and Escherichia/Shigella. Furthermore, YH1 inhibited specific phylotypes of bile salt hydrolase-expressing bacteria, including Parabacteroides, Bifidobacterium, and Bacteroides caccae. Stool tauro-conjugated BA levels increased after YH1 treatment. Plasma total BAs and 7α-hydroxy-4-cholesten-3-one (C4), a BA synthesis indicator, were elevated. The reduced deconjugation of BAs and increased plasma conjugated BAs, especially tauro-conjugated BAs, led to a decreased glyco- to tauro-conjugated BA ratio and reduced unconjugated secondary BAs. These results suggest that YH1 ameliorates T2D and hyperlipidemia by modulating microbiota constituents that alter fecal and plasma BA compositions and promote liver cholesterol-to-BA conversion and glucose homeostasis.
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Affiliation(s)
- Yueh-Hsiang Huang
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Yi-Hong Wu
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Hsiang-Yu Tang
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Szu-Tah Chen
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
| | - Chih-Ching Wang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
| | - Wan-Jing Ho
- Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
| | - Yi-Hsuan Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
| | - Geng-Hao Liu
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
| | - Pei-Yeh Lin
- Department of Medical Nutrition Therapy, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chi-Jen Lo
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
- Correspondence: (Y.-M.Y.); (M.-L.C.)
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan
- Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (Y.-M.Y.); (M.-L.C.)
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16
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Ong SC, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Rada P, Hrdý I, Narayanasamy RK, Smutná T, Lin R, Luo HW, Chiu CH, Tachezy J, Tang P. Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis. Genes (Basel) 2022; 13:genes13030531. [PMID: 35328084 PMCID: PMC8951798 DOI: 10.3390/genes13030531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal epithelial cells and animal models. These results prompted us to examine whether EVs released from TVV+ isolates contained TVV. We isolated small extracellular vesicles (sEVs) from six T. vaginalis isolates that were either TVV free (ATCC 50143), harbored a single (ATCC 30236, ATCC 30238, T1), two (ATCC PRA-98), or three TVV subspecies (ATCC 50148). The presence of TVV subspecies in the six isolates was observed using reverse transcription-polymerase chain reaction (RT-PCR). Transmission electron microscopy (TEM) confirmed the presence of cup-shaped sEVs with a size range from 30–150 nm. Trichomonas vaginalis tetraspanin (TvTSP1; TVAG_019180), the classical exosome marker, was identified in all the sEV preparations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that all the sEVs isolated from TVV+ isolates contain viral capsid proteins derived from the same TVV subspecies in that isolate as demonstrated by RT-PCR. To provide more comprehensive information on the TVV subspecies population in other T. vaginalis isolates, we investigated the distribution of TVV subspecies in twenty-four isolates by mining the New-Generation Sequencing (NGS) RNAseq datasets. Our results should be beneficial for future studies investigating the role of TVV on the pathogenicity of T. vaginalis and the possible transmission of virus subspecies among different isolates via sEVs.
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Affiliation(s)
- Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
| | - Wei-Hung Cheng
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung 824, Taiwan;
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
| | - Chih-Yu Tsai
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan District, Taoyuan 333, Taiwan;
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan; (C.-C.L.); (Y.-M.Y.)
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan; (C.-C.L.); (Y.-M.Y.)
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Taoyuan 333, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan; (C.-C.L.); (Y.-M.Y.)
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec (BIOCEV), Průmyslová 595, 252 42 Vestec, Czech Republic; (P.R.); (I.H.); (R.K.N.); (T.S.)
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec (BIOCEV), Průmyslová 595, 252 42 Vestec, Czech Republic; (P.R.); (I.H.); (R.K.N.); (T.S.)
| | - Ravi Kumar Narayanasamy
- Department of Parasitology, Faculty of Science, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec (BIOCEV), Průmyslová 595, 252 42 Vestec, Czech Republic; (P.R.); (I.H.); (R.K.N.); (T.S.)
| | - Tamara Smutná
- Department of Parasitology, Faculty of Science, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec (BIOCEV), Průmyslová 595, 252 42 Vestec, Czech Republic; (P.R.); (I.H.); (R.K.N.); (T.S.)
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
| | - Hong-Wei Luo
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec (BIOCEV), Průmyslová 595, 252 42 Vestec, Czech Republic; (P.R.); (I.H.); (R.K.N.); (T.S.)
- Correspondence: (J.T.); (P.T.)
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (S.-C.O.); (F.-M.K.); (C.-Y.T.); (R.L.); (H.-W.L.)
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
- Correspondence: (J.T.); (P.T.)
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Huang PJ, Huang CY, Li YX, Liu YC, Chu LJ, Yeh YM, Cheng WH, Chen RM, Lee CC, Chen LC, Lin HC, Chiu SF, Lin WN, Lyu PC, Tang P, Huang KY. Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death. Biomedicines 2021; 9:biomedicines9121817. [PMID: 34944632 PMCID: PMC8698965 DOI: 10.3390/biomedicines9121817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) is the mainstay of anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, the molecular events of MTZ-induced cell death in T. vaginalis remain elusive. To gain insight into the differential expression of genes related to MTZ resistance and cell death, we conducted RNA-sequencing of three paired MTZ-resistant (MTZ-R) and MTZ-sensitive (MTZ-S) T. vaginalis strains treated with or without MTZ. Comparative transcriptomes analysis identified that several putative drug-resistant genes were exclusively upregulated in different MTZ-R strains, such as ATP-binding cassette (ABC) transporters and multidrug resistance pumps. Additionally, several shared upregulated genes among all the MTZ-R transcriptomes were not previously identified in T. vaginalis, such as 5′-nucleotidase surE and Na+-driven multidrug efflux pump, which are a potential stress response protein and a multidrug and toxic compound extrusion (MATE)-like protein, respectively. Functional enrichment analysis revealed that purine and pyrimidine metabolisms were suppressed in MTZ-S parasites upon drug treatment, whereas the endoplasmic reticulum-associated degradation (ERAD) pathway, proteasome, and ubiquitin-mediated proteolysis were strikingly activated, highlighting the novel pathways responsible for drug-induced stress. Our work presents the most detailed analysis of the transcriptional changes and the regulatory networks associated with MTZ resistance and MTZ-induced signaling, providing insights into MTZ resistance and cell death mechanisms in trichomonads.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City 333, Taiwan;
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Ching-Yun Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
| | - Yu-Xuan Li
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Yi-Chung Liu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Lichieh-Julie Chu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City 333, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Wei-Hung Cheng
- Department of Medical Laboratory Science, College of Medicine, I-Shou University, Kaohsiung City 824, Taiwan;
| | - Ruei-Ming Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan;
| | - Hsin-Chung Lin
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
| | - Shu-Fang Chiu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Department of Inspection, Taipei City Hospital, Renai Branch, Taipei City 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Kuo-Yang Huang
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
- Correspondence: ; Tel.: +886-2-87923100 (ext. 18564)
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18
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Lee CC, Feng Y, Yeh YM, Lien R, Chen CL, Zhou YL, Chiu CH. Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants. Front Microbiol 2021; 12:746111. [PMID: 34690993 PMCID: PMC8529156 DOI: 10.3389/fmicb.2021.746111] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/08/2021] [Indexed: 01/14/2023] Open
Abstract
Gut dysbiosis may precede neonatal sepsis, but the association is still not well-understood. The goal of this study is to investigate the association between gut microbiota and neonatal sepsis, and to seek the evidence of colonization of pathogenic bacteria in the gut before evolving into an invasive infection. A prospective cohort study examined fecal microbiota composition in preterm infants with and without sepsis. Thirty-two very-low-birth-weight (VLBW) preterm infants and 10 healthy term infants as controls were enrolled. The fecal samples collected from the participants at the first, fourth, and seventh weeks of life underwent 16S rRNA amplicon sequencing for measurement of the diversity and composition of the microbiota. The bacterial isolates causing neonatal sepsis were genome sequenced. PCR was performed to confirm the translocation of the bacteria from the gut to the blood. The results showed that VLBW preterm infants with sepsis had lower microbial diversity in the gut at birth compared to preterm infants without sepsis and term infants. The composition of gut microbiome in preterm infants was similar to healthy terms at birth but evolved toward dysbiosis with increasing Proteobacteria and decreasing Firmicutes weeks later. The strain-specific PCR confirmed the presence of causative pathogens in the gut in 4 (40%) out of 10 VLBW preterms with sepsis before or at onset of sepsis, and persistence of the colonization for weeks after antibiotic treatment. The same bacterial strain could horizontally spread to cause infection in other infants. Prolonged antibiotic exposure significantly reduced beneficial Bifidobacterium and Lactobacillus in the gut. In conclusion, preterm infants with gut dysbiosis are at risk for neonatal sepsis, and the causative pathogens may be from the gut and persist to spread horizontally. The association of increased Proteobacteria abundance and decrease in microbiome diversity suggests the need for interventions targeting the gut microbiome to prevent dysbiosis and sepsis in VLBW preterm infants.
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Affiliation(s)
- Chien-Chung Lee
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ye Feng
- Sir Run Run Shaw Hospital, Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Reyin Lien
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ying-Li Zhou
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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Lee CC, Feng Y, Chen CL, Yeh YM, Hsu MH, Liao WT, Zhou YL, Tang P, Chiu CH. Genomic analysis of maternal carriage of group B Streptococcus and transmission routes of neonatal sepsis. J Infect 2021; 83:709-737. [PMID: 34627842 DOI: 10.1016/j.jinf.2021.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 01/30/2023]
Affiliation(s)
- Chien-Chung Lee
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ye Feng
- Sir Run Run Shaw Hospital, Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Mei-Hua Hsu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wan-Ting Liao
- Taiwan Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ying-Li Zhou
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Petrus Tang
- Department of Parasitology, Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No. 5, Fu-Hsin Street, Kweishan 333, Taoyuan, Taiwan.
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Lee CC, Huang PJ, Yeh YM, Li PH, Chiu CH, Cheng WH, Tang P. Helminth egg analysis platform (HEAP): An opened platform for microscopic helminth egg identification and quantification based on the integration of deep learning architectures. J Microbiol Immunol Infect 2021; 55:395-404. [PMID: 34511389 DOI: 10.1016/j.jmii.2021.07.014] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/26/2021] [Accepted: 07/18/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Millions of people throughout the world suffer from parasite infections. Traditionally, technicians use manual eye inspection of microscopic specimens to perform a parasite examination. However, manual operations have limitations that hinder the ability to obtain precise egg counts and cause inefficient identification of infected parasites on co-infections. The technician requirements for handling a large number of microscopic examinations in countries that have limited medical resources are substantial. We developed the helminth egg analysis platform (HEAP) as a user-friendly microscopic helminth eggs identification and quantification platform to assist medical technicians during parasite infection examination. METHODS Multiple deep learning strategies including SSD (Single Shot MultiBox Detector), U-net, and Faster R-CNN (Faster Region-based Convolutional Neural Network) are integrated to identify the same specimen allowing users to choose the best predictions. An image binning and egg-in-edge algorithm based on pixel density detection was developed to increase the performance. Computers with different operation systems can be gathered to lower the computation time using our easy-to-deploy software architecture. RESULTS A user-friendly interface is provided to substantially increase the efficiency of manual validation. To adapt to low-cost computers, we architected a distributed computing structure with high flexibilities. CONCLUSIONS HEAP serves not only as a prediction service provider but also as a parasitic egg database of microscopic helminth egg image collection, labeling data and pretrained models. All images and labeling resources are free and accessible at http://heap.cgu.edu.tw. HEAP can also be an ideal education and training resource for helminth egg examination.
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Affiliation(s)
- Chi-Ching Lee
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Artificial Intelligence Research Center, Chang Gung University, Taoyuan, Taiwan.
| | - Po-Jung Huang
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Pei-Hsuan Li
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Medical Laboratory Science, College of Medicine, I-Shou University, Kaohsiung City, Taiwan.
| | - Petrus Tang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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21
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Li HP, Huang CY, Lui KW, Chao YK, Yeh CN, Lee LY, Huang Y, Lin TL, Kuo YC, Huang MY, Lai YR, Yeh YM, Fan HC, Lin AC, Hsieh JCH, Chang KP, Lin CY, Wang HM, Chang YS, Hsu CL. Combination of Epithelial Growth Factor Receptor Blockers and CDK4/6 Inhibitor for Nasopharyngeal Carcinoma Treatment. Cancers (Basel) 2021; 13:cancers13122954. [PMID: 34204797 PMCID: PMC8231497 DOI: 10.3390/cancers13122954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/10/2021] [Accepted: 06/10/2021] [Indexed: 01/25/2023] Open
Abstract
Simple Summary Our findings indicated that the EGF-EGFR pathway was highly activated in very young patients with recurrent or metastatic NPC. High EGFR expression in patients with metastatic NPC resulted in poor clinical outcomes. To examine whether the EGFR pathway serves as a therapeutic target for NPC, NPC patient-derived xenograft (PDX) and NPC cell lines were treated with EGFR inhibitors (EGFRi) and a cell cycle blocker. Either EGFRi or cell cycle blocker treatment alone could reduce NPC cell growth and PDX tumor growth. Furthermore, combination treatment exerted an additive suppression effect on PDX tumor growth. This study provides promising evidence that EGFRi used in combination with a cell cycle blocker may be used to treat patients with NPC. Abstract Background: Nasopharyngeal carcinoma (NPC) involves host genetics, environmental and viral factors. In clinical observations, patients of young and old ages were found to have higher recurrence and metastatic rates. Methods: Cytokine array was employed to screen druggable target(s). The candidate target(s) were confirmed through patient-derived xenografts (PDXs) and a new EBV-positive cell line, NPC-B13. Results: Overexpression of epithelial growth factor (EGF) and EGF receptor (EGFR) was detected in young patients than in older patients. The growth of NPC PDX tumors and cell lines was inhibited by EGFR inhibitors (EGFRi) cetuximab and afatinib when used separately or in combination with the cell cycle blocker palbociclib. Western blot analysis of these drug-treated PDXs demonstrated that the blockade of the EGF signaling pathway was associated with a decrease in the p-EGFR level and reduction in PDX tumor size. RNA sequencing results of PDX tumors elucidated that cell cycle-related pathways were suppressed in response to drug treatments. High EGFR expression (IHC score ≥ grade 3) was correlated with poor survival in metastatic patients (p = 0.008). Conclusions: Our results provide encouraging preliminary data related to the combination treatment of EGFRi and palbociclib in patients with NPC.
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Affiliation(s)
- Hsin-Pai Li
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33305, Taiwan; (H.-P.L.); (M.-Y.H.); (Y.-R.L.); (Y.-S.C.)
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan 33305, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33305, Taiwan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Chen-Yang Huang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Kar-Wai Lui
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Yin-Kai Chao
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Chun-Nan Yeh
- Liver Research Center, Department of General Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Li-Yu Lee
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (L.-Y.L.); (Y.H.)
| | - Yenlin Huang
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (L.-Y.L.); (Y.H.)
| | - Tung-Liang Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Yung-Chia Kuo
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Mei-Yuan Huang
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33305, Taiwan; (H.-P.L.); (M.-Y.H.); (Y.-R.L.); (Y.-S.C.)
| | - Yi-Ru Lai
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33305, Taiwan; (H.-P.L.); (M.-Y.H.); (Y.-R.L.); (Y.-S.C.)
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Hsien-Chi Fan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - An-Chi Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Jason Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Chien-Yu Lin
- Department of Radiation, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Hung-Ming Wang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
| | - Yu-Sun Chang
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33305, Taiwan; (H.-P.L.); (M.-Y.H.); (Y.-R.L.); (Y.-S.C.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33305, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan;
| | - Cheng-Lung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; (C.-Y.H.); (T.-L.L.); (Y.-C.K.); (H.-C.F.); (A.-C.L.); (J.C.-H.H.); (H.-M.W.)
- School of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
- Correspondence: ; Tel.: +886-3-328-1200; Fax: +886-3-327-8211
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Yeh YM, Cheng HT, Le PH, Chen CC, Kuo CJ, Chen CL, Chiu CT, Chiu CH. Implementation of fecal microbiota transplantation in a medical center for recurrent or refractory Clostridioides difficile infection and report of preliminary outcome. Biomed J 2021; 45:504-511. [PMID: 34118466 PMCID: PMC9421926 DOI: 10.1016/j.bj.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/26/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022] Open
Abstract
Background Fecal microbiota transplantation (FMT) has been shown to highly effective in the treatment of recurrent or refractory Clostridioides difficile infection (rCDI) in many countries of the world. Not until 2018, Ministry of Health and Welfare, Taiwan approved the application of FMT for rCDI under a special law. The study reported the first implementation of the technology in the medical center in Taiwan and the preliminary outcome. Methods FMT was used to treat patients with rCDI in Chang Gung Memorial Hospital. FMT was delivered by gastroenterologists using colonoscope. Strict donor screening was performed according to the guidelines. We followed up the clinical course of patients after FMT. 16S rRNA sequencing of fecal samples for donor, and also recipient before and after FMT was carried out. Results From September 2018 to June 2020, 39 patients with rCDI received FMT, with a successful rate of 89.7%. Two patients died due to causes unrelated to FMT, and two other cases showed no clinical improvement after the procedure. High school and college students showed the best pass rate during donor screening. The presence of multi-drug resistant pathogen was the most common cause for screening failure. We demonstrated in a case the use of rRNA sequencing as a biomarker indicating for the improvement of dysbiosis in a patient after FMT. Conclusions FMT was successfully implemented in a medical center in Taiwan and showed a comparable successful rate in treating rCDI, compared to other countries. Safety remains the most important issue when applying FMT in the clinical setting.
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Affiliation(s)
- Yuan-Ming Yeh
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Hao-Tsai Cheng
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, New Taipei Municipal Tucheng Hospital, Tucheng, New Taipei City, Taiwan
| | - Puo-Hsien Le
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chien-Chang Chen
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Jung Kuo
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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23
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Chang SC, Lin SF, Chen ST, Chang PY, Yeh YM, Lo FS, Lu JJ. Alterations of Gut Microbiota in Patients With Graves' Disease. Front Cell Infect Microbiol 2021; 11:663131. [PMID: 34026662 PMCID: PMC8132172 DOI: 10.3389/fcimb.2021.663131] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/05/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Graves' disease (GD) is a systemic autoimmune disease characterized by hyperthyroidism. Evidence suggests that alterations to the gut microbiota may be involved in the development of autoimmune disorders. The aim of this study was to characterize the composition of gut microbiota in GD patients. Fecal samples were collected from 55 GD patients and 48 healthy controls. Using 16S rRNA gene amplification and sequencing, the overall bacterial richness and diversity were found to be similar between GD patients and healthy controls. However, principal coordinate analysis and partial least squares-discriminant analysis showed that the overall gut microbiota composition was significantly different (ANOSIM; p < 0.001). The linear discriminant analysis effect size revealed that Firmicutes phylum decreased in GD patients, with a corresponding increase in Bacteroidetes phylum compared to healthy controls. In addition, the families Prevotellaceae, and Veillonellaceae and the genus Prevotella_9 were closely associated with GD patients, while the families Lachnospiraceae and Ruminococcaceae and the genera Faecalibacterium, Lachnospira, and Lachnospiraceae NK4A136 were associated with healthy controls. Metagenomic profiles analysis yielded 22 statistically significant bacterial taxa: 18 taxa were increased and 4 taxa were decreased. Key bacterial taxa with different abundances between the two groups were strongly correlated with GD-associated clinical parameters using Spearman's correlation analysis. Importantly, the discriminant model based on predominant microbiota could effectively distinguish GD patients from healthy controls (AUC = 0.825). Thus, the gut microbiota composition between GD patients and healthy controls is significantly difference, indicating that gut microbiota may play a role in the pathogenesis of GD. Further studies are needed to fully elucidate the role of gut microbiota in the development of GD.
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Affiliation(s)
- Shih-Cheng Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Shu-Fu Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Szu-Tah Chen
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Fu-Sung Lo
- Department of Pediatrics, Division of Pediatric Endocrinology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
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24
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Yang CY, Li SW, Chin CY, Hsu CW, Lee CC, Yeh YM, Wu KA. Association of exacerbation phenotype with the sputum microbiome in chronic obstructive pulmonary disease patients during the clinically stable state. J Transl Med 2021; 19:121. [PMID: 33757530 PMCID: PMC7988976 DOI: 10.1186/s12967-021-02788-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/21/2020] [Accepted: 03/15/2021] [Indexed: 01/04/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung disease with increasing prevalence and incidence worldwide. Increasing evidence suggests that lung microbiomes might play a physiological role in acute exacerbations of COPD. The objective of this study was to characterize the association of the microbiota and exacerbation risk or airflow limitation in stable COPD patients. Methods The sputum microbiota from 78 COPD outpatients during periods of clinical stability was investigated using 16S rRNA V3-V4 amplicon sequencing. The microbiome profiles were compared between patients with different risks of exacerbation, i.e., the low risk exacerbator (LRE) or high risk exacerbator (HRE) groups, and with different airflow limitation severity, i.e., mild to moderate (FEV1 ≥ 50; PFT I) or severe to very severe (FEV1 < 50; PFT II). Results The bacterial diversity (Chao1 and observed OTUs) was significantly decreased in the HRE group compared to that in the LRE group. The top 3 dominant phyla in sputum were Firmicutes, Actinobacteria, and Proteobacteria, which were similar in the HRE and LRE groups. At the genus level, compared to that in the LRE group (41.24%), the proportion of Streptococcus was slightly decreased in the HRE group (28.68%) (p = 0.007). However, the bacterial diversity and the proportion of dominant bacteria at the phylum and genus levels were similar between the PFT I and PFT II groups. Furthermore, the relative abundances of Gemella morbillorum, Prevotella histicola, and Streptococcus gordonii were decreased in the HRE group compared to those in the LRE group according to linear discriminant analysis effect size (LEfSe). Microbiome network analysis suggested altered bacterial cooperative regulation in different exacerbation phenotypes. The proportions of Proteobacteria and Neisseria were negatively correlated with the FEV1/FVC value. According to functional prediction of sputum bacterial communities through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis, genes involved in lipopolysaccharide biosynthesis and energy metabolism were enriched in the HRE group. Conclusion The present study revealed that the sputum microbiome changed in COPD patients with different risks of exacerbation. Additionally, the bacterial cooperative networks were altered in the HRE patients and may contribute to disease exacerbation. Our results provide evidence that sputum microbiome community dysbiosis is associated with different COPD phenotypes, and we hope that by understanding the lung microbiome, a potentially modifiable clinical factor, further targets for improved COPD therapies during the clinically stable state may be elucidated. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02788-4.
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Affiliation(s)
- Chia-Yu Yang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yin Chin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Kuo-An Wu
- Department of Internal Medicine, Taoyuan Armed Forces General Hospital, No. 168, Zhongxing Rd., Longtan District, Taoyuan, 32551, Taiwan (R.O.C.). .,School of Medicine, Fu Jen Catholic University, New Taipei City, 24205, Taiwan.
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25
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Chuang YH, Fan WL, Chu YD, Liang KH, Yeh YM, Chen CC, Chiu CH, Lai MW. Whole-Exome Sequencing Identified Novel CLMP Mutations in a Family With Congenital Short Bowel Syndrome Presenting Differently in Two Probands. Front Genet 2021; 11:574943. [PMID: 33384711 PMCID: PMC7770137 DOI: 10.3389/fgene.2020.574943] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/23/2020] [Indexed: 11/13/2022] Open
Abstract
Congenital short bowel syndrome (CSBS) is a rare condition characterized by an inborn shortening of bowel length with loss of intestinal functions, which often combines malrotation. CXADR-like membrane protein (CLMP) and filamin A (FLNA) gene mutations are the two major causes of this inherited defect. We presented two siblings with the older brother suffering from a laparotomy for bowel obstruction due to malrotation on the 17th day after birth. The younger sister encountered a laparotomy for lactobezoar at 6 months old. CSBS was diagnosed by measurement of the bowel length during the operations. Compound heterozygous CLMP mutations with the paternal allele harboring a long deletion across exon 3-5 and the maternal allele bearing a non-sense mutation of exon 3 (c.235C > T, p.Q79∗) were identified in both cases. They are the first reported familial CSBS caused by novel CLMP mutations in Taiwan.
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Affiliation(s)
- Yao-Hung Chuang
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Children's Medical Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Wen-Lang Fan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Yu-De Chu
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Kung-Hao Liang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Chien-Chang Chen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Children's Medical Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan.,College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan City, Taiwan.,College of Medicine, Chang Gung University, Taoyuan City, Taiwan.,Division of Pediatric Infectious Disease, Department of Pediatrics, Chang Gung Children's Medical Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Ming-Wei Lai
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Children's Medical Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan.,College of Medicine, Chang Gung University, Taoyuan City, Taiwan
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26
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Cheng WH, Huang KY, Ong SC, Ku FM, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH, Tang P. Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency. Parasit Vectors 2020; 13:477. [PMID: 32948226 PMCID: PMC7501694 DOI: 10.1186/s13071-020-04355-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/11/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Iron plays essential roles in the pathogenesis and proliferation of Trichomonas vaginalis, the causative agent of the most prevalent non-viral human sexually transmitted infection. We previously demonstrated that under iron deficiency, the endogenous nitric oxide (NO) is accumulated and capable of regulating the survival of T. vaginalis. Herein, we aim to explore the influence of NO on the activity of the pyruvate-reducing enzyme lactate dehydrogenase in T. vaginalis (TvLDH). METHODS Levels of lactate and pyruvate were detected for determining glycolysis activity in T. vaginalis under iron deficiency. Quantitative PCR was performed to determine the expression of TvLDH. S-nitrosylated (SNO) proteomics was conducted to identify the NO-modified proteins. The activities of glyceraldehyde-3-phosphate dehydrogenase (TvGAPDH) and TvLDH were measured after sodium nitrate treatment. The effects of protein nitrosylation on the production of cellular reducing power were examined by measuring the amount of nicotinamide adenine dinucleotide (NAD) and the ratio of the NAD redox pair (NAD+/NADH). RESULTS We found that although the glycolytic pathway was activated in cells under iron depletion, the level of pyruvate was decreased due to the increased level of TvLDH. By analyzing the SNO proteome of T. vaginalis upon iron deficiency, we found that TvLDH is one of the glycolytic enzymes modified by SNO. The production of pyruvate was significantly reduced after nitrate treatment, indicating that protein nitrosylation accelerated the consumption of pyruvate by increasing TvLDH activity. Nitrate treatment also induced NAD oxidation, suggesting that protein nitrosylation was the key posttranslational modification controlling cellular redox status. CONCLUSIONS We demonstrated that NO-mediated protein nitrosylation plays pivotal roles in the regulation of glycolysis, pyruvate metabolism, and the activity of TvLDH. The recycling of oxidized NAD catalyzed by TvLDH provided the reducing power that allowed T. vaginalis to adapt to the iron-deficient environment.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan District, Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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27
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Wang LJ, Yang CY, Chou WJ, Lee MJ, Chou MC, Kuo HC, Yeh YM, Lee SY, Huang LH, Li SC. Gut microbiota and dietary patterns in children with attention-deficit/hyperactivity disorder. Eur Child Adolesc Psychiatry 2020; 29:287-297. [PMID: 31119393 DOI: 10.1007/s00787-019-01352-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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: 05/18/2018] [Accepted: 05/13/2019] [Indexed: 12/26/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder, but the underlying pathophysiological mechanisms of ADHD remain unclear. Gut microbiota has been recognized to influence brain function and behaviors. Therefore, this study aimed to determine whether imbalanced gut microbiomes identified by a 16S rRNA sequencing approach are involved in the pathophysiology of ADHD. We recruited a total of 30 children with ADHD (mean age: 8.4 years) and a total of 30 healthy controls (mean age: 9.3 years) for this study. The dietary patterns of all participants were assessed with the food frequency questionnaire. The microbiota of fecal samples were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. We found that the gut microbiota communities in ADHD patients showed a significantly higher Shannon index and Chao index than the control subjects. Furthermore, the linear discriminant analysis effect size (LEfSe) analysis was used to identify differentially enriched bacteria between ADHD patients and healthy controls. The relative abundance of Bacteroides coprocola (B. coprocola) was decreased, while the relative abundance of Bacteroides uniformis (B. uniformis), Bacteroides ovatus (B. ovatus), and Sutterella stercoricanis (S. stercoricanis) were increased in the ADHD group. Of all participants, S. stercoricanis demonstrated a significant association with the intake of dairy, nuts/seeds/legumes, ferritin and magnesium. B. ovatus and S. stercoricanis were positively correlated to ADHD symptoms. In conclusion, we suggest that the gut microbiome community is associated with dietary patterns, and linked to the susceptibility to ADHD.
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Affiliation(s)
- Liang-Jen Wang
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Chinese Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Department of Microbiology and Immunology/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wen-Jiun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Min-Jing Lee
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Miao-Chun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sheng-Yu Lee
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Psychiatry, College of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No.123, Ta-Pei Road, Kaohsiung City, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No.123, Ta-Pei Road, Kaohsiung City, Taiwan.
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Huang PJ, Chiu LY, Lee CC, Yeh YM, Huang KY, Chiu CH, Tang P. mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Res 2019; 46:D964-D970. [PMID: 29145625 PMCID: PMC5753213 DOI: 10.1093/nar/gkx1133] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/26/2017] [Indexed: 11/21/2022] Open
Abstract
Cancer is a genetic disease caused by somatic mutations; however, the understanding of the causative biological processes generating these mutations is limited. A cancer genome bears the cumulative effects of mutational processes during tumor development. Deciphering mutational signatures in cancer is a new topic in cancer research. The Wellcome Trust Sanger Institute (WTSI) has categorized 30 reference signatures in the COSMIC database based on the analyses of ∼10 000 sequencing datasets from TCGA and ICGC. Large cohorts and bioinformatics skills are required to perform the same analysis as WTSI. The quantification of known signatures in custom cohorts is not possible under the current framework of the COSMIC database, which motivates us to construct a database for mutational signatures in cancers and make such analyses more accessible to general researchers. mSignatureDB (http://tardis.cgu.edu.tw/msignaturedb) integrates R packages and in-house scripts to determine the contributions of the published signatures in 15 780 individual tumors from 73 TCGA/ICGC cancer projects, making comparison of signature patterns within and between projects become possible. mSignatureDB also allows users to perform signature analysis on their own datasets, quantifying contributions of signatures at sample resolution, which is a unique feature of mSignatureDB not available in other related databases.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ling-Ya Chiu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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Lee CC, Huang PJ, Yeh YM, Chen SY, Chiu CH, Cheng WH, Tang P. Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins. BMC Bioinformatics 2019; 20:382. [PMID: 31337335 PMCID: PMC6651900 DOI: 10.1186/s12859-019-2857-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. RESULTS We analyzed over one million protein sequences from 139 protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. CONCLUSIONS The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
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Affiliation(s)
- Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Po-Jung Huang
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sin-You Chen
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Petrus Tang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan. .,Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Huang PJ, Lin HH, Lee CC, Chiu LY, Wu SM, Yeh YM, Tang P, Chiu CH, Lyu PC, Tsai PC. CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts. BMC Med Genomics 2019; 12:99. [PMID: 31296206 PMCID: PMC6624176 DOI: 10.1186/s12920-019-0510-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND CoMut plot is widely used in cancer research publications as a visual summary of mutational landscapes in cancer cohorts. This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step for analyzing the recurrence and co-occurrence of gene mutations across samples. The cBioPortal and iCoMut are two web-based tools that allow users to create intricate visualizations from pre-loaded TCGA and ICGC data. For custom data analysis, only limited command-line packages are available now, making the production of CoMut plots difficult to achieve, especially for researchers without advanced bioinformatics skills. To address the needs for custom data and TCGA/ICGC data comparison, we have created CoMutPlotter, a web-based tool for the production of publication-quality graphs in an easy-of-use and automatic manner. RESULTS We introduce a web-based tool named CoMutPlotter to lower the barriers between complex cancer genomic data and researchers, providing intuitive access to mutational profiles from TCGA/ICGC projects as well as custom cohort studies. A wide variety of file formats are supported by CoMutPlotter to translate cancer mutation profiles into biological insights and clinical applications, which include Mutation Annotation Format (MAF), Tab-separated values (TSV) and Variant Call Format (VCF) files. CONCLUSIONS In summary, CoMutPlotter is the first tool of its kind that supports VCF file, the most widely used file format, as its input material. CoMutPlotter also provides the most-wanted function for comparing mutation patterns between custom cohort and TCGA/ICGC project. Contributions of COSMIC mutational signatures in individual samples are also included in the summary plot, which is a unique feature of our tool. CoMutPlotter is freely available at http://tardis.cgu.edu.tw/comutplotter .
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hou-Hsien Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Ling-Ya Chiu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shao-Min Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Pei-Chien Tsai
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. .,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Hsieh PC, Wang CC, Tsai CL, Yeh YM, Lee YS, Wu YR. POLG R964C and GBA L444P mutations in familial Parkinson's disease: Case report and literature review. Brain Behav 2019; 9:e01281. [PMID: 30941926 PMCID: PMC6520296 DOI: 10.1002/brb3.1281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 02/06/2023] Open
Abstract
Polymerase gamma (POLG) is an enzyme responsible for the replication and repair of mitochondrial DNA. Mutations in POLG may cause variable clinical manifestations, including parkinsonism, epilepsy, cerebellar ataxia, neuropathy, and progressive external ophthalmoplegia. However, mutations of this gene are rare in patients with typical Parkinson's disease (PD). We report a man (current age: 59 years) without any underlying disease presenting with right-hand tremor at the age of 39 years, followed by slow movement, rigidity, and postural instability. He developed motor fluctuation and levodopa-induced dyskinesia 8 years later. At the age of 58 years, cognitive decline and visual hallucination ensued; he was institutionalized thereafter. We used multiplex ligation-dependent probe amplification, which demonstrated no large deletions or duplications of relevant PD genes. Next, targeted sequencing panel covering 51 genes causative for PD was applied for the proband; it revealed a heterozygous missense substitution R964C in POLG and a heterozygous missense substitution L444P in GBA. The patient's father, who had been diagnosed as having PD and type 2 diabetes mellitus at the age of 70 years, demonstrated identical mutations. This is the first report of familial PD combined with POLG R964C and GBA L444P mutations. Two pathogenic gene mutations potentially cause double hit in pathological neurodegeneration. This finding extends our understanding of the PD genotype-phenotype correlation.
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Affiliation(s)
- Pei-Chen Hsieh
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Chun-Chieh Wang
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yun Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Yih-Ru Wu
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan.,Department of Neurology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Lin TC, Yeh YM, Fan WL, Chang YC, Lin WM, Yang TY, Hsiao M. Ghrelin Upregulates Oncogenic Aurora A to Promote Renal Cell Carcinoma Invasion. Cancers (Basel) 2019; 11:cancers11030303. [PMID: 30836712 PMCID: PMC6468656 DOI: 10.3390/cancers11030303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/21/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Ghrelin is a peptide hormone, originally identified from the stomach, that functions as an endogenous ligand of the growth hormone secretagogue receptor (GHSR) and promotes growth hormone (GH) release and food intake. Increasing reports point out ghrelin’s role in cancer progression. We previously characterized ghrelin’s prognostic significance in the clear cell subtype of renal cell carcinoma (ccRCC), and its pro-metastatic ability via Snail-dependent cell migration. However, ghrelin’s activity in promoting cell invasion remains obscure. In this study, an Ingenuity Pathway Analysis (IPA)-based investigation of differentially expressed genes in Cancer Cell Line Encyclopedia (CCLE) dataset indicated the potential association of Aurora A with ghrelin in ccRCC metastasis. In addition, a significant correlation between ghrelin and Aurora A expression level in 15 ccRCC cell line was confirmed by variant probes. ccRCC patients with high ghrelin and Aurora A status were clinically associated with poor outcome. We further observed that ghrelin upregulated Aurora A at the protein and RNA levels and that ghrelin-induced ccRCC in vitro invasion and in vivo metastasis occurred in an Aurora A-dependent manner. Furthermore, MMP1, 2, 9 and 10 expressions are associated with poor outcome. In particular, MMP10 is significantly upregulated and required for the ghrelin-Aurora A axis to promote ccRCC invasion. The results of this study indicated a novel signaling mechanism in ccRCC metastasis.
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Affiliation(s)
- Tsung-Chieh Lin
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou 33305, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou 33305, Taiwan.
| | - Wen-Lang Fan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou 33305, Taiwan.
| | - Yu-Chan Chang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Wei-Ming Lin
- Department of Diagnostic Radiology, Chang Gung Memorial Hospital, Chiayi Branch, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan.
| | - Tse-Yen Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40447, Taiwan.
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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Hsu CL, Lui KW, Chi LM, Kuo YC, Chao YK, Yeh CN, Lee LY, Huang Y, Lin TL, Huang MY, Lai YR, Yeh YM, Fan HC, Lin AC, Lu YJ, Hsieh CH, Chang KP, Tsang NM, Wang HM, Chang AY, Chang YS, Li HP. Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma. J Exp Clin Cancer Res 2018; 37:233. [PMID: 30236142 PMCID: PMC6149192 DOI: 10.1186/s13046-018-0873-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 05/16/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Background Patient-derived xenograft (PDX) tumor model has become a new approach in identifying druggable tumor mutations, screening and evaluating personalized cancer drugs based on the mutated targets. Methods We established five nasopharyngeal carcinoma (NPC) PDXs in mouse model. Subsequently, whole-exome sequencing (WES) and genomic mutation analyses were performed to search for genetic alterations for new drug targets. Potential drugs were applied in two NPC PDX mice model to assess their anti-cancer activities. RNA sequencing and transcriptomic analysis were performed in one NPC PDX mice to correlate with the efficacy of the anti-cancer drugs. Results A relative high incident rate of copy number variations (CNVs) of cell cycle-associated genes. Among the five NPC-PDXs, three had cyclin D1 (CCND1) amplification while four had cyclin-dependent kinase inhibitor CDKN2A deletion. Furthermore, CCND1 overexpression was observed in > 90% FFPE clinical metastatic NPC tumors (87/91) and was associated with poor outcomes. CNV analysis disclosed that plasma CCND1/CDKN2A ratio is correlated with EBV DNA load in NPC patients’ plasma and could serve as a screening test to select potential CDK4/6 inhibitor treatment candidates. Based on our NPC PDX model and RNA sequencing, Palbociclib, a cyclin-dependent kinase inhibitor, proved to have anti-tumor effects by inducing G1 arrest. One NPC patient with liver metastatic was treated with Palbociclib, had stable disease response and a drop in Epstein Barr virus (EBV) EBV titer. Conclusions Our integrated information of sequencing-based genomic studies and tumor transcriptomes with drug treatment in NPC-PDX models provided guidelines for personalized precision treatments and revealed a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for NPC. Electronic supplementary material The online version of this article (10.1186/s13046-018-0873-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng-Lung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Kar-Wai Lui
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Lang-Ming Chi
- Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yung-Chia Kuo
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yin-Kai Chao
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Chun-Nan Yeh
- Department of General Surgery, Liver Research Center, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Li-Yu Lee
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yenlin Huang
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Tung-Liang Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Mei-Yuan Huang
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China
| | - Yi-Ru Lai
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China
| | - Hsien-Chi Fan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - An-Chi Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yen-Jung Lu
- ACT Genomics, Co. Ltd., 1F., No.280, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan, Republic of China
| | - Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Ngan-Ming Tsang
- Department of Radiation, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Hung-Ming Wang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Alex Y Chang
- Johns Hopkins Singapore International Medical Centre, 11 Jalan Tan Tock Seng, Singapore City, 308433, Singapore
| | - Yu-Sun Chang
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Hsin-Pai Li
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China. .,Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China. .,Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China.
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Abstract
Background High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes. Results We introduce a workflow named VAReporter to facilitate the management of variant assessment in disease-targeted sequencing, the identification of pathogenic variants, the interpretation of biological effects and the prioritization of clinically actionable targets. State-of-art algorithms that account for mutation phenotypes are used to rank the importance of mutated genes through visual analytic strategies. We established an extensive annotation source by integrating a wide variety of biomedical databases and followed the American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation and reporting of sequence variations. Conclusions In summary, VAReporter is the first web server designed to provide a “one-stop” resource for individual’s diagnosis and large-scale cohort studies, and is freely available at http://rnd.cgu.edu.tw/vareporter.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Ling-Ya Chiu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan. .,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. .,Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
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Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP, Chang YL. Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging. Front Microbiol 2018; 9:862. [PMID: 29774014 PMCID: PMC5943489 DOI: 10.3389/fmicb.2018.00862] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [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: 01/09/2018] [Accepted: 04/13/2018] [Indexed: 12/15/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. The oral microbiota communities from stage 4 patients showed significantly higher complexity than those from healthy controls. The populations also dynamically changed with the cancer's progression from stage 1 to stage 4. The predominant phyla in the oral samples showed variation in the relative abundance of Fusobacteria, Bacteroidetes, and Actinobacteria. The abundance of Fusobacteria increased significantly with the progression of oral cancer from the healthy controls (2.98%) to OSCC stage 1 (4.35%) through stage 4 (7.92%). At the genus level, the abundance of Fusobacterium increased, while the number of Streptococcus, Haemophilus, Porphyromonas, and Actinomyces decreased with cancer progression. Fusobacterium periodonticum, Parvimonas micra, Streptococcus constellatus, Haemophilus influenza, and Filifactor alocis were associated with OSCC, and they progressively increased in abundance from stage 1 to stage 4. The abundances of Streptococcus mitis, Haemophilus parainfluenzae, and Porphyromonas pasteri were inversely associated with OSCC progression. We selected a bacterial marker panel of three bacteria (upregulated F. periodonticum, down-regulated S. mitis, and P. pasteri), which had an AUC of 0.956 (95% CI = 0.925-0.986) in discriminating OSCC stage 4 from the healthy controls. Furthermore, the functional prediction of oral bacterial communities showed that genes involved in carbohydrate-related metabolism, such as methane metabolism, and energy-metabolism-related parameters, such as oxidative phosphorylation and carbon fixation in photosynthetic organisms, were enriched in late-stage OSCC, while those responsible for amino acid metabolism, such as folate biosynthesis and valine, leucine, and isoleucine biosynthesis, were significantly associated with the healthy controls. In conclusion, our results provided evidence of oral bacteria community changes during oral cancer progression and suggested the possibility of using bacteria as OSCC diagnostic markers.
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Affiliation(s)
- Chia-Yu Yang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hai-Ying Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chia-Yin Chin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Jung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Song-Nian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chun-Ta Liao
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kai-Ping Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Liang Chang
- Department of Oral & Maxillofacial Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YM, Ku FM, Lin R, Cheng ML, Chiu CH, Tang P. γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasit Vectors 2017; 10:443. [PMID: 28950916 PMCID: PMC5615479 DOI: 10.1186/s13071-017-2381-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/12/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND γ-Carboxymuconolactone decarboxylase (CMD) participates in the β-ketoadipate pathway, which catalyzes aromatic compounds to produce acetyl- or succinyl-CoA, in prokaryotes and yeast. Our previous study demonstrated that expression of a CMD homologue that contains two signatures (dualCMD) is negatively regulated by iron in Trichomonas vaginalis. However, we were not able to identify the components of the β-ketoadipate pathway in the parasite's genome. These observations prompted us to investigate the biological functions of this novel CMD homologue in T. vaginalis. METHODS The specific anti-TvCMD1 antibody was generated, and the expression of TvCMD1 in T. vaginalis cultured under iron-rich and iron-deficient were evaluated. Phylogenetic, metabolomic and substrate induction (protocatechuate and benzoate) analysis were conducted to clarify the function of dualCMD in trichomonad cells. Subcellular localization of TvCMD1 was observed by confocal microscopy. The cell cycle-related role of TvCMD1 was assessed by treating cells with G2/M inhibitor nocodazole. RESULTS We confirmed that T. vaginalis is not able to catabolize the aromatic compounds benzoate and protocatechuate, which are known substrates of the β-ketoadipate pathway. Using immunofluorescence microscopy, we found that TvCMD1 is spatially associated with the basal body, a part of the cytoskeletal organizing center in T. vaginalis. TvCMD1 accumulated upon treatment with the G2/M inhibitor nocodazole. Additionally, TvCMD1 was expressed and transported to/from the basal body during cytokinesis, suggesting that TvCMD1 plays a role in cell division. CONCLUSION We demonstrated that TvCMD1 is unlikely to participate in the β-ketoadipate pathway and demonstrated that it is a novel basal body-localizing (associated) protein. This model sheds light on the importance of genes that are acquired laterally in the coevolution of ancient protists, which surprisingly functions in cell cycle regulation of T. vaginalis.
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Affiliation(s)
- Wei-Hung Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Po-Jung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Fu-Man Ku
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Rose Lin
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Mei-Ling Cheng
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IYF, Yeh YM, Chen CD, Li HP, Luo JD, Tan BCM, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun 2017; 8:465. [PMID: 28878238 PMCID: PMC5587710 DOI: 10.1038/s41467-017-00493-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/04/2017] [Indexed: 12/29/2022] Open
Abstract
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0.004). The frequency of APOBEC3B-deletion alleles is ~50% in 143 genotyped oral squamous cell carcinoma -Taiwan samples (27A3B−/−:89A3B+/−:27A3B+/+), compared to the 5.8% found in 314 OSCC-TCGA samples. We thus report a frequent APOBEC mutational profile, which relates to a APOBEC3B-deletion germline polymorphism in Taiwanese oral squamous cell carcinoma that impacts expression of APOBEC3A, and is shown to be of clinical prognostic relevance. Our finding might be recapitulated by genomic studies in other cancer types. Oral squamous cell carcinoma is a prevalent malignancy in Taiwan. Here, the authors show that OSCC in Taiwanese show a frequent deletion polymorphism in the cytidine deaminases gene cluster APOBEC3 resulting in increased expression of A3A, which is shown to be of clinical prognostic relevance.
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Affiliation(s)
- Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chi-Ching Lee
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biochemistry, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Chi-Sheng Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Curtis R Pickering
- Departments of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Po-Jung Huang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jing Wang
- Departments of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-De Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsin-Pai Li
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Ji-Dung Luo
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Timothy En Haw Chan
- Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chuen Hsueh
- Pathology Core of the Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bing Zhang
- Department of Molecular and Human Genetics Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Chia-Yu Yang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-Ching Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Lai-Chu See
- Department of Public Health, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Biostatistics Core Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Regulation and Bioinformatics Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Cell and Molecular Biology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, 736, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, 112, Taiwan
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jeffrey N Myers
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan. .,College of Medicine, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.
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Gan RC, Chen TW, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P. PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. BMC Bioinformatics 2016; 17:513. [PMID: 28155708 PMCID: PMC5260104 DOI: 10.1186/s12859-016-1366-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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] [Indexed: 02/23/2023] Open
Abstract
Background Next-generation sequencing promises the de novo genomic and transcriptomic analysis of samples of interests. However, there are only a few organisms having reference genomic sequences and even fewer having well-defined or curated annotations. For transcriptome studies focusing on organisms lacking proper reference genomes, the common strategy is de novo assembly followed by functional annotation. However, things become even more complicated when multiple transcriptomes are compared. Results Here, we propose a new analysis strategy and quantification methods for quantifying expression level which not only generate a virtual reference from sequencing data, but also provide comparisons between transcriptomes. First, all reads from the transcriptome datasets are pooled together for de novo assembly. The assembled contigs are searched against NCBI NR databases to find potential homolog sequences. Based on the searched result, a set of virtual transcripts are generated and served as a reference transcriptome. By using the same reference, normalized quantification values including RC (read counts), eRPKM (estimated RPKM) and eTPM (estimated TPM) can be obtained that are comparable across transcriptome datasets. In order to demonstrate the feasibility of our strategy, we implement it in the web service PARRoT. PARRoT stands for Pipeline for Analyzing RNA Reads of Transcriptomes. It analyzes gene expression profiles for two transcriptome sequencing datasets. For better understanding of the biological meaning from the comparison among transcriptomes, PARRoT further provides linkage between these virtual transcripts and their potential function through showing best hits in SwissProt, NR database, assigning GO terms. Our demo datasets showed that PARRoT can analyze two paired-end transcriptomic datasets of approximately 100 million reads within just three hours. Conclusions In this study, we proposed and implemented a strategy to analyze transcriptomes from non-reference organisms which offers the opportunity to quantify and compare transcriptome profiles through a homolog based virtual transcriptome reference. By using the homolog based reference, our strategy effectively avoids the problems that may cause from inconsistencies among transcriptomes. This strategy will shed lights on the field of comparative genomics for non-model organism. We have implemented PARRoT as a web service which is freely available at http://parrot.cgu.edu.tw.
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Affiliation(s)
- Ruei-Chi Gan
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan.,Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Wen Chen
- Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Timothy H Wu
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei City, Taiwan
| | - Po-Jung Huang
- Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan. .,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan.
| | - Petrus Tang
- Bioinformatics Center, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. .,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Molecular Regulation & Bioinformatics Laboratory, Chang Gung University, Taoyuan, Taiwan.
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Huang PJ, Lee CC, Tan BCM, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS, Liu H, Tang P. Vanno: a visualization-aided variant annotation tool. Hum Mutat 2015; 36:167-74. [PMID: 25196204 DOI: 10.1002/humu.22684] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/25/2014] [Indexed: 01/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have revolutionized the field of genetics and are trending toward clinical diagnostics. Exome and targeted sequencing in a disease context represent a major NGS clinical application, considering its utility and cost-effectiveness. With the ongoing discovery of disease-associated genes, various gene panels have been launched for both basic research and diagnostic tests. However, the fundamental inconsistencies among the diverse annotation sources, software packages, and data formats have complicated the subsequent analysis. To manage disease-associated NGS data, we developed Vanno, a Web-based application for in-depth analysis and rapid evaluation of disease-causative genome sequence alterations. Vanno integrates information from biomedical databases, functional predictions from available evaluation models, and mutation landscapes from TCGA cancer types. A highly integrated framework that incorporates filtering, sorting, clustering, and visual analytic modules is provided to facilitate exploration of oncogenomics datasets at different levels, such as gene, variant, protein domain, or three-dimensional structure. Such design is crucial for the extraction of knowledge from sequence alterations and translating biological insights into clinical applications. Taken together, Vanno supports almost all disease-associated gene tests and exome sequencing panels designed for NGS, providing a complete solution for targeted and exome sequencing analysis. Vanno is freely available at http://cgts.cgu.edu.tw/vanno.
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Affiliation(s)
- Po-Jung Huang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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Huang PJ, Lee CC, Tan BCM, Yeh YM, Julie Chu L, Chen TW, Chang KP, Lee CY, Gan RC, Liu H, Tang P. CMPD: cancer mutant proteome database. Nucleic Acids Res 2014; 43:D849-55. [PMID: 25398898 PMCID: PMC4383976 DOI: 10.1093/nar/gku1182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents the most cost-effective method to-date for deciphering the association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute and TCGA, to provide a comprehensive catalogue of coding variants in diverse tissue samples and cell lines. Further functional and clinical interrogation of these sequence variations must rely on extensive cross-platforms integration of sequencing information and a proteome database that explicitly and comprehensively archives the corresponding mutated peptide sequences. While such data resource is a critical for the mass spectrometry-based proteomic analysis of exomic variants, no database is currently available for the collection of mutant protein sequences that correspond to recent large-scale genomic data. To address this issue and serve as bridge to integrate genomic and proteomics datasets, CMPD (http://cgbc.cgu.edu.tw/cmpd) collected over 2 millions genetic alterations, which not only facilitates the confirmation and examination of potential cancer biomarkers but also provides an invaluable resource for translational medicine research and opportunities to identify mutated proteins encoded by mutated genes.
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Affiliation(s)
- Po-Jung Huang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | | | - Yuan-Ming Yeh
- Bioinformatics Division, Tri-I Biotech, Inc., Taipei 221, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Ting-Wen Chen
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Lin-Kou, Taoyuan 333, Taiwan
| | - Cheng-Yang Lee
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Ruei-Chi Gan
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
| | - Hsuan Liu
- Department of Molecular and Cellular Biology, Chang Gung University, Taoyuan 333, Taiwan
| | - Petrus Tang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 333, Taiwan
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Yeh YM, Chen CY, Huang PR, Hsu CW, Wu CC, Wang TCV. Proteomic analyses of genes regulated by heterogeneous nuclear ribonucleoproteins A/B in Jurkat cells. Proteomics 2014; 14:1357-66. [PMID: 24634410 DOI: 10.1002/pmic.201300549] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/20/2014] [Accepted: 03/04/2014] [Indexed: 11/06/2022]
Abstract
Several lines of evidence suggest that hnRNPs A/B (hnRNPs A1, A2/B1, and A3) play an important role in proliferation, although the functional overlap among members of hnRNPs A/B remains largely unknown. In this study, we have employed RNAi knockdown and proteomic approaches to investigate the biological functions of hnRNPs A/B. Depletion of hnRNP A2, but not A1 or A3, produced a significant inhibition of cellular proliferation in Jurkat cells. Analysis of the proteomes in the cells depleted for hnRNP A1, A2, or A3 has identified a total of 167 differentially expressed proteins in the depleted cells. Network analysis of the proteins altered in the cells depleted for hnRNP A2 revealed that the biological processes likely affected by these proteins are related to cell cycle, cytoskeleton rearrangement, and transcription regulation. Indeed, we have confirmed that the level of RhoA and CrkL was selectively reduced in the cells depleted of hnRNP A2, but not in the cells depleted for hnRNP A1 or A3. Therefore, we suggest that the reduced proliferation observed in the cells depleted of hnRNP A2 may result from its effects on cell adhesion processes in the Jurkat cells.
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Affiliation(s)
- Yuan-Ming Yeh
- Department of Molecular and Cellular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
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Huang PJ, Yeh YM, Gan RC, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P. CPAP: Cancer Panel Analysis Pipeline. Hum Mutat 2013; 34:1340-6. [PMID: 23893859 DOI: 10.1002/humu.22386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 04/16/2013] [Accepted: 07/12/2013] [Indexed: 12/14/2022]
Abstract
Targeted sequencing using next-generation sequencing technologies is currently being rapidly adopted for clinical sequencing and cancer marker tests. However, no existing bioinformatics tool is available for the analysis and visualization of multiple targeted sequencing datasets. In the present study, we use cancer panel targeted sequencing datasets generated by the Life Technologies Ion Personal Genome Machine Sequencer as an example to illustrate how to develop an automated pipeline for the comparative analyses of multiple datasets. Cancer Panel Analysis Pipeline (CPAP) uses standard output files from variant calling software to generate a distribution map of SNPs among all of the samples in a circular diagram generated by Circos. The diagram is hyperlinked to a dynamic HTML table that allows the users to identify target SNPs by using different filters. CPAP also integrates additional information about the identified SNPs by linking to an integrated SQL database compiled from SNP-related databases, including dbSNP, 1000 Genomes Project, COSMIC, and dbNSFP. CPAP only takes 17 min to complete a comparative analysis of 500 datasets. CPAP not only provides an automated platform for the analysis of multiple cancer panel datasets but can also serve as a model for any customized targeted sequencing project.
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Affiliation(s)
- Po-Jung Huang
- Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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Yeh YM, Huang KY, Richie Gan RC, Huang HD, Wang TCV, Tang P. Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis. J Microbiol Immunol Infect 2012; 46:366-73. [PMID: 22921107 DOI: 10.1016/j.jmii.2012.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/13/2012] [Accepted: 07/10/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND/PURPOSE(S) Trichomoniasis caused by Trichomonas vaginalis is the most common non-viral sexually transmitted infection. Morphological transformation from the trophozoite stage to the amoeboid or pseudocyst stage is crucial for T. vaginalis infection and survival. Protein phosphorylation is a key post-translational modification involved in the regulation of several biological processes in various prokaryotes and eukaryotes. More than 880 protein kinases have been identified in the T. vaginalis genome. However, little is known about the phosphorylation of specific proteins and the distribution of phosphorylated proteins in different stages of the morphological transformation of T. vaginalis. METHODS To obtain a more comprehensive understanding of the T. vaginalis phosphoproteome, we analyzed phosphorylated proteins in the three morphological stages using titanium dioxide combined with LC-MS/MS. RESULTS A total of 93 phosphopeptides originating from 82 unique proteins were identified. Among these proteins, 21 were detected in all stages, 29 were identified in two different stages, and 32 were stage specific. CONCLUSION Identification of stage-specific phosphorylated proteins indicates that phosphorylation of these proteins may play a key role in the morphological transformation of T. vaginalis.
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Affiliation(s)
- Yuan-Ming Yeh
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Molecular and Cellular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Huang PR, Yeh YM, Pao CC, Chen CY, Wang TCV. N-(1-Pyrenyl) maleimide inhibits telomerase activity in a cell free system and induces apoptosis in Jurkat cells. Mol Biol Rep 2012; 39:8899-905. [PMID: 22707200 DOI: 10.1007/s11033-012-1757-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/07/2012] [Indexed: 02/04/2023]
Abstract
Telomerase activity is repressed in normal human somatic cells, but is activated in most cancers, suggesting that telomerase may be an important target for cancer therapy. Agents that interact selectively with telomerase are anticipated to exert specific action on cancer cells. In this study, we evaluated maleimide derivatives for their potency and selectivity of telomerase inhibition. Among the several N-substituted derivatives of maleimide tested, N-(1-Pyrenyl) maleimide was shown to exert the greatest inhibition of telomerase in a cell free system, with an IC50 value of 0.25 μM. Importantly, we demonstrated that N-(1-pyrenyl) maleimide induces apoptosis in Jurkat T cells and displays the greatest differential cytotoxicity against hematopoietic cancer cells. These results suggest that N-(1-pyrenyl) maleimide is an attractive maleimide to be tested and developed as anti-cancer drug.
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Affiliation(s)
- Pei-Rong Huang
- Department of Molecular and Cellular Biology, Chang Gung University, Kwei-San, Tao-Yuan, 333, Taiwan
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Wang TCV, Huang PR, Yeh YM, Hung SC. Abstract 2999: Role of heterogeneous nuclear ribonucleoprotein A/Bs in telomere maintenance. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-2999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a large family of proteins that associate with nascent pre-mRNAs, packaging them into hnRNP particles. In addition to their action as RNA-binding proteins, several members of the hnRNP family are thought to play roles in telomere maintenance because they are known to bind to telomeric DNA and to TERRA RNA, which is now identified as an integral component of telomeric heterochromatin. Using affinity purification and proteomic approach, we have previously shown that the members of hnRNP A/B family are the most abundant proteins in the nuclear extracts that bound specifically to G-strand telomeric DNA. To address if members of hnRNP A/B family are essential components of a functional telomere (i.e., does hnRNP A/Bs play a structural role) and to determine the functional overlap among members of hnRNP A/Bs in telomere length regulation, we initiated to investigate the biological effects of single, double, or triple knock-down of hnRNP A1, A2/B1 or A3. Preliminary results obtained from transient depletion of single hnRNP A1, A2 or A3 by RNA interference (RNAi) indicated that depletion of hnRNP A2 or A3 significantly reduced cell growth and colony formation. The percentage of cells in the sub-G1 phase was increased following the knockdown of hnRNP A2 or A3. In addition, the expression of S-phase kinase-associated protein-2 (skp2) was decreased in the transient knock-down cells. Surprisingly, however, studies of stable clones derived from single knock-down experiments indicated that knock-down of hnRNP A2, but not A1 or A3, produced a profound effect on cellular growth. This effect does not appear to result from reduced viability and/or apoptosis. We noted that an increased expression of hnRNP A1 was always observed in the stable clones depleted of hnRNP A3. Similarly, increased expression of A3 was observed in the cells depleted of hnRNP A1, suggesting that hnRNP A1 and A3 may have functional redundancy in vivo. Works are in progress to determine whether the anti-proliferation effects of depleting hnRNP A/B may result from telomere dysfunction, and to investigate the functional overlap between hnRNP A/Bs using double knock-down approach.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2999. doi:10.1158/1538-7445.AM2011-2999
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Chi LM, Lee CW, Chang KP, Hao SP, Lee HM, Liang Y, Hsueh C, Yu CJ, Lee IN, Chang YJ, Lee SY, Yeh YM, Chang YS, Chien KY, Yu JS. Enhanced interferon signaling pathway in oral cancer revealed by quantitative proteome analysis of microdissected specimens using 16O/18O labeling and integrated two-dimensional LC-ESI-MALDI tandem MS. Mol Cell Proteomics 2009; 8:1453-74. [PMID: 19297561 PMCID: PMC2709179 DOI: 10.1074/mcp.m800460-mcp200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 03/09/2009] [Indexed: 11/06/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) remains one of the most common cancers worldwide, and the mortality rate of this disease has increased in recent years. No molecular markers are available to assist with the early detection and therapeutic evaluation of OSCC; thus, identification of differentially expressed proteins may assist with the detection of potential disease markers and shed light on the molecular mechanisms of OSCC pathogenesis. We performed a multidimensional (16)O/(18)O proteomics analysis using an integrated ESI-ion trap and MALDI-TOF/TOF MS system and a computational data analysis pipeline to identify proteins that are differentially expressed in microdissected OSCC tumor cells relative to adjacent non-tumor epithelia. We identified 1233 unique proteins in microdissected oral squamous epithelia obtained from three pairs of OSCC specimens with a false discovery rate of <3%. Among these, 977 proteins were quantified between tumor and non-tumor cells. Our data revealed 80 dysregulated proteins (53 up-regulated and 27 down-regulated) when a 2.5-fold change was used as the threshold. Immunohistochemical staining and Western blot analyses were performed to confirm the overexpression of 12 up-regulated proteins in OSCC tissues. When the biological roles of 80 differentially expressed proteins were assessed via MetaCore analysis, the interferon (IFN) signaling pathway emerged as one of the most significantly altered pathways in OSCC. As many as 20% (10 of 53) of the up-regulated proteins belonged to the IFN-stimulated gene (ISG) family, including ubiquitin cross-reactive protein (UCRP)/ISG15. Using head-and-neck cancer tissue microarrays, we determined that UCRP is overexpressed in the majority of cheek and tongue cancers and in several cases of larynx cancer. In addition, we found that IFN-beta stimulates UCRP expression in oral cancer cells and enhances their motility in vitro. Our findings shed new light on OSCC pathogenesis and provide a basis for the future development of novel biomarkers.
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MESH Headings
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/chemistry
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Chromatography, Liquid/methods
- Databases, Protein
- Gene Expression Regulation, Neoplastic
- Humans
- Immunohistochemistry
- Interferons/metabolism
- Male
- Microdissection
- Molecular Sequence Data
- Mouth Neoplasms/chemistry
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/pathology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oxygen Isotopes/metabolism
- Proteome/analysis
- Signal Transduction/physiology
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Tandem Mass Spectrometry/methods
- Tissue Array Analysis
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Affiliation(s)
- Lang-Ming Chi
- From the ‡Molecular Medicine Research Center
- Departments of §Medical Research and Development
| | | | | | | | | | - Ying Liang
- From the ‡Molecular Medicine Research Center
| | - Chuen Hsueh
- From the ‡Molecular Medicine Research Center
- ‖Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333, Taiwan
| | - Chia-Jung Yu
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
| | - I-Neng Lee
- From the ‡Molecular Medicine Research Center
| | | | | | - Yuan-Ming Yeh
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University and
| | - Yu-Sun Chang
- From the ‡Molecular Medicine Research Center
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University and
| | - Kun-Yi Chien
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
| | - Jau-Song Yu
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
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Abstract
Telomerase activity is repressed in normal human somatic cells, but is activated in most cancers, suggesting that telomerase may be an important target for cancer therapy. Inhibition of telomerase in cancer cells has been shown to limit the growth of human cancer cells in culture. In this study, we report that helenalin, a natural sesquiterpene lactone, is a potent and selective inhibitor for human telomerase. In vitro studies indicate that this drug can inactivate telomerase directly in a manner that is dependent on concentration and time. The inhibitory action of this drug on telomerase is selective since the presence of excessive externally added proteins did not protect the inhibition and all of the other enzymes tested in this study were not inhibited by this drug. Furthermore, we demonstrated that helenalin can inhibit the expression of hTERT and telomerase in hematopoietic cancer cells. Therefore, the anti-tumor activity of helenalin is attributed, at least in part, to the inhibition of telomerase.
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Affiliation(s)
- Pei-Rong Huang
- Department of Molecular and Cellular Biology, Chang Gung University, Kwei-San, Tao-Yuan 333, Taiwan, ROC
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Yeh YM, Pan YT, Wang TCV. Cdc42/Rac1 participates in the control of telomerase activity in human nasopharyngeal cancer cells. Cancer Lett 2005; 218:207-13. [PMID: 15670898 DOI: 10.1016/j.canlet.2004.06.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 06/29/2004] [Accepted: 06/30/2004] [Indexed: 01/20/2023]
Abstract
Telomerase, a specialized ribonucleoprotein reverse transcriptase that directs the synthesis of telomeric DNA, is repressed in normal human somatic cells, but is activated in most cancers. Little is known concerning how telomerase activity is activated and maintained in cancer cells. We have previously shown that protein kinase C-zeta (PKC zeta) controls telomerase activity in nasopharyngeal cancer (NPC) cells. Since PKC zeta activity is known to be modulated by Cdc42/Rac1, we investigated the effects of inhibiting Cdc42 and Rac1 on the telomerase activity of NPC-076 cells. Treatment of NPC cells with antisense oligonucleotides against Cdc42 or Rac1 produced an inhibition of telomerase activity. Similarly, transient expression of dominant-negative mutants of Cdc42 or Rac1, but not the wild-type Cdc42 or Rac1, also produced an inhibition of telomerase activity in NPC cells. This inhibition of telomerase activity is not associated with a transcriptional down-regulation of hTERT, the key regulator of telomerase. We suggest that Cdc42/Rac1 participates in the posttranscriptional control of telomerase activity in NPC cells.
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Affiliation(s)
- Yuan-Ming Yeh
- Department of Molecular and Cellular Biology, Chang Gung University, Kwei-San, Tao-Yuan 333, Taiwan, ROC
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Boots MR, Yeh YM, Boots SG. Hypocholesterolemic agents VII: Inhibition of beta-hydroxy-beta-methylglutaryl-CoA reductase by monoesters of substituted glutaric acids. J Pharm Sci 1980; 69:506-9. [PMID: 7381731 DOI: 10.1002/jps.2600690507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A series of 1-(4-biphenylyl)pentyl hydrogen 3-alkylglutarates and 3-hydroxy-3-alkylglutarates was synthesized and assayed for inhibition of rat liver beta-hydroxy-beta-methylglutaryl-CoA reductase. Limited solubility of the monoesters in the enzyme assay system prevented the determination of the I50 values. However, the limited data indicated no significant changes in the activity of the analogs when they were assayed at identical concentrations.
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