76
|
Zhao L, Ni Y, Su M, Li H, Dong F, Chen W, Wei R, Zhang L, Guiraud SP, Martin FP, Rajani C, Xie G, Jia W. High Throughput and Quantitative Measurement of Microbial Metabolome by Gas Chromatography/Mass Spectrometry Using Automated Alkyl Chloroformate Derivatization. Anal Chem 2017; 89:5565-5577. [PMID: 28437060 DOI: 10.1021/acs.analchem.7b00660] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ability to identify and quantify small molecule metabolites derived from gut microbial-mammalian cometabolism is essential for the understanding of the distinct metabolic functions of the microbiome. To date, analytical protocols that quantitatively measure a complete panel of microbial metabolites in biological samples have not been established but are urgently needed by the microbiome research community. Here, we report an automated high-throughput quantitative method using a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) platform to simultaneously measure over one hundred microbial metabolites in human serum, urine, feces, and Escherichia coli cell samples within 15 min per sample. A reference library was developed consisting of 145 methyl and ethyl chloroformate (MCF and ECF) derivatized compounds with their mass spectral and retention index information for metabolite identification. These compounds encompass different chemical classes including fatty acids, amino acids, carboxylic acids, hydroxylic acids, and phenolic acids as well as benzoyl and phenyl derivatives, indoles, etc., that are involved in a number of important metabolic pathways. Within an optimized range of concentrations and sample volumes, most derivatives of both reference standards and endogenous metabolites in biological samples exhibited satisfactory linearity (R2 > 0.99), good intrabatch reproducibility, and acceptable stability within 6 days (RSD < 20%). This method was further validated by examination of the analytical variability of 76 paired human serum, urine, and fecal samples as well as quality control samples. Our method involved using high-throughput sample preparation, measurement with automated derivatization, and rapid GC/TOFMS analysis. Both techniques are well suited for microbiome metabolomics studies.
Collapse
|
77
|
Lo J, Kawakubo M, Juneja V, Su M, Freeman G, Sharpe A, Manstein D, Fisher D. 136 A novel combination therapy rescues response to checkpoint blockade in neoantigen-deficient cancers. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
78
|
Wang Q, Wang LH, Wang AL, Wang F, Wang XY, Qiao YP, Su M, Dou LX, Fang LW. [Mode of delivery among HIV-positive pregnant women in areas with high prevalence of HIV in China, 2007-2013]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2017; 50:620-4. [PMID: 27412839 DOI: 10.3760/cma.j.issn.0253-9624.2016.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To describe the changing demographic profile over time of pregnant women diagnosed with HIV infection, and trends in mode of delivery and pregnancy outcome. METHODS An observational investigation was conducted based on a population of 1 128 HIV-positive pregnant women at eight sites in China in provinces with high prevalence of HIV among pregnant women and children between 2007 and 2013. The study area included Shangcai and Weishi counties in Henan province; Ruili and Longchuan counties and Linxiang prefecture in Yunnan province; Yining County in Xinjiang; and Lingshan county and Babu district in Guangxi province. Main outcome measures were maternal characteristics, mode of delivery, and related trends over time by Cochram-Mantel-Haenszel(CMH) χ(2)-test. RESULTS A total hospital delivery rate of 96.4% was reported. For each year during the period 2007-2013, hospital delivery rates were 95.1% (253/266), 94.8% (188/198), 93.7% (164/175), 98.8% (159/161), 98.6% (141/143), 97.4% (114/117), and 100.0% (68/68), respectively (χ(2)CMH=7.68, P=0.006). The neonatal survival rate increased by 0.7% incrementally from 2007 to 2013, with 98.5% (262/266), 99.0% (196/198), 99.4% (174/175), 99.4% (160/161), 100.0% (143/143), 100.0% (117/117), and 100.0% (68/68), respectively (χ(2)CMH=4.58, P=0.030). The proportions of vaginal deliveries in those years were 62.2% (166/266), 54.8% (109/198), 59.9% (105/175), 61.7% (100/161), 66.7% (96/143), 58.8% (69/117), and 66.7% (46/68), respectively (χ(2)CMH=1.19, P= 0.276). The average rate for midwives skilled in procedures such as artificial rupture of membranes and episiotomy was 37.8% (261/691), with proportions decreasing during the study period at 39.2% (65/166), 47.4% (52/109), 35.9% (38/105), 46.0% (46/100), 25.5% (25/96), 31.2% (22/69), and 28.3% (13/46), respectively (χ(2CMH)=6.76, P=0.009). CONCLUSION The annual rate of reported hospital delivery increased between 2007 and 2013, with a declining rate of skilled midwifery over the same period. Survival of neonates born to HIV-infected mothers in China has increased to nearly equivalent levels as those of developed countries.
Collapse
|
79
|
Xu X, Wu A, Zhang X, Su M, Jiang T, Yuan ZM. MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets. BIOPHYSICS REPORTS 2017; 2:106-115. [PMID: 28317014 PMCID: PMC5334392 DOI: 10.1007/s41048-016-0033-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023] Open
Abstract
High-throughput sequencing-based metagenomics has garnered considerable interest in recent years. Numerous methods and tools have been developed for the analysis of metagenomic data. However, it is still a daunting task to install a large number of tools and complete a complicated analysis, especially for researchers with minimal bioinformatics backgrounds. To address this problem, we constructed an automated software named MetaDP for 16S rRNA sequencing data analysis, including data quality control, operational taxonomic unit clustering, diversity analysis, and disease risk prediction modeling. Furthermore, a support vector machine-based prediction model for intestinal bowel syndrome (IBS) was built by applying MetaDP to microbial 16S sequencing data from 108 children. The success of the IBS prediction model suggests that the platform may also be applied to other diseases related to gut microbes, such as obesity, metabolic syndrome, or intestinal cancer, among others (http://metadp.cn:7001/).
Collapse
|
80
|
Zhao L, Ni Y, Yu H, Zhang P, Zhao A, Bao Y, Liu J, Chen T, Xie G, Panee J, Chen W, Rajani C, Wei R, Su M, Jia W, Jia W. Serum stearic acid/palmitic acid ratio as a potential predictor of diabetes remission after Roux-en-Y gastric bypass in obesity. FASEB J 2016; 31:1449-1460. [PMID: 28007782 DOI: 10.1096/fj.201600927r] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/12/2016] [Indexed: 12/18/2022]
Abstract
Endogenous fatty acid metabolism that results in elongation and desaturation lipid products is thought to play a role in the development of type 2 diabetes mellitus (T2DM). In this study, we evaluated the potential of estimated elongase and desaturase activities for use as predictive markers for T2DM remission after Roux-en-Y gastric bypass (RYGB). The results of a targeted metabolomics approach from 2 independent studies were used to calculate 24 serum FA concentration ratios (product/precursor). Gene expression data from an open public data set was also analyzed. In a longitudinal study of 38 obese diabetic patients with RYGB, we found higher baseline stearic acid/palmitic acid (S/P) ratio. This ratio reflects an elovl6-encoded elongase enzyme activity that has been found to be associated with greater possibility for diabetes remission after RYGB [odds ratio, 2.16 (95% CI 1.10-4.26)], after adjustment for age, gender, body mass index, diabetes duration, glycosylated hemoglobin A1c, and fasting C-peptide. Our results were validated by examination of postsurgical elovl6 gene expression in morbidly obese patients. The association of S/P with the metabolic status of obese individuals was further validated in a cross-sectional cohort of 381 participants. In summary, higher baseline S/P was associated with greater probability of diabetes remission after RYGB and may serve as a diagnostic marker in preoperative patient assessment. - Zhao, L., Ni, Y., Yu, H., Zhang, P., Zhao, A., Bao, Y., Liu, J., Chen, T., Xie, G., Panee, J., Chen, W., Rajani, C., Wei, R., Su, M., Jia, W., Jia, W. Serum stearic acid/palmitic acid ratio as a potential predictor of diabetes remission after Roux-en-Y gastric bypass in obesity.
Collapse
|
81
|
Chen WL, Wang YY, Zhao A, Xia L, Xie G, Su M, Zhao L, Liu J, Qu C, Wei R, Rajani C, Ni Y, Cheng Z, Chen Z, Chen SJ, Jia W. Enhanced Fructose Utilization Mediated by SLC2A5 Is a Unique Metabolic Feature of Acute Myeloid Leukemia with Therapeutic Potential. Cancer Cell 2016; 30:779-791. [PMID: 27746145 PMCID: PMC5496656 DOI: 10.1016/j.ccell.2016.09.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/08/2016] [Accepted: 09/13/2016] [Indexed: 12/28/2022]
Abstract
Rapidly proliferating leukemic progenitor cells consume substantial glucose, which may lead to glucose insufficiency in bone marrow. We show that acute myeloid leukemia (AML) cells are prone to fructose utilization with an upregulated fructose transporter GLUT5, which compensates for glucose deficiency. Notably, AML patients with upregulated transcription of the GLUT5-encoding gene SLC2A5 or increased fructose utilization have poor outcomes. Pharmacological blockage of fructose uptake ameliorates leukemic phenotypes and potentiates the cytotoxicity of the antileukemic agent, Ara-C. In conclusion, this study highlights enhanced fructose utilization as a metabolic feature of AML and a potential therapeutic target.
Collapse
|
82
|
Wang X, Wang J, Zhao H, Li N, Ge S, Chen L, Li J, Jing J, Su M, Zheng Z, Zhang J, Gao G, Wang X. Clinical analysis and treatment of symptomatic intracranial hemorrhage after deep brain stimulation surgery. Br J Neurosurg 2016; 31:217-222. [PMID: 27760466 DOI: 10.1080/02688697.2016.1244252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
83
|
Ni Y, Su M, Qiu Y, Jia W, Du X. ADAP-GC 3.0: Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics Studies. Anal Chem 2016; 88:8802-11. [PMID: 27461032 DOI: 10.1021/acs.analchem.6b02222] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ADAP-GC is an automated computational pipeline for untargeted, GC/MS-based metabolomics studies. It takes raw mass spectrometry data as input and carries out a sequence of data processing steps including construction of extracted ion chromatograms, detection of chromatographic peak features, deconvolution of coeluting compounds, and alignment of compounds across samples. Despite the increased accuracy from the original version to version 2.0 in terms of extracting metabolite information for identification and quantitation, ADAP-GC 2.0 requires appropriate specification of a number of parameters and has difficulty in extracting information on compounds that are in low concentration. To overcome these two limitations, ADAP-GC 3.0 was developed to improve both the robustness and sensitivity of compound detection. In this paper, we report how these goals were achieved and compare ADAP-GC 3.0 against three other software tools including ChromaTOF, AnalyzerPro, and AMDIS that are widely used in the metabolomics community.
Collapse
|
84
|
Lan K, Su M, Xie G, Ferslew BC, Brouwer KLR, Rajani C, Liu C, Jia W. Key Role for the 12-Hydroxy Group in the Negative Ion Fragmentation of Unconjugated C24 Bile Acids. Anal Chem 2016; 88:7041-8. [PMID: 27322813 DOI: 10.1021/acs.analchem.6b00573] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Host-gut microbial interactions contribute to human health and disease states and an important manifestation resulting from this cometabolism is a vast diversity of bile acids (BAs). There is increasing interest in using BAs as biomarkers to assess the health status of individuals and, therefore, an increased need for their accurate separation and identification. In this study, the negative ion fragmentation behaviors of C24 BAs were investigated by UPLC-ESI-QTOF-MS. The step-by-step fragmentation analysis revealed a distinct fragmentation mechanism for the unconjugated BAs containing a 12-hydroxyl group. The unconjugated BAs lacking 12-hydroxylation fragmented via dehydration and dehydrogenation. In contrast, the 12-hydroxylated ones, such as deoxycholic acid (DCA) and cholic acid (CA), employed dissociation routes including dehydration, loss of carbon monoxide or carbon dioxide, and dehydrogenation. All fragmentations of the 12-hydroxylated unconjugated BAs, characterized by means of stable isotope labeled standards, were associated with the rotation of the carboxylate side chain and the subsequent rearrangements accompanied by proton transfer between 12-hydroxyl and 24-carboxyl groups. Compared to DCA, CA underwent further cleavages of the steroid skeleton. Accordingly, the effects of stereochemistry on the fragmentation pattern of CA were investigated using its stereoisomers. Based on the knowledge gained from the fragmentation analysis, a novel BA, 3β,7β,12α-trihydroxy-5β-cholanic acid, was identified in the postprandial urine samples of patients with nonalcoholic steatohepatitis. The analyses used in this study may contribute to a better understanding of the chemical diversity of BAs and the molecular basis of human liver diseases that involve BA synthesis, transport, and metabolism.
Collapse
|
85
|
Xie G, Wang X, Huang F, Zhao A, Chen W, Yan J, Zhang Y, Lei S, Ge K, Zheng X, Liu J, Su M, Liu P, Jia W. Dysregulated hepatic bile acids collaboratively promote liver carcinogenesis. Int J Cancer 2016; 139:1764-75. [PMID: 27273788 DOI: 10.1002/ijc.30219] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/02/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022]
Abstract
Dysregulated bile acids (BAs) are closely associated with liver diseases and attributed to altered gut microbiota. Here, we show that the intrahepatic retention of hydrophobic BAs including deoxycholate (DCA), taurocholate (TCA), taurochenodeoxycholate (TCDCA), and taurolithocholate (TLCA) were substantially increased in a streptozotocin and high fat diet (HFD) induced nonalcoholic steatohepatitis-hepatocellular carcinoma (NASH-HCC) mouse model. Additionally chronic HFD-fed mice spontaneously developed liver tumors with significantly increased hepatic BA levels. Enhancing intestinal excretion of hydrophobic BAs in the NASH-HCC model mice by a 2% cholestyramine feeding significantly prevented HCC development. The gut microbiota alterations were closely correlated with altered BA levels in liver and feces. HFD-induced inflammation inhibited key BA transporters, resulting in sustained increases in intrahepatic BA concentrations. Our study also showed a significantly increased cell proliferation in BA treated normal human hepatic cell lines and a down-regulated expression of tumor suppressor gene CEBPα in TCDCA treated HepG2 cell line, suggesting that several hydrophobic BAs may collaboratively promote liver carcinogenesis.
Collapse
|
86
|
Zheng N, Wang K, He J, Qiu Y, Xie G, Su M, Jia W, Li H. Effects of ADMA on gene expression and metabolism in serum-starved LoVo cells. Sci Rep 2016; 6:25892. [PMID: 27180883 PMCID: PMC4867623 DOI: 10.1038/srep25892] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Serum starvation is a typical way for inducing tumor cell apoptosis and stress. Asymmetric dimethylarginine (ADMA) is an endogenous metabolite. Our previous study reveals the plasma ADMA level is elevated in colon cancer patients, which can attenuate serum starvation-induced apoptosis in LoVo cells. In current study, we evaluated the effects of ADMA on gene expression and metabolism in serum-starved LoVo cells with gene microarray and metabolomic approaches. Our results indicated that 96 h serum starvation induced comprehensive alterations at transcriptional level, and most of them were restored by ADMA. The main signaling pathways induced by serum starvation included cancers-related pathways, pathways in cell death, apoptosis, and cell cycle etc. Meanwhile, the metabolomic data showed serum-starved cells were clearly separated with control cells, but not with ADMA-treated cells in PCA model. The identified differential metabolites indicated serum starvation significantly suppressed TCA cycle, altered glucose and fatty acids metabolism, as well as nucleic acids metabolism. However, very few differential metabolites were identified between ADMA and serum-starved cells. In summary, our current results indicated serum starvation profoundly altered the gene expression and metabolism of LoVo cells, whereas ADMA could restore most of the changes at transcriptional level, but not at metabolic level.
Collapse
|
87
|
Hwang B, Brozowski J, Liu Z, Lin L, Li N, Su M, Thomas N, Diaz L, Liu Z. 083 The loss function of BP180 Collagen type XVII in skin, leads to a mast cell dependent pro-inflammatory microenvironment which promotes melanoma progression. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.02.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
88
|
Shi G, Su M, Liang J, Duan R, Gu W, Xiao Y, Zhang Z, Qiu H, Zhang Z, Li Y, Zhang X, Ling Y, Song L, Chen M, Zhao Y, Wu J, Jing H, Xiao J, Wang X. Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica. Arch Microbiol 2016; 198:673-87. [PMID: 27129539 DOI: 10.1007/s00203-016-1229-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 04/15/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
Yersinia enterocolitica is the most diverse species among the Yersinia genera and shows more polymorphism, especially for the non-pathogenic strains. Individual non-pathogenic Y. enterocolitica strains are wrongly identified because of atypical phenotypes. In this study, we isolated an unusual Y. enterocolitica strain LC20 from Rattus norvegicus. The strain did not utilize urea and could not be classified as the biotype. API 20E identified Escherichia coli; however, it grew well at 25 °C, but E. coli grew well at 37 °C. We analyzed the genome of LC20 and found the whole chromosome of LC20 was collinear with Y. enterocolitica 8081, and the urease gene did not exist on the genome which is consistent with the result of API 20E. Also, the 16 S and 23 SrRNA gene of LC20 lay on a branch of Y. enterocolitica. Furthermore, the core-based and pan-based phylogenetic trees showed that LC20 was classified into the Y. enterocolitica cluster. Two plasmids (80 and 50 k) from LC20 shared low genetic homology with pYV from the Yersinia genus, one was an ancestral Yersinia plasmid and the other was novel encoding a number of transposases. Some pathogenic and non-pathogenic Y. enterocolitica-specific genes coexisted in LC20. Thus, although it could not be classified into any Y. enterocolitica biotype due to its special biochemical metabolism, we concluded the LC20 was a Y. enterocolitica strain because its genome was similar to other Y. enterocolitica and it might be a strain with many mutations and combinations emerging in the processes of its evolution.
Collapse
|
89
|
Panneerselvam J, Xie G, Che R, Su M, Zhang J, Jia W, Fei P. Distinct Metabolic Signature of Human Bladder Cancer Cells Carrying an Impaired Fanconi Anemia Tumor-Suppressor Signaling Pathway. J Proteome Res 2016; 15:1333-41. [PMID: 26956768 DOI: 10.1021/acs.jproteome.6b00076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metabolic profiling has great potential to help the diagnosis and prognosis of cancer patients. Fanconi Anemia (FA) tumor-suppressor signaling has been instrumental in understanding human tumorigenesis. However, this instrumental understanding has never been demonstrated at the metabolic level. Here, we show that impaired FA signaling can lead cells to exhibit metabolic signatures of tumorigenesis. This is consistent with our original studies of the roles of FA signaling in suppressing non-FA tumorigenesis at functional and genetic levels. Using ultraperformance liquid chromatography-mass spectroscopy and gas chromatography-mass spectrometry, we characterized metabolic alterations in bladder cancer cells carrying an intact or impaired FA pathway. The latter was obtained by ectopically expressing FAVL (FAVL-high), which we previously found to be capable of inactivating FA signaling. A total of 18 metabolites, end products of cell proliferation or apoptosis, were significantly different between FAVL-high and -low cells. Methionine, phenylalanine, and threonine, resulting from a tumorigenic process, were substantially increased in FAVL-high cells. With this study, we achieved genomic, functional, and metabolomic characterization of the roles of FA signaling in the development of human cancer. Furthermore, this study provides novel insights into how to translate FA basic research into strategies for producing effective biomarkers in human cancer diagnosis and prognosis.
Collapse
|
90
|
Liang J, Li X, Zha T, Chen Y, Hao H, Liu C, Duan R, Xiao Y, Su M, Wang X, Jing H. DTDP-rhamnosyl transferase RfbF, is a newfound receptor-related regulatory protein for phage phiYe-F10 specific for Yersinia enterocolitica serotype O:3. Sci Rep 2016; 6:22905. [PMID: 26965493 PMCID: PMC4786787 DOI: 10.1038/srep22905] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/24/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages and their hosts are continuously engaged in evolutionary competition. Here we isolated a lytic phage phiYe-F10 specific for Yersinia enterocolitica serotype O:3. We firstly described the phage receptor was regulated by DTDP-rhamnosyl transferase RfbF, encoded within the rfb cluster that was responsible for the biosynthesis of the O antigens. The deletion of DTDP-rhamnosyl transferase RfbF of wild type O:3 strain caused failure in phiYe-F10 adsorption; however, the mutation strain retained agglutination with O:3 antiserum; and complementation of its mutant converted its sensitivity to phiYe-F10. Therefore, DTDP-rhamnosyl transferase RfbF was responsible for the phage infection but did not affect recognition of Y. enterocolitica O:3 antiserum. Further, the deletions in the putative O-antigen biosynthesis protein precursor and outer membrane protein had no effect on sensitivity to phiYe-F10 infection. However, adsorption of phages onto mutant HNF10-ΔO-antigen took longer time than onto the WT, suggesting that deletion of the putative O-antigen biosynthesis protein precursor reduced the infection efficiency.
Collapse
|
91
|
Kuo ML, Lee MBE, Tang M, den Besten W, Hu S, Sweredoski MJ, Hess S, Chou CM, Changou CA, Su M, Jia W, Su L, Yen Y. PYCR1 and PYCR2 Interact and Collaborate with RRM2B to Protect Cells from Overt Oxidative Stress. Sci Rep 2016; 6:18846. [PMID: 26733354 PMCID: PMC4702135 DOI: 10.1038/srep18846] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022] Open
Abstract
Ribonucleotide reductase small subunit B (RRM2B) is a stress response protein that protects normal human fibroblasts from oxidative stress. However, the underlying mechanism that governs this function is not entirely understood. To identify factors that interact with RRM2B and mediate anti-oxidation function, large-scale purification of human Flag-tagged RRM2B complexes was performed. Pyrroline-5-carboxylate reductase 1 and 2 (PYCR1, PYCR2) were identified by mass spectrometry analysis as components of RRM2B complexes. Silencing of both PYCR1 and PYCR2 by expressing short hairpin RNAs induced defects in cell proliferation, partial fragmentation of the mitochondrial network, and hypersensitivity to oxidative stress in hTERT-immortalized human foreskin fibroblasts (HFF-hTERT). Moderate overexpression of RRM2B, comparable to stress-induced level, protected cells from oxidative stress. Silencing of both PYCR1 and PYCR2 completely abolished anti-oxidation activity of RRM2B, demonstrating a functional collaboration of these metabolic enzymes in response to oxidative stress.
Collapse
|
92
|
He J, Wang K, Zheng N, Qiu Y, Xie G, Su M, Jia W, Li H. Metformin suppressed the proliferation of LoVo cells and induced a time-dependent metabolic and transcriptional alteration. Sci Rep 2015; 5:17423. [PMID: 26616174 PMCID: PMC4663508 DOI: 10.1038/srep17423] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/29/2015] [Indexed: 12/24/2022] Open
Abstract
Metformin is a widely used anti-diabetic drug with potential anti-tumor activity. However, little is known about its global metabolic and transcriptional impacts on tumor cells. In current study, we performed a metabolic profiling on human-derived colon cancer LoVo cells treated by 10 mM metformin for 8, 24 and 48 h. An obvious time-dependent metabolic alteration was observed from 8 to 48 h, prior to the reduction of cell viability. A total of 47, 45 and 66 differential metabolites were identified between control and metformin-treated cells at three time points. Most of the metabolites were up-regulated at 8 h, but down-regulated at 24 and 48 h by metformin. These metabolites were mainly involved in carbohydrates, lipids, amino acids, vitamins and nucleotides metabolism pathways. Meanwhile, the transcirptomic profile revealed 134 and 3061 differentially expressed genes at 8 and 24 h by metformin. In addition to the cancer signaling pathways, expression of genes involved in cell energy metabolism pathways was significantly altered, which were further validated with genes in glucose metabolism pathway. Altogether, our current data indicate that metformin suppressed the proliferation of LoVo cells, which may be due to the modulation on cell energy metabolism at both metabolic and transcriptional levels in a time-dependent way.
Collapse
|
93
|
Yu H, Ni Y, Bao Y, Zhang P, Zhao A, Chen T, Xie G, Tu Y, Zhang L, Su M, Wei L, Jia W, Jia W. Chenodeoxycholic Acid as a Potential Prognostic Marker for Roux-en-Y Gastric Bypass in Chinese Obese Patients. J Clin Endocrinol Metab 2015; 100:4222-30. [PMID: 26425885 DOI: 10.1210/jc.2015-2884] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONTEXT Bile acids (BAs) have been suggested as key mediators of the improvements in glucose metabolism after Roux-en-Y gastric bypass (RYGB). OBJECTIVE The objective of the study was to test whether the individual or a group of BAs have potential value to predict diabetes remission after RYGB. DESIGN AND PATIENTS A retrospective cohort of 38 Chinese obese patients with type 2 diabetes mellitus (T2DM) who had undergone RYGB and a cross-sectional cohort of 327 subjects from the Shanghai Obesity Study were involved in the study. MAIN OUTCOME AND MEASURES We applied a targeted metabolomics approach to quantitatively measure 26 serum BAs. The relative proportion of each BA in total BAs was calculated. RESULTS In the metabolic surgery study, RYGB was effective in the reduction of body weight in both remission and nonremission groups. The reductions of body mass index (BMI) in both groups were 7.34 ± 2.10 kg/m(2) and 6.31 ± 2.38 kg/m(2), respectively (P = .14). Patients in the remission group had a shorter duration of diabetes, lower glycated hemoglobin, and higher C-peptide and chenodeoxycholic acid (CDCA) proportion at baseline compared with the nonremission group. Multiple logistic regression indicated that a higher level of CDCA relative to total BA (CDCA%) and shorter duration of diabetes at baseline were associated with a greater chance of diabetes remission. The odd ratios were 0.19 (95% confidence interval 0.05-0.74) and 1.77 (95% confidence interval 1.13-2.76), respectively, after adjustment for age, gender, and BMI. In the cross-sectional study, CDCA% was significantly higher in obese individuals with T2DM than the normal glucose tolerance group. Correlation analysis showed CDCA% was positively correlated with BMI, glycated hemoglobin, triglycerides, and low-density lipoprotein cholesterol and negatively correlated with high-density lipoprotein cholesterol and diabetes duration. CONCLUSION Increased CDCA, a major primary BA, was correlated with a shorter duration of T2DM, which was associated with a higher possibility of remission after surgery. CDCA% might act as a potential prognostic marker of RYGB.
Collapse
|
94
|
Ferslew BC, Xie G, Johnston CK, Su M, Stewart PW, Jia W, Brouwer KL, Barritt AS. Altered Bile Acid Metabolome in Patients with Nonalcoholic Steatohepatitis. Dig Dis Sci 2015; 60:3318-28. [PMID: 26138654 PMCID: PMC4864493 DOI: 10.1007/s10620-015-3776-8] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/17/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The prevalence of nonalcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) is increasing at an alarming rate. The role of bile acids in the development and progression of NAFLD to NASH and cirrhosis is poorly understood. This study aimed to quantify the bile acid metabolome in healthy subjects and patients with non-cirrhotic NASH under fasting conditions and after a standardized meal. METHODS Liquid chromatography tandem mass spectroscopy was used to quantify 30 serum and 16 urinary bile acids from 15 healthy volunteers and 7 patients with biopsy-confirmed NASH. Bile acid concentrations were measured at two fasting and four post-prandial time points following a high-fat meal to induce gallbladder contraction and bile acid reabsorption from the intestine. RESULTS Patients with NASH had significantly higher total serum bile acid concentrations than healthy subjects under fasting conditions (2.2- to 2.4-fold increase in NASH; NASH 2595-3549 µM and healthy 1171-1458 µM) and at all post-prandial time points (1.7- to 2.2-fold increase in NASH; NASH 4444-5898 µM and healthy 2634-2829 µM). These changes were driven by increased taurine- and glycine-conjugated primary and secondary bile acids. Patients with NASH exhibited greater variability in their fasting and post-prandial bile acid profile. CONCLUSIONS Results indicate that patients with NASH have higher fasting and post-prandial exposure to bile acids, including the more hydrophobic and cytotoxic secondary species. Increased bile acid exposure may be involved in liver injury and the pathogenesis of NAFLD and NASH.
Collapse
|
95
|
Su M, Yang B, Han Z. Improve the effect of the mandibular reconstruction by using the digital technique. Int J Oral Maxillofac Surg 2015. [DOI: 10.1016/j.ijom.2015.08.819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
96
|
Su M, Yang CC, Trikamji B, Mishra S. History of neurology in Taiwan. Neurology 2015; 84:1803-4. [DOI: 10.1212/wnl.0000000000001513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
97
|
Zhou K, Xie G, Wang J, Zhao A, Liu J, Su M, Ni Y, Zhou Y, Pan W, Che Y, Zhang T, Xiao Y, Wang Y, Wen J, Jia W, Cai W. Metabonomics reveals metabolite changes in biliary atresia infants. J Proteome Res 2015; 14:2569-74. [PMID: 25899098 DOI: 10.1021/acs.jproteome.5b00125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biliary atresia (BA) is a rare neonatal cholestatic disorder caused by obstruction of extra- and intra-hepatic bile ducts. If untreated, progressive liver cirrhosis will lead to death within 2 years. Early diagnosis and operation improve the outcome significantly. Infants with neonatal hepatitis syndrome (NHS) present similar symptoms, confounding the early diagnosis of BA. The lack of noninvasive diagnostic methods to differentiate BA from NHS greatly delays the surgery of BA infants, thus deteriorating the outcome. Here we performed a metabolomics study in plasma of BA, NHS, and healthy infants using gas chromatography-time-of-flight mass spectrometry. Scores plots of orthogonal partial least-squares discriminant analysis clearly separated BA from NHS and healthy infants. Eighteen metabolites were found to be differentially expressed between BA and NHS, among which seven (l-glutamic acid, l-ornithine, l-isoleucine, l-lysine, l-valine, l-tryptophan, and l-serine) were amino acids. The altered amino acids were quantitatively verified using ultraperformance liquid chromatography-tandem mass spectrometry. Ingenuity pathway analysis revealed the network of "Cellular Function and Maintenance, Hepatic System Development and Function, Neurological Disease" was altered most significantly. This study suggests that plasma metabolic profiling has great potential in differentiating BA from NHS, and amino acid metabolism is significantly different between the two diseases.
Collapse
|
98
|
Yen K, Wang F, Travins J, Chen Y, Yang H, Straley K, Choe S, Dorsch M, Agresta S, Schenkein D, Biller S, Su M. AG-221 offers a survival advantage in a primary human IDH2 mutant AML xenograft model. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv089.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
99
|
Su M, Tomás-Gamasa M, Serdjukow S, Mayer P, Carell T. Synthesis and properties of a Cu(II) complexing pyrazole ligandoside in DNA. Chem Commun (Camb) 2014; 50:409-11. [PMID: 24263097 DOI: 10.1039/c3cc47561a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development of metal base pairs is of immense importance for the construction of DNA nanostructures. Here we report the synthesis of a biaryl pyrazole-phenol nucleoside that forms in DNA a stable self-pair upon complexation of a Cu(II) ion. A sequence with five consecutive pyrazole nucleotides allows the complexation of five Cu(II) ions in a row.
Collapse
|
100
|
Su M, Sura S. SU-E-T-596: Axillary Nodes Radiotherapy Boost Field Dosimetric Impact Study: Oblique Field and Field Optimization in 3D Conventional Breast Cancer Radiation Treatment. Med Phys 2014. [DOI: 10.1118/1.4888932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|