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Zhang Y, Yu CY, Song E, Li SC, Mechref Y, Tang H, Liu X. Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry. J Proteome Res 2015; 14:5099-108. [DOI: 10.1021/acs.jproteome.5b00299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Song E, Hu Y, Hussein A, Yu CY, Tang H, Mechref Y. Characterization of the Glycosylation Site of Human PSA Prompted by Missense Mutation using LC-MS/MS. J Proteome Res 2015; 14:2872-83. [PMID: 26022737 DOI: 10.1021/acs.jproteome.5b00362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prostate specific antigen (PSA) is currently used as a diagnostic biomarker for prostate cancer. It is a glycoprotein possessing a single glycosylation site at N69. During our previous study of PSA N69 glycosylation, additional glycopeptides were observed in the PSA sample that were not previously reported and did not match glycopeptides of impure glycoproteins existing in the sample. This extra glycosylation site of PSA is associated with a mutation in KLK3 genes. Among single nucleotide polymorphisms (SNPs) of KLKs families, the rs61752561 in KLK3 genes is an unusual missense mutation resulting in the conversion of D102 to N in PSA amino acid sequence. Accordingly, a new N-linked glycosylation site is created with an N102MS motif. Here we report the first qualitative and quantitative glycoproteomic study of PSA N102 glycosylation site by LC-MS/MS. We successfully applied tandem MS to verify the amino acid sequence possessing N102 glycosylation site and associated glycoforms of PSA samples acquired from different suppliers. Among the three PSA samples, HexNAc2Hex5 was the predominant glycoform at N102, while HexNAc4Hex5Fuc1NeuAc1 or HexNAc4Hex5Fuc1NeuAc2 was the primary glycoforms at N69. D102 is the first amino acid of "kallikrein loop", which is close to a zinc-binding site and catalytic triad. The different glycosylation of N102 relative to N69 might be influenced by the close vicinity of N102 to these functional sites and steric hindrance.
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Hu Y, Zhou S, Yu CY, Tang H, Mechref Y. Automated annotation and quantitation of glycans by liquid chromatography/electrospray ionization mass spectrometric analysis using the MultiGlycan-ESI computational tool. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:135-42. [PMID: 25462374 PMCID: PMC4516131 DOI: 10.1002/rcm.7093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 05/20/2023]
Abstract
RATIONALE Liquid chromatography/mass spectrometry (LC/MS) is currently considered to be a conventional glycomics analysis strategy due to the high sensitivity and ability to handle complex biological samples. Interpretation of LC/MS data is a major bottleneck in high-throughput glycomics LC/MS-based analysis. The complexity of LC/MS data associated with biological samples prompts the needs to develop computational tools capable of facilitating automated data annotation and quantitation. METHODS An LC/MS-based automated data annotation and quantitation software, MultiGlycan-ESI, was developed and utilized for glycan quantitation. Data generated by the software from LC/MS analysis of permethylated N-glycans derived from fetuin were initially validated by manual integration to assess the performance of the software. The performance of MultiGlycan-ESI was then assessed for the quantitation of permethylated fetuin N-glycans analyzed at different concentrations or spiked with permethylated N-glycans derived from human blood serum. RESULTS The relative abundance differences between data generated by the software and those generated by manual integration were less than 5%, indicating the reliability of MultiGlycan-ESI in quantitation of permethylated glycans analyzed by LC/MS. Automated quantitation resulted in a linear relationship for all six N-glycans derived from 50 ng to 400 ng fetuin with correlation coefficients (R(2) ) greater than 0.93. Spiking of permethylated fetuin N-glycans at different concentrations in permethylated N-glycan samples derived from a 0.02 μL of HBS also exhibited linear agreement with R(2) values greater than 0.9. CONCLUSIONS With a variety of options, including mass accuracy, merged adducts, and filtering criteria, MultiGlycan-ESI allows automated annotation and quantitation of LC/ESI-MS N-glycan data. The software allows the reliable quantitation of glycan LC/MS data. The software is reliable for automated glycan quantitation, thus facilitating rapid and reliable high-throughput glycomics studies.
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Song E, Mayampurath A, Yu CY, Tang H, Mechref Y. Glycoproteomics: identifying the glycosylation of prostate specific antigen at normal and high isoelectric points by LC-MS/MS. J Proteome Res 2014; 13:5570-80. [PMID: 25327667 PMCID: PMC4261947 DOI: 10.1021/pr500575r] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Prostate
specific antigen (PSA) is currently used as a biomarker
to diagnose prostate cancer. PSA testing has been widely used to detect
and screen prostate cancer. However, in the diagnostic gray zone,
the PSA test does not clearly distinguish between benign prostate
hypertrophy and prostate cancer due to their overlap. To develop more
specific and sensitive candidate biomarkers for prostate cancer, an
in-depth understanding of the biochemical characteristics of PSA (such
as glycosylation) is needed. PSA has a single glycosylation site at
Asn69, with glycans constituting approximately 8% of the protein by
weight. Here, we report the comprehensive identification and quantitation
of N-glycans from two PSA isoforms using LC–MS/MS. There were
56 N-glycans associated with PSA, whereas 57 N-glycans were observed
in the case of the PSA-high isoelectric point (pI) isoform (PSAH).
Three sulfated/phosphorylated glycopeptides were detected, the identification
of which was supported by tandem MS data. One of these sulfated/phosphorylated
N-glycans, HexNAc5Hex4dHex1s/p1 was identified in both PSA and PSAH
at relative intensities of 0.52 and 0.28%, respectively. Quantitatively,
the variations were monitored between these two isoforms. Because
we were one of the laboratories participating in the 2012 ABRF Glycoprotein
Research Group (gPRG) study, those results were compared to that presented
in this study. Our qualitative and quantitative results summarized
here were comparable to those that were summarized in the interlaboratory
study.
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Mayampurath A, Song E, Mathur A, Yu CY, Hammoud Z, Mechref Y, Tang H. Label-free glycopeptide quantification for biomarker discovery in human sera. J Proteome Res 2014; 13:4821-32. [PMID: 24946017 DOI: 10.1021/pr500242m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycan moieties of glycoproteins modulate many biological processes in mammals, such as immune response, inflammation, and cell signaling. Numerous studies show that many human diseases are correlated with quantitative alteration of protein glycosylation. In some cases, these changes can occur for certain types of glycans over specific sites in a glycoprotein rather than on the global abundance of the glycoprotein. Conventional analytical techniques that analyze the abundance of glycans cleaved from glycoproteins cannot reveal these subtle effects. Here we present a novel statistical method to quantify the site-specific glycosylation of glycoproteins in complex samples using label-free mass spectrometric techniques. Abundance variations between sites of a glycoprotein as well as different glycoforms, that is, glycopeptides with different glycans attached to the same site, can be detected using these techniques. We applied our method to an esophageal cancer study based on blood serum samples from cancer patients in an attempt to detect potential biomarkers of site-specific N-linked glycosylation. A few glycoproteins, including vitronectin, showed significantly different site-specific glycosylations within cancer/control samples, indicating that our method is ready to be used for the discovery of glycosylated biomarkers.
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Liao CC, Chen TY, Tsang LC, Ou SY, Yu CY, Hsu HW, Cheng YF, Chiu KW, Eng HL, Chen CL, Huang TL. The acoustic radiation force impulse elastography evaluation of liver fibrosis in posttransplantation dysfunction of living donor liver transplantation. Transplant Proc 2014; 46:876-9. [PMID: 24767370 DOI: 10.1016/j.transproceed.2013.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/25/2013] [Accepted: 12/10/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND The acoustic radiation force impulse elastography (ARFI) is a new technology of elastography integrated into B-mode ultrasonography. It has been a reliable method to evaluate liver fibrosis of chronic liver disease in recent years, but less applied in the posttransplantation liver. The aim of the study was to evaluate liver fibrosis by the ARFI with correlation of pathological stages in living donor liver transplantation (LDLT). MATERIALS AND METHODS From August 2010 to August 2012, there were 57 LDLT patients with liver biopsy (LB) due to posttransplantation dysfunction; all patients also received posttransplantation ARFI liver stiffness measurement (LSM) after transplantation for liver fibrosis staging. The ARFI elastography was performed using a Siemens Acuson S2000 ultrasound system with 4V1 transducers (Acusion, Siemens Medical Systems Co. Ltd. Erlangen, Germany). The ARFI LSM value was presented by shear wave velocity (SWV, m/s). The fibrosis staging as F0 to F4 was in accordance with the Metavir scoring system. RESULTS A total of 57 patients had both posttransplantation LB and effective ARFI fibrosis staging for correlation. The ARFI LSM value increased with severity of liver fibrosis and had significant linear correlation with the results of histological fibrosis staging. The ARFI LSM sensitivities (Se), specificities (Sp), and cutoff values based on receiver-operator characteristic curve were F0: 0.75 m/s (Se: 93.8%, Sp: 4%), F1: 1.06 m/s (Se: 95.5%, Sp: 25.7%), F2: 1.81 m/s (Se: 50%, Sp: 83.6%) and F3: 2.33 m/s (Se: 100%, Sp: 92.9%). Predictive value of ARFI LSM reported a significant difference between early fibrosis stage (F0-F1) and advanced fibrosis stage (F ≧ 2) (P < .05). CONCLUSION In this study, ARFI demonstrated a strong linear correlation and severity of liver fibrosis with LB pathologic staging. ARFI can be an alternative and compensatory method for frequent LB in the posttransplantation liver.
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Mayampurath A, Yu CY, Song E, Balan J, Mechref Y, Tang H. Computational framework for identification of intact glycopeptides in complex samples. Anal Chem 2013; 86:453-63. [PMID: 24279413 DOI: 10.1021/ac402338u] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycosylation is an important protein modification that involves enzymatic attachment of sugars to amino acid residues. Understanding the structure of these sugars and the effects of glycosylation are vital for developing indicators of disease development and progression. Although computational methods based on mass spectrometric data have proven to be effective in monitoring changes in the glycome, developing such methods for the glycoproteome are challenging, largely due to the inherent complexity in simultaneously studying glycan structures with their corresponding glycosylation sites. This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. Scoring algorithms are presented for tandem mass spectra of glycopeptides resulting from collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD) fragmentation modes. An empirical false-discovery rate estimation method, based on a target-decoy search approach, is derived for assigning confidence. The power of our method is further enhanced when multiple data sets are pooled together to increase identification confidence. Using this framework, 103 highly confident N-linked glycopeptides from 53 sites across 33 glycoproteins were identified in complex human serum proteome samples using conventional proteomic platforms with standard depletion of the 7-most abundant proteins. These results indicate that our method is ready to be used for characterizing site-specific protein glycosylation in complex samples.
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Yu CY, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H. Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry. Bioinformatics 2013; 29:1706-7. [PMID: 23610369 DOI: 10.1093/bioinformatics/btt190] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED As a common post-translational modification, protein glycosylation plays an important role in many biological processes, and it is known to be associated with human diseases. Mass spectrometry (MS)-based glycomic profiling techniques have been developed to measure the abundances of glycans in complex biological samples and applied to the discovery of putative glycan biomarkers. To automate the annotation of glycomic profiles in the liquid chromatography-MS (LC-MS) data, we present here a user-friendly software tool, MultiGlycan, implemented in C# on Windows systems. We tested MultiGlycan by using several glycomic profiling datasets acquired using LC-MS under different preparations and show that MultiGlycan executes fast and generates robust and reliable results. AVAILABILITY MultiGlycan can be freely downloaded at http://darwin.informatics.indiana.edu/MultiGlycan/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Abstract
We introduce three software tools, Cartoonist, GlycoWorkbench, and MultiGlycan, for N-glycan profiling of complex biological samples. Detailed instructions for using these tools are provided, and their performances are demonstrated by using real glycan profiling data.
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Birmingham DJ, Hebert LA, Song H, Noonan WT, Rovin BH, Nagaraja HN, Yu CY. Evidence that abnormally large seasonal declines in vitamin D status may trigger SLE flare in non-African Americans. Lupus 2012; 21:855-64. [PMID: 22433915 PMCID: PMC3839052 DOI: 10.1177/0961203312439640] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cross-sectional studies have shown that low vitamin D (25-hydroxyvitamin D (25(OH)D)) is associated with increased systemic lupus erythematosus (SLE) activity. This study is the first to assess the temporal relationship between 25(OH)D levels and onset of SLE flare. This assessment was made possible because of the specimen bank and database of the Ohio SLE Study (OSS), a longitudinal study of frequently relapsing SLE that involved regular bimonthly patient follow-up. We identified for this study 82 flares from 46 patients that were separated by at least 8 months from previous flares. Serum 25(OH)D levels were measured at 4 and 2 months before flare, and at the time of flare (a flare interval). We found that for flares occurring during low daylight months (LDM, Oct-Mar), 25(OH)D levels were decreased at the time of flare, but only in non-African American (non-AA) patients (32% decrease at flare, compared to 4 months prior, p < 0.001). To control for seasonal effects, we also measured 25(OH)D levels in the LDM "no-flare" intervals, which were intervals that matched to the same calendar months of the patients' LDM flare intervals, but that didn't end in flare (n = 24). For these matches, a significant decrease occurred in 25(OH)D levels during the flare intervals (18.1% decrease, p < 0.001), but not during the matching no-flare intervals (6.2% decrease, p = 0.411). For flares occurring during high daylight months (HDM), 25(OH)D levels changed only in non-AA patients, increasing slightly (5.6%, p = 0.010). Analysis of flare rates for the entire OSS cohort (n = 201 flares) revealed a tendency for higher flare rates during LDM compared to HDM, but again only in non-AA patients (p = 0.060). Flare rates were lower during HDM for non-AA patients compared to AA patients (p = 0.028). In conclusion, in non-AA SLE patients, unusually large declines in 25(OH)D during LDM may be mechanistically related to SLE flare, whereas relatively high 25(OH)D levels during HDM may protect against flare.
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Mitra I, Zhuang Z, Zhang Y, Yu CY, Hammoud ZT, Tang H, Mechref Y, Jacobson SC. N-glycan profiling by microchip electrophoresis to differentiate disease states related to esophageal adenocarcinoma. Anal Chem 2012; 84:3621-7. [PMID: 22397697 DOI: 10.1021/ac203431s] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report analysis of N-glycans derived from disease-free individuals and patients with Barrett's esophagus, high-grade dysplasia, and esophageal adenocarcinoma by microchip electrophoresis with laser-induced fluorescence detection. Serum samples in 10 μL aliquots are enzymatically treated to cleave the N-glycans that are subsequently reacted with 8-aminopyrene-1,3,6-trisulfonic acid to add charge and a fluorescent label. Separations at 1250 V/cm and over 22 cm yielded efficiencies up to 700,000 plates for the N-glycans and analysis times under 100 s. Principal component analysis (PCA) and analysis of variance (ANOVA) tests of the peak areas and migration times are used to evaluate N-glycan profiles from native and desialylated samples and determine differences among the four sample groups. With microchip electrophoresis, we are able to distinguish the three patient groups from each other and from disease-free individuals.
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Huang TL, Chen TY, Tsang LL, Ou HY, Yu CY, Wang CC, Wang SH, Lin CC, Liu YW, Yong CC, Chiu KW, Eng HL, Jawan B, Cheng YF, Chen CL. Hemodynamics of portal venous stenosis before and after treatment in pediatric liver transplantation: evaluation with Doppler ultrasound. Transplant Proc 2012; 44:481-3. [PMID: 22410051 DOI: 10.1016/j.transproceed.2012.01.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIM The aim of this study was to evaluate portal vein stenosis (PVS) in pediatric liver transplantation (PLT) using Doppler ultrasound (DUS) before and after interventional management for hemodynamic changes. MATERIALS AND METHODS From 2000 to 2010, we encountered 11 PVS cases among 180 PLT that were evaluated using DUS and computed tomography (CT) angiography (CTA); all underwent portal stenting. DUS was used to monitor portal hemodynamics. For the diagnosis of PVS, we investigated multiple parameters including stenotic size (SS), stenotic ratio (SR) (SR [%]=PRE-SS/PRE [PRE=stenotic size]), portal flow velocity ratio (VR) (VR=VS/PRE [PRE=velocity at prestenotic site; VS=peak velocity at stenotic site]), spleen size, and platelet count. RESULTS The incidence of PVS was 5.6% (11/180). The PV was 2.5 mm using DUS and 2.7 mm using CTA. The average SR was 65% fitting the criterion. Low prestenotic portal flow<12 cm/sec and high peak velocity in the stenotic segment (up to 147 cm/sec) were observed in 6 cases. The VR value was high at 7.5:1 and there was splenomegaly with thrombocytopenia. After portal vein stenting, hyperperfusion occurred might after reopening the stenosis: the flow increased to an average of 34 cm/sec and then flow decreased slowly to a stable level 2 weeks later. The size of the spleen decreased from 17 to 12 cm and the thrombocytopenia also improved with platelet counts increasing from 67×10(3) to 178×10(3)/μl at 2 months follow-up. The changes in portal flow, portal vein size, spleen size, and platelet count were significant (P<.05). CONCLUSION PVS is diagnosed using DUS by increased intrahepatic PV dilatation, peak flow at the stenotic site, discrepant VR. Early portal stenting showed a better prognosis. DUS is essential and effective for hemodynamic monitoring and management of PVS.
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M. Mayampurath A, Yu CY, Mechref Y, Tang H. Bioinformatic Approaches in Glycomics and Glycoproteomics. CURR PROTEOMICS 2011. [DOI: 10.2174/157016411798220817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wu YL, Brookshire BP, Verani RR, Arnett FC, Yu CY. Clinical presentations and molecular basis of complement C1r deficiency in a male African-American patient with systemic lupus erythematosus. Lupus 2011; 20:1126-34. [PMID: 21784777 DOI: 10.1177/0961203311404914] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Homozygous deficiencies of early components for complement activation are among the strongest genetic risk factors for human systemic lupus erythematosus (SLE). Eleven cases of C1r deficiency are documented but this is the first report on the molecular basis of C1r deficiency. The proband is an African-American male who developed SLE at 3 months of age. He had a discoid lupus rash and diffuse proliferative glomerulonephritis. Serum complement analysis of the patient showed zero CH50 activity, undetectable C1r, and reduced levels of C1s, but highly elevated levels of complement C4, C2, and C1-inhibitor. The coding regions of the mutant C1R gene with 11 exons located at chromosome 12p13 were polymerase chain reaction (PCR)-amplified and sequenced to completion. DNA sequencing revealed a homozygous C→T mutation at nucleotide-6392 in exon 10 of the C1R gene, resulting in a nonsense mutation from Arg-380 (R380X). The patient's clinically normal mother was heterozygous for this mutation. A sequence-specific primer (SSP) PCR coupled with StuI-restriction fragment length polymorphism (RFLP) was developed to detect the novel mutation. Screening of 209 African-American SLE patients suggested that the R380X mutation is a rare causal variant. Mutations leading to early complement component deficiencies in SLE are mostly private variants with large effects.
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Hsieh CB, Chung KP, Chu CM, Yu JC, Hsieh HF, Chu HC, Yu CY, Chen TW. Appropriate liver resection type for patients with the American joint committee on cancer classification T1 and T2 hepatocellular carcinoma. Eur J Surg Oncol 2011; 37:497-504. [PMID: 21450438 DOI: 10.1016/j.ejso.2011.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 03/02/2011] [Accepted: 03/07/2011] [Indexed: 12/12/2022] Open
Abstract
SYNOPSIS Major liver resection prevents intrahepatic tumor recurrence in T2 hepatocellular carcinoma patients with microvascular invasion or daughter nodules. BACKGROUND AND OBJECTIVES There is no consensus on whether major or minor hepatectomy is better for hepatocellular carcinoma (HCC) patients. We investigated the outcomes of liver resection type in resectable HCC patients. METHODS Two hundred sixty-three HCC patients with Child-Pugh class A liver function who underwent curative hepatectomy were enrolled. Among them, 186 patients had pathologic stage T1 HCC and 77 had stage T2 HCC. Patients were also classed according to the type of resection (major or minor). Clinicopathologic characteristics and outcomes were compared. RESULTS Patients with T1 HCC who underwent major resection had a higher rate of blood transfusion than those who underwent minor resection (P < 0.001). The disease-free survival rate of T2 patients who underwent major resection was better than that of patients who underwent minor resection (P = 0.004). The overall survival rates of T1 and T2 HCC patients did not differ significantly between those with major or minor resection. CONCLUSIONS Major liver resection is recommended for T2 HCC patients with adequate remnant liver function because it results in a better disease-free survival rate than does minor resection in these patients. Minor liver resection is suggested for T1 HCC patients, except for those with a tumor sitting close to vessels, because it is associated with a low incidence of blood transfusion and a good survival rate.
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Birmingham DJ, Irshaid F, Nagaraja HN, Zou X, Tsao BP, Wu H, Yu CY, Hebert LA, Rovin BH. The complex nature of serum C3 and C4 as biomarkers of lupus renal flare. Lupus 2010; 19:1272-80. [PMID: 20605879 DOI: 10.1177/0961203310371154] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To assess the relationship between serum C3 or C4 levels and lupus renal flare, C3 and C4 levels were measured bimonthly in 71 lupus nephritis patients for a mean of 35 months, during which time 70 renal flares were identified. Comparing baseline, pre-flare, and at-flare values indicated that neither C3 nor C4 levels decreased pre-flare, but both decreased on average significantly at flare. However, sensitivity/specificity for C3 (75%/71%) and C4 (48%/71%) were low. To account for other influencing factors, multiple regression was performed that included bimonthly values of C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), and genotype data on C3 (S/F), CRP (1846G > A), and the complement regulator factor H (Y402H). This analysis revealed that reduced levels of C4, but not C3, were independently associated with the two-month pre-flare period. Conversely, reduced levels of C3, but not C4, were independently associated with the flare visit. Significant pro-flare interactions included low C3 levels with the factor H 402HH-encoding genotype, and low CRP levels with the C3 F allele. Together these data suggest that C4 activation is critical for initiating renal flare while C3 activation is involved in the actual tissue damage, and that these effects are influenced by genetic variability in complement activation and regulation.
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Soto K, Wu YL, Ortiz A, Aparício SR, Yu CY. Familial C4B deficiency and immune complex glomerulonephritis. Clin Immunol 2010; 137:166-75. [PMID: 20580617 DOI: 10.1016/j.clim.2010.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 05/29/2010] [Accepted: 06/02/2010] [Indexed: 11/16/2022]
Abstract
Homozygous complement C4B deficiency is described in a Southern European young female patient with Membranoproliferative Glomerulonephritis (MPGN) type III characterized by renal biopsies with strong complement C4 and IgG deposits. Low C4 levels were independent of clinical evolution or type of immunosuppression and were found in three other family members without renal disease or infections. HLA typing revealed that the patient has homozygous A*02, Cw*06, B*50 at the class I region, and DRB1*08 and DQB1*03 at the class II region. Genotypic and phenotypic studies demonstrated that the patient has homozygous monomodular RCCX in the HLA class III region, with single long C4A genes coding for C4A3 and complete C4B deficiency. Her father, mother, son and niece have heterozygous C4B deficiency. The patient's deceased brother had a history of Henoch-Schönlein Purpura (HSP), an immune complex-mediated proliferative glomerulonephritis. These findings challenge the putative pathophysiological roles of C4A and C4B and underscore the need to perform functional assays, C4 allotyping and genotyping on patients with persistently low serum levels of a classical pathway complement component and glomerulopathy associated with immune deposits.
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Kuo SM, Chang WK, Yu CY, Hsieh CB. Silent hepatic portal venous gas following upper gastrointestinal endoscopy. Endoscopy 2009; 41 Suppl 2:E121-2. [PMID: 19544258 DOI: 10.1055/s-0029-1214657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Tsou CC, Tsui YH, Yian YH, Chen YJ, Yang HY, Yu CY, Lynn KS, Chen YJ, Sung TY, Hsu WL. MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS. Nucleic Acids Res 2009; 37:W661-9. [PMID: 19528069 PMCID: PMC2703943 DOI: 10.1093/nar/gkp476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Isotope labeling combined with liquid chromatography-mass spectrometry (LC-MS) provides a robust platform for analyzing differential protein expression in proteomics research. We present a web service, called MaXIC-Q Web (http://ms.iis.sinica.edu.tw/MaXIC-Q_Web/), for quantitation analysis of large-scale datasets generated from proteomics experiments using various stable isotope-labeling techniques, e.g. SILAC, ICAT and user-developed labeling methods. It accepts spectral files in the standard mzXML format and search results from SEQUEST, Mascot and ProteinProphet as input. Furthermore, MaXIC-Q Web uses statistical and computational methods to construct two kinds of elution profiles for each ion, namely, PIMS (projected ion mass spectrum) and XIC (extracted ion chromatogram) from MS data. Toward accurate quantitation, a stringent validation procedure is performed on PIMSs to filter out peptide ions interfered with co-eluting peptides or noise. The areas of XICs determine ion abundances, which are used to calculate peptide and protein ratios. Since MaXIC-Q Web adopts stringent validation on spectral data, it achieves high accuracy so that manual validation effort can be substantially reduced. Furthermore, it provides various visualization diagrams and comprehensive quantitation reports so that users can conveniently inspect quantitation results. In summary, MaXIC-Q Web is a user-friendly, interactive, robust, generic web service for quantitation based on ICAT and SILAC labeling techniques.
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Yang SY, Chieh JJ, Wang WC, Yu CY, Lan CB, Chen JH, Horng HE, Hong CY, Yang HC, Huang W. Ultra-highly sensitive and wash-free bio-detection of H5N1 virus by immunomagnetic reduction assays. J Virol Methods 2008; 153:250-2. [PMID: 18760307 DOI: 10.1016/j.jviromet.2008.07.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 07/08/2008] [Accepted: 07/22/2008] [Indexed: 10/21/2022]
Abstract
A platform for assaying avian influenza H5N1 viruses that involves measuring the ac immunomagnetic reduction of a magnetic reagent mixed with a detected sample is developed. The magnetic reagent contained magnetic nanoparticles coated with antibodies. To achieve an ultra-high sensitivity assay, a system utilizing a high-transition-temperature superconducting quantum interference device was used to sense the immunomagnetic reduction of the reagents. The results confirmed the ultra-high sensitivity of the immunomagnetic reduction assay on H5N1.
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Zhao ZG, Jiang L, Zhang WW, Yu CY, Zhu SS, Xie K, Tian H, Liu LL, Ikehashi H, Wan JM. Fine mapping of S31, a gene responsible for hybrid embryo-sac abortion in rice (Oryza sativa L.). PLANTA 2007; 226:1087-96. [PMID: 17549514 DOI: 10.1007/s00425-007-0553-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2006] [Accepted: 05/08/2007] [Indexed: 05/15/2023]
Abstract
Partial abortion of female gametes and the resulting semi-sterility of indica x japonica inter-subspecific rice hybrids have been ascribed to an allelic interaction, which can be avoided by the use of wide compatibility varieties. To further understand the genetic mechanism of hybrid sterility, we have constructed two sets of hybrids, using as male parent either the typical japonica variety Asominori, or the wide compatibility variety 02428; and as female, a set of 66 chromosome segment substitution lines in which various chromosomal segments from the indica variety IR24 have been introduced into a common genetic background of Asominori. Spikelet semi-sterility was observed in hybrid between CSSL34 and Asominori, which is known to carry the sterility gene S31 (Zhao et al. in Euphytica 151:331-337, 2006). Cytological analysis revealed that the semi-sterility of the CSSL34 x Asominori hybrid was caused primarily by partial abortion of the embryo sac at the stage of the mitosis of the functional megaspore. A population of 1,630 progeny of the three-way cross (CSSL34 x 02428) x Asominori was developed to map S31. Based on the physical location of linked molecular markers, S31 was thereby delimited to a 54-kb region on rice chromsome 5. This fragment contains eight predicted open reading frames, four of which encode known proteins and four putative proteins. These results are relevant to the map-based cloning of S31, and the development of marker-assisted transfer of non-sterility allele inducing alleles to breeding germplasm, to allow for a more efficient exploitation of heterosis in hybrid rice.
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Yu CY, Tsui YH, Yian YH, Sung TY, Hsu WL. The Multi-Q web server for multiplexed protein quantitation. Nucleic Acids Res 2007; 35:W707-12. [PMID: 17553828 PMCID: PMC1933177 DOI: 10.1093/nar/gkm345] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Multi-Q web server provides an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. The web server is designed as a platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. Compared to the previous stand-alone version, the new web server version provides many enhanced features and flexible options for quantitation. The workflow of the web server is represented by a quantitation wizard so that the tool is easy to use. It also provides a friendly interface that helps users configure their parameter settings before running the program. The web server generates a standard report for quantitation results. In addition, it allows users to customize their output reports and information of interest can be easily highlighted. The output also provides visualization of mass spectral data so that users can conveniently validate the results. The Multi-Q web server is a fully automated and easy to use quantitation tool that is suitable for large-scale multiplexed protein quantitation. Users can download the Multi-Q Web Server from http://ms.iis.sinica.edu.tw/Multi-Q-Web.
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Liao GS, Yu CY, Shih ML, Chan DC, Liu YC, Yu JC, Chen TW, Hsieh CB. Radiofrequency ablation after transarterial embolization as therapy for patients with unresectable hepatocellular carcinoma. Eur J Surg Oncol 2007; 34:61-6. [PMID: 17434711 DOI: 10.1016/j.ejso.2007.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 02/09/2007] [Indexed: 10/23/2022] Open
Abstract
PURPOSE To evaluate the usefulness of transcatheter arterial embolization (TAE) followed by radiofrequency ablation (RFA) as combined treatment for unresectable hepatocellular carcinoma (HCC). PATIENTS AND METHODS Thirty-six consecutive patients (cirrhosis, Child-Pugh class A or B) with solitary or oligonodular HCC were treated (41 lesions; mean size, 58.9 mm; range, 30-120 mm). RFA was performed after one TAE treatment. Local efficacy was evaluated with multiphasic computed tomography (CT) performed an average of two months after RFA and once during later follow-up. RESULTS The mean follow-up period was 16 months (range, 2-45 months). Technical success (namely, complete tumor devascularization during the arterial phase) was achieved for 59% of lesions at the first CT evaluation and for 46% at the second evaluation. Among prognostic factors included in the analysis, only lesion diameter (< 50 mm versus > or = 50 mm) was statistically significant in terms of predicting local success (Fisher's exact test: 85% versus 43% at first CT, p<0.01; 70% versus 36% during follow-up, p=0.05). There were no major periprocedural complications. Kaplan-Meier analysis showed survival rates of 84% at 12 months and 57% at 24 months. CONCLUSIONS Combined therapy--TAE then RFA--for unresectable HCC lesions in patients with cirrhosis produces a relatively high complete local response rate compared with TAE or RFA alone. Our results, considered with those from other case series, may help design prospective, randomized clinical trials to test combination therapy versus single-modality therapy in terms of risks and benefits.
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Chen TW, Tsai CH, Chou SJ, Yu CY, Shih ML, Yu JC, Hsieh CB. Intrapericardial isolation of the inferior vena cava through a transdiaphragmatic pericardial window for tumor resection without sternotomy or thoracotomy. Eur J Surg Oncol 2007; 33:239-42. [PMID: 17174512 DOI: 10.1016/j.ejso.2006.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2006] [Accepted: 11/09/2006] [Indexed: 02/08/2023] Open
Abstract
AIMS The prognosis for patients with advanced tumors invading the inferior vena cava (IVC) is dismal and surgical treatments for these tumors are challenging. A surgical approach that avoids sternotomy and thoracotomy for tumors invading the IVC even to the level of the hepatocaval junction would be extremely helpful. METHODS The intrapericardial IVC was isolated via a transdiaphragmatic pericardial window using a transabdominal approach. Hepatectomy was then applied via an anterior approach until the IVC was seen. Total hepatic vascular exclusion was achieved by clamping the portal triad, intrapericardial IVC and infrahepatic IVC. We removed the primary tumor, the liver portion involved and the tumor thrombi, with segmental resection of the IVC. Vascular continuity was reestablished using a 20-mm-diameter polytetrafluoroethylene graft. RESULTS Four patients with tumors invading the IVC were treated with this method. All underwent gross en-bloc tumor resections and all survived. CONCLUSION This method for the resection of IVC tumors could avoid emboli dislodging from the tumor thrombi, prevent the complications of sternotomy, cardiopulmonary bypass and shorten operative times.
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Cheng YF, Huang TL, Chen TY, Concejero A, Tsang LLC, Wang CC, Wang SH, Sun CK, Lin CC, Liu YW, Yang CH, Yong CC, Ou SY, Yu CY, Chiu KW, Jawan B, Eng HL, Chen CL. Liver graft-to-recipient spleen size ratio as a novel predictor of portal hyperperfusion syndrome in living donor liver transplantation. Am J Transplant 2006; 6:2994-9. [PMID: 17061990 DOI: 10.1111/j.1600-6143.2006.01562.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Portal hyperperfusion in a small-size liver graft is one cause of posttransplant graft dysfunction. We retrospectively analyzed the potential risk factors predicting the development of portal hyperperfusion in 43 adult living donor liver transplantation recipients. The following were evaluated: age, body weight, native liver disease, spleen size, graft size, graft-to-recipient weight ratio (GRWR), total portal flow, recipient portal venous flow per 100 g graft weight (RPVF), graft-to-recipient spleen size ratio (GRSSR) and portosystemic shunting. Spleen size was directly proportional to the total portal flow (p = 0.001) and RPVF (p = 0.014). Graft hyperperfusion (RPVF flow > 250 mL/min/100 g graft) was seen in eight recipients. If the GRSSR was < 0.6, 5 of 11 cases were found to have graft hyperperfusion (p = 0.017). The presence of portosystemic shunting was significant in decreasing excessive RPVF (p = 0.059). A decrease in portal flow in the hyperperfused grafts was achieved by intraoperative splenic artery ligation or splenectomy. Spleen size is a major factor contributing to portal flow after transplant. The GRSSR is associated with posttransplant graft hyperperfusion at a ratio of < 0.6.
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