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Xi Y, Rocke DM. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics 2008; 9:324. [PMID: 18664284 PMCID: PMC2516527 DOI: 10.1186/1471-2105-9-324] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 07/29/2008] [Indexed: 11/14/2022] Open
Abstract
Background We propose a statistically principled baseline correction method, derived from a parametric smoothing model. It uses a score function to describe the key features of baseline distortion and constructs an optimal baseline curve to maximize it. The parameters are determined automatically by using LOWESS (locally weighted scatterplot smoothing) regression to estimate the noise variance. Results We tested this method on 1D NMR spectra with different forms of baseline distortions, and demonstrated that it is effective for both regular 1D NMR spectra and metabolomics spectra with over-crowded peaks. Conclusion Compared with the automatic baseline correction function in XWINNMR 3.5, the penalized smoothing method provides more accurate baseline correction for high-signal density metabolomics spectra.
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Xi Y, Bruheim S, Kudo K, Fodstad O, Ju J. Use of microRNAs expression profiles to classify the responsiveness of human osteosarcoma to doxorubicin, cisplatin, and ifosfamide. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.10515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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He Z, Hu Y, Feng L, Li Y, Liu G, Xi Y, Wen L, Lucia A. NRF-1 genotypes and endurance exercise capacity in young Chinese men. Br J Sports Med 2008; 42:361-6. [DOI: 10.1136/bjsm.2007.042945] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Xi Y, de Ropp JS, Viant MR, Woodruff DL, Yu P. Improved identification of metabolites in complex mixtures using HSQC NMR spectroscopy. Anal Chim Acta 2008; 614:127-33. [PMID: 18420042 DOI: 10.1016/j.aca.2008.03.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 02/13/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
Abstract
The automated and robust identification of metabolites in a complex biological sample remains one of the greatest challenges in metabolomics. In our experiments, HSQC carbon-proton correlation NMR data with a model that takes intensity information into account improves upon the identification of metabolites that was achieved using COSY proton-proton correlation NMR data with the binary model of [Y. Xi, J.S. de Ropp, M.R. Viant, D.L. Woodruff, P. Yu, Metabolomics, 2 (2006) 221-233]. In addition, using intensity information results in easier-to-interpret "grey areas" for cases where it is not clear if the compound might be present. We report on highly successful experiments that identify compounds in chemically defined mixtures as well as in biological samples, and compare our two-dimensional HSQC analyses against quantification of metabolites in the corresponding one-dimensional proton NMR spectra. We show that our approach successfully employs a fully automated algorithm for identifying the presence or absence of predefined compounds (held within a library) in biological HSQC spectra, and in addition calculates upper bounds on the compound intensities.
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He Z, Hu Y, Feng L, Bao D, Xi Y, Wen L, Lucia A. Relationship between TFAM Gene Polymorphisms and Endurance Capacity in Response to Training. Int J Sports Med 2007; 28:1059-64. [PMID: 17497594 DOI: 10.1055/s-2007-965064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aim of this study was to explore whether polymorphisms in mitochondrial transcription factor A ( TFAM) gene are associated with endurance capacity in a pretraining state (baseline) and/or in response to a supervised 18-wk endurance training (changes) in 102 young Chinese males (nonathletes). Phenotypes measured were running economy (RE) and V(.)O (2max). Genomic DNA was extracted from white blood cells and the genotypes were analyzed by PCR-RFLP in single nucleotide polymorphisms (SNP) rs1937, rs2306604 and rs1049432. Genotype distributions were in Hardy-Weinberg equilibrium at three loci (p > 0.05). When the three polymorphisms were considered together, three haplotypes were estimated, i.e., G (rs1937)-A (rs2306604)-G (rs1049432) (49 %), G (rs1937)-G (rs2306604)-G (rs1049432) (33 %) and C (rs1937)-G (rs2306604)-T (rs1049432) (18 %). SNPrs1937 and rs1049432 achieved near complete linkage disequilibrium (LD) (D' = 1 and r (2) = 0.903). We found no significant differences in baseline levels of V(.)O (2max) and RE between TFAM genotypes or haplotypes. Similarly, we found no differences for the training-induced changes of both variables. It was concluded that the three polymorphisms in TFAM gene rs1937, rs2306604 and rs1049432 do not predict endurance capacity/trainability, at least in Chinese males.
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Sun Y, Kong F, Ren S, Yuan F, Liang F, Liu N, Jin L, Xi Y. Severe acute graft-vs-host disease in a patient with acute monocytic leukemia having a recombination event between HLA-A/B loci from a multiple recombinant family. ACTA ACUST UNITED AC 2007; 70:499-505. [PMID: 17990988 DOI: 10.1111/j.1399-0039.2007.00953.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human leukocyte antigen (HLA) recombination, particularly multiple recombinations can produce novel haplotypes, thereby complicating donor-recipient selection and possibly inducing severe graft-vs-host disease (GVHD) after nonfully matched allogeneic hematopoietic stem cell transplantation. Here, we report for the first time that a 30-year-old female acute monocytic leukemia patient with an HLA-A/B recombinant haplotype, who has three unmatched and one HLA-B/DRB1 recombinant haplotype siblings, presented grade IV acute GVHD (aGVHD) after transplantation from a sibling with a single allele only mismatch at the classical HLA-A locus. Furthermore, using a new three-dimensional structure modeling application, we inferred that the structural differences in peptide-binding and T-cell receptor interaction sites can significantly change the immunogenicity of mismatched HLA molecules, potentially one of the main causes of aGVHD.
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Gao L, Sun Y, Chen C, Xi Y, Wang J, Wang Z. Primary mechanism of apoptosis induction in a leukemia cell line by fraction FA-2-b-ß prepared from the mushroom Agaricus blazei Murill. Braz J Med Biol Res 2007; 40:1545-55. [DOI: 10.1590/s0100-879x2007001100015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 08/06/2007] [Indexed: 11/22/2022] Open
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He Z, Hu Y, Feng L, Lu Y, Liu G, Xi Y, Wen L, McNaughton LR. NRF2 Genotype Improves Endurance Capacity in Response to Training. Int J Sports Med 2007; 28:717-21. [PMID: 17357964 DOI: 10.1055/s-2007-964913] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aim of this work was to examine the association between the polymorphisms in nuclear respiratory factor (NRF2) gene and endurance capacity measured prior to and after an 18-wk endurance training program in young Chinese men. The phenotypes measured were running economy (RE) and VO(2max). The RE was determined by measuring submaximal VO(2) for 5 min at a constant running speed of 12 km x h (-1) and VO(2max) was measured during an incremental test to volitional exhaustion. Genomic DNA was extracted from white cells of peripheral blood and the genotypes were examined in SNPrs12594956, rs8031031 and rs7181866 by PCR-RFLP. Genotype distributions were in Hardy-Weinberg equilibrium at three loci, and linkage disequilibrium was observed (LD D' = 1 and r (2) = 0.903) between rs8031031 and rs7181866. The VO(2max) was associated with rs12594956 at baseline while the training response of VO(2) at RE, was associated with rs12594956, rs8031031 and rs7181866. When the three SNPs were considered together, those carrying the ATG haplotype had 57.5 % higher training response in VO(2) at RE (p = 0.006) than non-carriers. In conclusion, polymorphisms in NRF2 gene may explain some of the between-person variance in endurance capacity.
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Fodstad O, Xi Y, Risberg K, Ju J, Anderson YG. Synergistic antitumor efficacy and altered gene expression signature in breast cancer cells treated with immunotoxins and cyclosporin A. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.13505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
13505 Background: Immunotoxins (ITs) has shown limited clinical success related to liver toxicity and development of anti-IT antibodies. To delay the immune response we tested combinations of ITs and the Cyclosporin A (CsA). we have shown that one IT, currently in a phase I/II clinical trial, acts by inducing apoptosis and protein synthesis inhibition, but gene expression analysis of IT treated cells has never been reported. Hence, we also studied changes in gene expression induced by ITs alone and the effects of adding (CsA) on both treatment efficacy and gene expression signature. Methods: Human MA-11 breast cancer cells were treated in vitro with antiEGFR- and antiEPCAM-based ITs alone and in combinations with CsA. Therapeutic efficay was assessed by MTS cell viability assay. Total RNA from untreated and treated cells was isolated and CodeLink Uniset Human 20 k Oligo Bioarray (GE Healthcare, Amersham Biosciences, NJ), containing approximately 20,289 gene probes, was used to generate gene expression profiles. Gene expression analysis was carried out using GeneSpring software version 7.2 using One-way ANOVA with p<0.05. Comparisons of gene list across different groups were performed using Venn Diagrams. Results: Combination therapy produced remarkable synergistic effects in MA-11 cells in vitro and in metastasis models in vivo. Moreover, in conventional rats receiving repeated injections of ITs and CsA the formation of anti-IT antibodies was virtually abrogated. Changes in gene expression profiles induced by the ITs alone and in combination with CsA were evaluated to elucidate the underlying molecular mechanisms for the synergistic effects. The ITs each induced specific changes in expression of some apoptosis-related genes but also fogenes in pathways unrelated to apoptosis and protein synthesis. The addition of CsA induced up- or down-regulation of a number of interesting non-immune-associated genes Conclusions: Important shortcomings for successful clinical use of ITs may be overcome by combination therapy with CsA. The possibility for further improvement is provided by results of gene profiling studies identifying therapy-induced genes belonging to different cell signaling pathways. No significant financial relationships to disclose.
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He Z, Hu Y, Feng L, Bao D, Wang L, Li Y, Wang J, Liu G, Xi Y, Wen L, Lucia A. Is there an association between PPARGC1A genotypes and endurance capacity in Chinese men? Scand J Med Sci Sports 2007; 18:195-204. [PMID: 17490458 DOI: 10.1111/j.1600-0838.2007.00648.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our purpose was to determine the possible association between genotypes of three polymorphisms (Gly482Ser, Thr394Thr and A2962G) of the peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) gene, on one hand, and both the pre- (baseline) and post-training levels of maximal (i.e., maximal oxygen uptake [VO2max]) and submaximal human endurance capacity (i.e., running economy [RE]). We studied 102 young males (physically active, non-athletes; age: 19+/-1 yrs) from Northern China (of Han origin) who underwent a 18-week endurance training (running) program and were tested on a treadmill (for VO2max and RE determination) before and after training. None of the VO2max and RE related traits were associated with the Gly482Ser and Thr394Thr polymorphisms at baseline or after training. The A2962G polymorphism was however associated with VO2max at baseline, as carriers of the G allele (AG+GG genotypes; n=49) had higher levels of VO2max than the AA group (n=53) (58.2+/-4.3 vs 56.3+/-3.9 mL/kg/min; P=0.017). Our results do not support previous data on Caucasians showing an association between the Gly482Ser variant and VO2max but suggest the potential role of another polymorphism (A2962G) to explain individual VO2max differences in Chinese men.
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Zhang J, Xi Y, Li J. The relationships between environment and plant communities in the middle part of Taihang Mountain Range, North China. COMMUNITY ECOL 2006. [DOI: 10.1556/comec.7.2006.2.3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sun Y, Liu S, Luo Y, Liang F, Xi Y. Identification and frequency of a novel HLA-A allele, A*110104. ACTA ACUST UNITED AC 2006; 68:453-4. [PMID: 17092262 DOI: 10.1111/j.1399-0039.2006.00687.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhou DQ, Hu Y, Liu G, Gong L, Xi Y, Wen L. Muscle-specific creatine kinase gene polymorphism and running economy responses to an 18-week 5000-m training programme. Br J Sports Med 2006; 40:988-91. [PMID: 17000714 PMCID: PMC2577470 DOI: 10.1136/bjsm.2006.029744] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To investigate the association between muscle-specific creatine kinase (CKMM) gene polymorphism and the effects of endurance training on running economy. METHODS 102 biologically unrelated male volunteers from northern China performed a 5000-m running programme, with an intensity of 95-105% ventilatory threshold. The protocol was undertaken three times per week and lasted for 18 weeks. Running economy indexes were determined by making the participants run on a treadmill before and after the protocol, and the A/G polymorphism in the 3' untranslated region of CKMM was detected by polymerase chain reaction-restricted fragment length polymorphism (NcoI restriction enzyme). RESULTS Three expected genotypes for CKMM-NcoI (AA, AG and GG) were observed in the participants. After training, all running economy indexes declined markedly. Change in steady-state consumption of oxygen, change in steady-state consumption of oxygen by mean body weight, change in steady-state consumption of oxygen by mean lean body weight and change in ventilatory volume in AG groups were larger than those in AA and GG groups. CONCLUSIONS The findings indicate that the CKMM gene polymorphism may contribute to individual running economy responses to endurance training.
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He Z, Hu Y, Feng L, Lu Y, Liu G, Xi Y, Wen L, Xu X, Xu K. Polymorphisms in the HBB gene relate to individual cardiorespiratory adaptation in response to endurance training. Br J Sports Med 2006; 40:998-1002. [PMID: 16990440 PMCID: PMC2577474 DOI: 10.1136/bjsm.2006.030866] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE The crucial role of haemoglobin in endurance performance has been well documented. We examined whether polymorphisms in the HBB gene modified aerobic capacity. METHODS 102 recruits were trained by running 5000 m three times per week for 18 weeks. Exercise intensity progressively increased from an initial heart rate corresponding to 95% of the individual baseline ventilatory threshold during the first 10 weeks to 105% during the last 8 weeks. The phenotypes measured were running economy and VO(2)max. Running economy was determined by measuring submaximal VO(2) for 5 min at a constant running speed of 12 km.h(-1) and VO(2)max was obtained during an incremental test to exhaustion. Genomic DNA was extracted from white cells of peripheral blood and the -551C/T, intron2,+16C/G and +340 A/T genotypes were examined relative to the TAA site variants by PCR-RFLP. RESULTS Genotype distributions were in Hardy-Weinberg equilibrium at three loci. None of the running economy and VO(2)max-related traits were associated with the three polymorphisms or haplotypes at baseline, while the training response of running economy was associated with -551C/T and intron2,+16C/G polymorphisms. Subjects homozygous for intron2,+16C/C or -551C/C had decreased oxygen cost of running compared to the other individuals. DISCUSSION It was concluded that the -551C/C or intron2,+16C/C genotype might explain part of the individual variation in the cardiorespiratory adaptation to endurance training.
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Nakajima G, Uchida K, Hayashi K, Xi Y, Takasaki K, Ju J. Non-coding microRNA hsa-let-7g as a novel chemoresponse biomarker for S-1 in colon cancer. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
13513 Background: MicroRNAs (miRNAs) are small non-cording RNAs (∼ 22 nucleotide) that regulate gene expression by suppressing their target mRNAs at post-transcriptional level. Previous studies from our group have identified a number of dis-regulated miRNAs due to the loss of p53 tumor suppressor in cancer cell lines. As part of the efforts to further investigate the in vivo biological significance of these miRNAs, the expression of both hsa-let-7g and hsa-miR-200c were investigated using formalin-fixed paraffin embedded (FFPE) colon cancer specimens to evaluate the potential correlation with chemosensitivity and tumorigenesis. Methods: Forty-six patients with recurrent or residual colon cancer lesion assessable were treated with 5-FU based antimetabolite S-1. This includes twenty-one pair of tumor and normal samples. Total RNAs were isolated from these samples FFPE specimens (contains either > 90% normal or > 90% tumor tissue). cDNAs were synthesized using primers specific for hsa-let-7g, hsa-miR-200c and internal control 5S. The expression levels of each particular miRNAs were quantified using real time qRT-PCR analysis. The expression level of each miRNAs was quantified by measuring the difference of threshold cycle (CT) of candidate miRNAs and internal control 5S (Δ-CT). Results: The expression level of hsa-let-7g was significantly higher in tumor tissues compare to normal tissues (p=0.0026; Wilcoxon test). In the forty-six tumor tissues, the expression level of hsa-let-7g in disease response group (patients group of complete response, partial response and no change after chemotherapy) was significantly lower than the disease progression group (p=0.03; Mann-Whitney test). The expression of hsa-miR-200c was significantly over-expressed in tumor tissues compare to normal tissues (p=0.0001; Wilcoxon test). Although hsa-let-7g is strongly associated with patient’s response to S-1 treatment, it is not a prognostic factor for predicting survival. Conclusion: hsa-let-7g and hsa-miR-200c may be associated with tumorigenesis in colon cancer. In addition, hsa-let-7g may be a significant indicator for chemoresponse to S-1 based chemotherapy. No significant financial relationships to disclose.
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Bruheim S, Xi Y, Ju J, Fodstad O. Chemo-response biomarker discovery via expression profiling using soft-tissue sarcoma xenografts. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.9569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9569 Background: Soft-tissue sarcoma (STS) constitute a heterogeneous group of tumours of mesenchymal origin. Whereas the mainstay of treatment has been surgery and radiation, these tumours are generally considered as quite chemoresistant. However, it is well known that subgroups of patients benefit from chemotherapy. Markers that could predict drug response would therefore be beneficial for the management of this malignancy. We have previously established panel of 17 unique human soft tissue xenografts, representing 7 different histological subgroups and assessed their responsiveness to doxorubicin, ifosfamide, etoposide, and cisplatin. We wanted to utilize these xenografts as a model system to discover for novel candidate marker genes for STS chemo-response. Methods: GE Uniset Human 20K microarrays were used to obtain gene expression profiles from the each xenografts. One-way ANOVA test with a Benjamini-Hochberg multiple test correction allowing a false discovery rate of 5% was used to identify genes with significantly differential expression. Results: Doxorubicin, ifosfamide, etoposide and cisplatin were efficient in 6/17, 10/17, 1/17 and 7/17 xenografts respectively. However, in the expression profiles obtained none of the genes showed significantly correlation with chemo-responsiveness to any of the drugs. Two of the xenografts, TAX 1 and TAX 2, both originate from a malignant fibrous histiocytoma (MFH) in the same patient, but show strikingly different sensitivity to ifosfamide (TAX1 resistant, TAX2 sensitive). When triplicate hybridizations of TAX1 and 2 were compared, 294 genes met the above criteria. In addition we identified a subset of 122 genes that were flagged absent in one of the specimens, present in the other. Among genes with an already described role in mediating drug resistance are GST-pi and glutathione peroxidase. Taken together, these results indicate that discovery of general response markers in STSs may be difficult due to the heterogeneity of the different subgroups constituting this malignancy. Conclusions: Gene expression profiling of the TAX 1 and TAX 2 xenografts revealed a number of interesting candidate marker genes for ifosfamide sensitivity of MFH. This list of genes will be further refined by validation in clinical samples. No significant financial relationships to disclose.
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Ju J, Formentini A, Nakajima G, Kornmann M, Xi Y. MBD4 and SEI1 as new prognostic markers in colorectal cancer patients receiving adjuvant 5-fluorouracil. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.20085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
20085 Background: Previous studies from our laboratory have identified a number of marker genes associated with chemosensitivity to 5-fluorouracil (5-FU). In this study, the in vivo significance of several marker genes in terms of prognostic potential were evaluated using colorectal cancer patient samples treated with 5-FU based therapy. Eight marker genes were selected based on their functional roles and significant fold changes in expression. They are SERTA domain containing 1(SEI1), Ribonucleotide reductase M2 polypeptide (RRM2), Origin recognition complex, subunit 6 homolog-like (ORC6L), Eukaryotic translation initiation factor 4E (EIF4E), Thymidylate Synthase (TS), SET and MYND domain containing 3 (SMYD3), Dickkopf homolog 4 (DKK4) and Methyl-CpG binding domain protein 4 (MBD4). Methods: Forty eight snap frozen clinical colorectal samples (24 normal and 24 paired colorectal cancer patient samples) were selected with detailed clinical follow-up information. cDNAs were synthesized and the expression levels of marker genes were quantified via qRT-PCR analysis. The statistical significance of these markers for disease prognosis was evaluated using two tailed paired T-test. Kaplan-Meier survival curve was generated and analyzed by Logrank test. Results: Based on the quantitative expression analysis, RRM2 (p = 0.0001, 95% CI, 2.0 to 4.5), ORC6L (p = 0.0001, 95% CI, 1.8 to 4.6), EIF4E (p = 0.0002, 95% CI, 0.3 to 0.9), TS (p = 0.0005, 95% CI, 0.7 to 2.2) and SMYD3 (p = 0.0001, 95% CI, 0.8 to 1.5) was over-expressed in tumor tissues. However, the expression of SEI1 was decreased in tumors (p = 0.02, 95% CI, 0.1 to 1.3), consistent with the function of SEI1 as a potential tumor suppressor. Kaplan-Meier survival analysis indicated that MBD4 is a significant prognostic factor for patient’s survival (p = 0.03). MBD4 was a key protein involved in DNA methylation. The expression of TS was associated with tumor stage as it had significant higher expression level in UICC stage I and II compared to stage IV patients (p = 0.03). Conclusion: MBD4 may be potential novel prognostic markers for predicting patient survival for colorectal cancer. No significant financial relationships to disclose.
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Xi Y, Formentini A, Kornmann M, Ju J. Noncoding miRNAs as novel prognostic factor for 5-fluorouracil adjuvant therapy in colorectal cancer. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.3609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3609 Background: The roles of non-coding miRNAs in tumorgenesis are just emerging. miRNAs regulate gene expression at post-transcriptional level by influencing translation efficiency of their target mRNAs. Previous studies from our laboratory have identified a number of miRNAs that were dis-regulated in colon cancer cell lines related to the loss of p53 tumor suppressor gene. In this study, the in vivo significance of some of these miRNAs was further evaluated using clinical samples. Ten miRNAs (hsa-let-7b, hsa-let-7g, hsa-miR-15b, hsa-miR-181b, hsa-miR-191, hsa-miR-200c, hsa-miR-26a, hsa-miR-27a, hsa-miR-30a-5p and hsa-miR-30c) were evaluated for their potential prognostic value in colorectal cancer patients receiving 5-fluorouracil (5-FU) based therapy. Methods: Forty eight snap frozen clinical colorectal samples (24 normal and 24 paired colorectal cancer patient samples) were selected with detailed clinical follow-up information. RNAs were isolated from these samples using TRIzol reagent. After cDNA synthesis with miRNA specific primers, the expression levels of 10 miRNAs were quantified via qRT-PCR analysis. The statistical significance of these markers for disease prognosis was evaluated using two tailed paired T-test. Kaplan-Meier survival curve was generated and followed by Logrank test. Result: Among the ten miRNAs, hsa-miR-15b (p=0.02), hsa-miR-181b (p=0.01), hsa-miR-191 (p=0.03) and hsa-miR-200c (p=0.005) were significantly over-expressed in tumors compared to normal colorectal samples. Kaplan-Meier survival analysis indicates that hsa-miR-200c was a significant prognostic marker for predicting patient’s survival (p=0.01). The patients (n=15) with higher hsa-miR-200c expression had shorter survival interval (median survival = 26 months) compared to patients (n=9) with lower expression (median survival = 38 months). Conclusions: Some of these miRNAs may function as oncogenes due to their over-expression in tumors. Hsa-miR-200c may be a potential novel prognostic factor for 5-FU based chemotherapy in colorectal cancer. No significant financial relationships to disclose.
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Bruheim S, Xi Y, Nakajima G, Ju J, Fodstad O. Gene expression profiles classifies the responsiveness of human osteosarcoma to doxorubicin, cisplatin and ifosfamide. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.9534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9534 Background: Despite the increased survival rates of osteosarcoma patients attributed to adjuvant chemotherapy, at least one third of the patients still succumb to their disease. Furthermore, ultra-aggressive combination chemotherapy is associated with considerable acute and long term toxicity. This is of particular concern in patients who may be cured by a simpler and less toxic regimens or do not have micrometastatic disease. Hence, further improvements in the management of osteosarcoma seemingly depend on diagnostic and prognostic tools that may allow for a more risk adapted and individualized treatment. Methods: We have used GE Uniset Human 20K microarrays to obtain gene expression profiles from a panel of ten unique human osteosarcoma xenografts. For each of the three drugs doxorubicin, cisplatin or ifosfamide the xenografts were grouped according to their response to chemotherapy, resistant, weakly sensitive or sensitive. For each individual drug, a one-way ANOVA test with a Benjamini and Hochberg multiple test correction allowing a false discovery rate of 5% (doxorubicin, cisplatin) or 2% (ifosfamide) was used to identify genes with significantly differential expression. In addition a 2-fold cut off was applied to exclude smaller but yet significant differences. Results: For doxorubicin and cisplatin, respectively 59 and 120 genes met these criteria. The expression levels of 25 genes overlapped between these two groups. For ifosfamide, 148 genes were selected, for 5 of them the expression overlapped with cisplatin sensitivity related genes. In the lists, genes involved in mediating and regulating apoptosis were abundant, such as regulators of TGF signaling, ubiquitin mediated protein degradation and members of the immediate early response protein family. Several genes which products interact with components of the cytoskeleton were also identified. Conclusion: We have used a unique strategy to screen for potential chemosensitivity markers by utilizing xenografts as training sets. No significant financial relationships to disclose.
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Xi Y, Nakajima G, Chu E, Ju J. Systematic analysis of both steady state and actively translated mRNA transcripts regulated by thymidylate synthase and 5-FU treatment in human colon cancer. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.2034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ju J, Xi Y, Fodstad O, Bruheim S. Prediction of the response of human osteosarcoma xenografts to chemotherapy via gene expression profiling. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.9521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Huang Y, Tang R, Dai J, Gu S, Zhao W, Cheng C, Xu M, Zhou Z, Ying K, Xi Y, Mao Y. A novel human hydroxysteroid dehydrogenase like 1 gene (HSDL1) is highly expressed in reproductive tissues. Mol Biol Rep 2002; 28:185-91. [PMID: 12153137 DOI: 10.1023/a:1015726217890] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report the cloning and characterization of a novel human hydroxysteroid dehydrogenase like gene (HSDL1) located on human chromosome 16q24.2. The HSDL1 cDNA is 3407 base pair in length, encoding a 309 amino acid polypeptide related to human 17beta-HSD3. Northern blot reveals that the HSDL1 is highly expressed in testis and ovary. In situ hybridization indicates that the expression of HSDL1 is predominantly increased in the prostate cancer tissue compared with the normal prostate tissue, which suggests that the gene expression is important to the arising of prostate cancer.
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173
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Kacena MA, Merrel GA, Konda SR, Wilson KM, Xi Y, Horowitz MC. Inflammation and bony changes at the temporomandibular joint. Cells Tissues Organs 2001; 169:257-64. [PMID: 11455121 DOI: 10.1159/000047889] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cytokines help mediate the acute and chronic inflammation and associated destruction of connective tissue in arthritic temporomandibular joints (TMJ). The proinflammatory cytokines TNFalpha, IL-1beta, IL-6, IL-8, and IFN-gamma are associated with inflammation in synovial joints and connective tissue destruction. Therefore, the increased levels of these cytokines in the synovial fluid of temporomandibular disorder (TMD) patients would be expected. Conversely, IL-1ra and IL-10 acts as inhibitors to these proinflammatory cytokines. Thus, in TMD patients, low levels of IL-1ra and IL-10 might be expected. A review of studies from multiple investigators confirms that proinflammatory cytokine levels increase in TMD patients, IL-1ra levels are also increased, and IL-10 levels remain unchanged. Because IL-10 can inhibit TNFalpha, IL-1, IL-6, and IL-8, the lack of IL-10 in the TMJ in the face of the other studies showing increases in TNFalpha, IL-1beta, IL-6, and IL-8 could partially explain the exacerbation of the associated osteoarthritis. In addition, although IL-1ra levels are elevated in most of the TMD patients, the increases do not appear to be sufficient to inhibit the inflammation and connective tissue degradation associated with IL-1beta. Thus, it appears that treatment of TMD requires a delicate balance between proinflammatory cytokines and cytokine inhibitors such as IL-1ra and IL-10.
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Horowitz MC, Xi Y, Wilson K, Kacena MA. Control of osteoclastogenesis and bone resorption by members of the TNF family of receptors and ligands. Cytokine Growth Factor Rev 2001; 12:9-18. [PMID: 11312114 DOI: 10.1016/s1359-6101(00)00030-7] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Skeletal mass is maintained by a balance between cells which resorb bone (osteoclasts) and cells which form bone (osteoblasts). Bone development and growth is an on-going, life-long process. Bone is formed during embryonic life, grows rapidly through childhood, and peaks around 20 years of age (formation exceeds resorption). For humans the skeleton then enters a long period, approximately 40 years, when bone mass remains relatively stable. Skeletal turnover continues but the net effect of resorption and formation on bone mass is zero. For women this ends when they enter menopause and similar bone loss occurs for men, but later in life. These opposite functions are coupled, resorption precedes formation, and osteoblasts, or their precursors, stromal cells, regulate osteoclast formation and activity. Until recently, the molecular nature of this regulation, was poorly understood. However, recent observations have identified members of the TNF family of ligands and receptors as critical regulators of osteoclastogenesis. Osteoprotegerin (OPG) a decoy receptor was first identified. Its ligand, receptor activator of nuclear factor-kappaB ligand (RANKL), was quickly found, and shown to be expressed on stromal cells and osteoblasts. Its cognate receptor, RANK, was found to be expressed in high levels on osteoclast precursors. The interaction between RANKL and RANK was shown to be required for osteoclast formation. These observations have provided a molecular understanding of the coupling between osteoclastic bone resorption and osteoblastic bone formation. Moreover, they provide a framework on which to base a clear understanding of normal (e.g. postmenopausal osteoporosis and age associated bone loss) and pathologic skeletal changes (e.g. osteopetrosis, glucocorticoid-induced osteoporosis, periodontal disease, bone metastases, Paget's disease, hyperparathyroidism, and rheumatoid arthritis).
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Meng X, Cheng Q, Xi Y. [Retrospective analysis of endometrial neoplasms treated by different therapeutic modalities]. ZHONGHUA FU CHAN KE ZA ZHI 2001; 36:153-5. [PMID: 11783391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To compare the therapeutic effects of different remedies in patients with endometrial carcinoma. METHODS Total of 386 patients with metracarcinoma underwent 3 different treatments: (1) operation only 145 cases; (2) operation and complemental radiotherapy 161 cases; (3) radiotherapy only 80 cases. Then they were followed up for 5 years and more. RESULTS The 5-year survival rates of operation group were 78.9% (56/71), 61.0% (25/41) and 18.2% (6/33) in stage I, stage II, and stage III-IV respectively, for operation and complemental radiotherapy, they were 75.0% (33/44), 59.5% (44/74) and 48.8% (21/43), for radiotherapy, 34.8% (8/23), 18.8% (3/16) and 0.0% (0/41). There was no difference between operation group and operation plus radiotherapy in patients with stage I and stage II (P > 0.05). However the 5-year survival rates were significantly higher in operation plus complemental radiotherapy group and those only received operation in stage III stage IV patients (P < 0.001). And no matter in what stages, the therapeutic effect was worse in radiotherapy group than other two groups (P < 0.001). CONCLUSION The remedies with operation as main measure are the best choice for metacarcinoma, radiotherapy merely is fit with those who can not be operated on.
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