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Articles by J Luo
Total Records ( 6 ) for J Luo
  C Cheng , K Shen , C Song , J Luo and G. C. Tseng
 

Motivation: Reproducibility analyses of biologically relevant microarray studies have mostly focused on overlap of detected biomarkers or correlation of differential expression evidences across studies. For clinical utility, direct inter-study prediction (i.e. to establish a prediction model in one study and apply to another) for disease diagnosis or prognosis prediction is more important. Normalization plays a key role for such a task. Traditionally, sample-wise normalization has been a standard for inter-array and inter-study normalization. For gene-wise normalization, it has been implemented for intra-study or inter-study predictions in a few papers while its rationale, strategy and effect remain unexplored.

Results: In this article, we investigate the effect of gene-wise normalization in microarray inter-study prediction. Gene-specific intensity discrepancies across studies are commonly found even after proper sample-wise normalization. We explore the rationale and necessity of gene-wise normalization. We also show that the ratio of sample sizes in normal versus diseased groups can greatly affect the performance of gene-wise normalization and an analytical method is developed to adjust for the imbalanced ratio effect. Both simulation results and applications to three lung cancer and two prostate cancer data sets, considering both binary classification and survival risk predictions, showed significant and robust improvement of the new adjustment. A calibration scheme is developed to apply the ratio-adjusted gene-wise normalization for prospective clinical trials. The number of calibration samples needed is estimated from existing studies and suggested for future applications. The result has important implication to the translational research of microarray as a practical disease diagnosis and prognosis prediction tool.

  J. S Barnholtz Sloan , P. B Shetty , X Guan , S. J Nyante , J Luo , D. J Brennan and R. C. Millikan
 

Twenty-nine single-nucleotide polymorphisms (SNPs) from previously published genome-wide association studies (GWAS) and multiple ancestry informative markers were genotyped in the Carolina Breast Cancer Study (CBCS) (742 African-American (AA) cases, 1230 White cases; 658 AA controls, 1118 White controls). In the entire study population, 9/10 SNPs in fibroblast growth factor receptor 2 (FGFR2) were significantly associated with breast cancer after adjusting for age, race and European ancestry [odds ratios (OR) range 1.17–1.81]. Associations were observed for SNPs in FGFR2, LSP1, H19, TLR1/TLR6 and RELN for AA; FGFR2, TNRC9, H19 and MAP3K1 for Whites; FGFR2, TNRC9, Msc5A1 and chromosome 8q for women ≥50 years old and FGFR2 and TNRC9 for women <50 years old. FGFR2 haplotypes based upon rs11200014, rs2981579, rs1219648 and rs2420946 were associated with increased risk of breast cancer, including the GTGT haplotype in AAs [OR = 1.27, 95% confidence interval (CI) 1.04–1.56] and younger women of either race [OR = 1.35, 95% CI 1.02–1.78) and the ATGT haplotype in Whites (OR = 1.30, 95% CI 1.15–1.46). Recent GWAS hits for breast cancer in Europeans and Whites (i.e. women of European descent) thus showed evidence of replication among AAs and Whites in the CBCS. Several new haplotypes were associated with breast cancer in AA and younger women, particularly the FGFR2 GTGT haplotype. These results highlight the need to conduct GWAS among younger women and in a variety of racial–ethnic populations.

  Y Dong , B Lu , X Zhang , J Zhang , L Lai , D Li , Y Wu , Y Song , J Luo , X Pang , Z Yi and M. Liu
 

Cucurbitacin E (CuE, -elaterin), a tetracyclic triterpenes compound from folk traditional Chinese medicine plants, has been shown to inhibit cancer cell growth, inflammatory response and bilirubin–albumin binding. However, the effects of CuE on tumor angiogenesis and its potential molecular mechanism are still unknown. Here, we demonstrated that CuE significantly inhibited human umbilical vascular endothelial cell (HUVEC) proliferation, migration and tubulogenesis in vitro and blocked angiogenesis in chick embryo chorioallantoic membrane assay and mouse corneal angiogenesis model in vivo. Furthermore, we found that CuE remarkably induced HUVEC apoptosis, inhibited tumor angiogenesis and suppressed human prostate tumor growth in xenograft tumor model. Finally, we showed that CuE blocked vascular endothelial growth factor receptor (VEGFR) 2-mediated Janus kinase (Jak) 2–signal transducer and activator of transcription (STAT) 3 signaling pathway in endothelial cells and suppressed the downstream protein kinases, such as extracellular signal-regulated kinase and p38 mitogen-activated protein kinases. Therefore, our studies provided the first evidence that CuE inhibited tumor angiogenesis by inhibiting VEGFR2-mediated Jak–STAT3 and mitogen-activated protein kinases signaling pathways and CuE is a potential candidate in angiogenesis-related disease therapy.

  P Wang , J Liu , Y Li , S Wu , J Luo , H Yang , R Subbiah , J Chatham , O Zhelyabovska and Q. Yang
 

Rationale: Peroxisome proliferator-activated receptors (PPARs) (, , and /β) are nuclear hormone receptors and ligand-activated transcription factors that serve as key determinants of myocardial fatty acid metabolism. Long-term cardiomyocyte-restricted PPAR deficiency in mice leads to depressed myocardial fatty acid oxidation, bioenergetics, and premature death with lipotoxic cardiomyopathy.

Objective: To explore the essential role of PPAR in the adult heart.

Methods and Results: We investigated the consequences of inducible short-term PPAR knockout in the adult mouse heart. In addition to a substantial transcriptional downregulation of lipid metabolic proteins, short-term PPAR knockout in the adult mouse heart attenuated cardiac expression of both Cu/Zn superoxide dismutase and manganese superoxide dismutase, leading to increased oxidative damage to the heart. Moreover, expression of key mitochondrial biogenesis determinants such as PPAR coactivator-1 were substantially decreased in the short-term PPAR deficient heart, concomitant with a decreased mitochondrial DNA copy number. Rates of palmitate and glucose oxidation were markedly depressed in cardiomyocytes of PPAR knockout hearts. Consequently, PPAR deficiency in the adult heart led to depressed cardiac performance and cardiac hypertrophy.

Conclusions: PPAR is an essential regulator of cardiac mitochondrial protection and biogenesis and PPAR activation can be a potential therapeutic target for cardiac disorders.

  S Lu , Y. M Xie , X Li , J Luo , X. Q Shi , X Hong , Y. H Pan and X. Ma
 

TH2B, an important testis histone, plays a key role in remodeling chromatin structure during spermatogenesis. We present a detailed study of post-translational modifications (PTMs) of histone TH2B from different developmental stages of sperm cells, using a combination of high performance liquid chromatography, enzymatic Glu-c digestions of peptides, liquid chromatography–mass spectrometry (LC–MS) and LC–MS/MS analysis. The results showed modification patterns of the intact histone TH2B during spermatogenesis. Acetylated TH2B was most abundant in spermatogonia (28.9%) when compared with the spermatocytes (8.3%) and round spermatids (11.2%). Several new PTMs of TH2B were identified. In spermatogonia, spermatocytes and round spermatids, T116 and K117, were modified by phosphorylation and methylation, respectively, forming a novel ‘phospho switch’ site. The identified modification patterns of histone TH2B in spermatogenic cells provides a basis for future studies on histone coding and epigenetic regulation during spermatogenesis.

  S. J Wu , J Luo , K. T O'Neil , J Kang , E. R Lacy , G Canziani , A Baker , M Huang , Q. M Tang , T. S Raju , S. A Jacobs , A Teplyakov , G. L Gilliland and Y. Feng
 

Protein aggregation is of great concern to pharmaceutical formulations and has been implicated in several diseases. We engineered an anti-IL-13 monoclonal antibody CNTO607 for improved solubility. Three structure-based engineering approaches were employed in this study: (i) modifying the isoelectric point (pI), (ii) decreasing the overall surface hydrophobicity and (iii) re-introducing an N-linked carbohydrate moiety within a complementarity-determining region (CDR) sequence. A mutant was identified with a modified pI that had a 2-fold improvement in solubility while retaining the binding affinity to IL-13. Several mutants with decreased overall surface hydrophobicity also showed moderately improved solubility while maintaining a similar antigen affinity. Structural studies combined with mutagenesis data identified an aggregation ‘hot spot’ in heavy-chain CDR3 (H-CDR3) that contains three residues (99FHW100a). The same residues, however, were found to be essential for high affinity binding to IL-13. On the basis of the spatial proximity and germline sequence, we reintroduced the consensus N-glycosylation site in H-CDR2 which was found in the original antibody, anticipating that the carbohydrate moiety would shield the aggregation ‘hot spot’ in H-CDR3 while not interfering with antigen binding. Peptide mapping and mass spectrometric analysis revealed that the N-glycosylation site was generally occupied. This variant showed greatly improved solubility and bound to IL-13 with affinity similar to CNTO607 without the N-linked carbohydrate. All three engineering approaches led to improved solubility and adding an N-linked carbohydrate to the CDR was the most effective route for enhancing the solubility of CNTO607.

 
 
 
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