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1.  Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease 
Nature genetics  2012;44(8):890-894.
We performed a meta-analysis of 2 genome-wide association studies of coronary artery disease comprising 1,515 cases with coronary artery disease and 5,019 controls, followed by de novo replication studies in 15,460 cases and 11,472 controls, all of Chinese Han descent. We successfully identified four new loci for coronary artery disease reaching genome-wide significance (P < 5 × 10−8), which mapped in or near TTC32-WDR35, GUCY1A3, C6orf10-BTNL2 and ATP2B1. We also replicated four loci previously identified in European populations (PHACTR1, TCF21, CDKN2A/B and C12orf51). These findings provide new insights into biological pathways for the susceptibility of coronary artery disease in Chinese Han population.
PMCID: PMC3927410  PMID: 22751097
2.  Moth-eaten alopecia: a sign of secondary syphilis 
PMCID: PMC3537782  PMID: 22761476
3.  Predictors of Organ Damage in Systemic Lupus Erythematosus: the Hopkins’ Lupus Cohort 
Arthritis and rheumatism  2012;64(12):4021-4028.
The SLICC/ACR Damage Index (SDI) is the accepted measure of permanent organ damage in SLE. We analyzed data from a large SLE cohort to identify variables associated with rates of damage accrual as measured by the SDI.
2054 SLE patients (92% female, 56% Caucasian, 37% African-American, mean age at diagnosis 33 years) were included. The SDI was calculated retrospectively at the time of cohort entry, and prospectively during follow-up. The relationships between time-invariant patient characteristics and rates of damage accrual were assessed based on the damage score at last available follow-up. The relationships between time-varying patient characteristics and damage accrual were assessed based on the timing of damage accrual during cohort participation..
Overall, the SDI increased at a rate of 0.13 per year. Higher rates of damage were observed for those who were older, male, African American, low income, low education, hypertensive, had lupus anticoagulant, or who had proteinuria. During follow-up, the risk of damage was higher for those who were older with more disease activity, low complement, anti-dsDNA, satisfied more ACR-11 criteria, and using corticosteroids. Lower risk was observed among those using hydroxychloroquine. After adjustment for other variables, age, hypertension, and use of corticosteroids emerged as the most important predictors of damage accrual.
Rates of damage vary in demographic subgroups, but much variation appears to be explained by hypertension and corticosteroid use. These data clearly point to the need for tight control of disease activity without reliance on corticosteroids.
PMCID: PMC3510359  PMID: 22932985
SLICC/ACR Damage index (SDI); SLE
4.  PKCa Agonists Enhance the Protective Effect of Hyaluronic Acid on Nitric Oxide-Induced Apoptosis of Articular Chondrocytes in Vitro 
Objective(s): Protein kinase C (PKCα) is involved in modulating articular chondrocytes apoptosis induced by nitric oxide (NO). Hyaluronic acid (HA) inhibits nitric oxide-induced apoptosis of articular chondrocytes by protecting PKCα, but the mechanism remains unclear. The present study was performed to investigate the effects and mechanisms of PKCα regulate protective effect of hyaluronic acid.
Materials and Methods The ratio of apoptotic cell and cell viability was surveyed by PCNA and MTT assay. The expression of caspase-3 was determined by real-time PCR and western blot.
Results: It was showed that HA was able to reduce the nuclei fragment and PCNA expression, and NO-induced articular apoptosis blocked by HA, pretreated chondrocytes with PMA, HA significantly inhibits the activation of caspase-3 induced by NO, but pretrement with CHR, HA significantly incresed the expression of caspase-3.
Conclusion: The results may be showed that PKCa regulate the expresion of caspase-3, which contribute to the apoptosis of chondrocytes induced by NO. PKC α agonists enhance the protective effect of hyaluronic acid on nitric oxide-induced articular chondrocytes apoptosis.
PMCID: PMC3933806  PMID: 24570835
Apoptosis; Nitric Oxide; PKC-α; PMA
5.  A systems approach for analysis of high content screening assay data with topic modeling 
BMC Bioinformatics  2013;14(Suppl 14):S11.
High Content Screening (HCS) has become an important tool for toxicity assessment, partly due to its advantage of handling multiple measurements simultaneously. This approach has provided insight and contributed to the understanding of systems biology at cellular level. To fully realize this potential, the simultaneously measured multiple endpoints from a live cell should be considered in a probabilistic relationship to assess the cell's condition to response stress from a treatment, which poses a great challenge to extract hidden knowledge and relationships from these measurements.
In this work, we applied a text mining method of Latent Dirichlet Allocation (LDA) to analyze cellular endpoints from in vitro HCS assays and related to the findings to in vivo histopathological observations. We measured multiple HCS assay endpoints for 122 drugs. Since LDA requires the data to be represented in document-term format, we first converted the continuous value of the measurements to the word frequency that can processed by the text mining tool. For each of the drugs, we generated a document for each of the 4 time points. Thus, we ended with 488 documents (drug-hour) each having different values for the 10 endpoints which are treated as words. We extracted three topics using LDA and examined these to identify diagnostic topics for 45 common drugs located in vivo experiments from the Japanese Toxicogenomics Project (TGP) observing their necrosis findings at 6 and 24 hours after treatment.
We found that assay endpoints assigned to particular topics were in concordance with the histopathology observed. Drugs showing necrosis at 6 hour were linked to severe damage events such as Steatosis, DNA Fragmentation, Mitochondrial Potential, and Lysosome Mass. DNA Damage and Apoptosis were associated with drugs causing necrosis at 24 hours, suggesting an interplay of the two pathways in these drugs. Drugs with no sign of necrosis we related to the Cell Loss and Nuclear Size assays, which is suggestive of hepatocyte regeneration.
The evidence from this study suggests that topic modeling with LDA can enable us to interpret relationships of endpoints of in vitro assays along with an in vivo histological finding, necrosis. Effectiveness of this approach may add substantially to our understanding of systems biology.
PMCID: PMC3851019  PMID: 24267543
6.  Data mining tools for Salmonella characterization: application to gel-based fingerprinting analysis 
BMC Bioinformatics  2013;14(Suppl 14):S15.
Pulsed field gel electrophoresis (PFGE) is currently the most widely and routinely used method by the Centers for Disease Control and Prevention (CDC) and state health labs in the United States for Salmonella surveillance and outbreak tracking. Major drawbacks of commercially available PFGE analysis programs have been their difficulty in dealing with large datasets and the limited availability of analysis tools. There exists a need to develop new analytical tools for PFGE data mining in order to make full use of valuable data in large surveillance databases.
In this study, a software package was developed consisting of five types of bioinformatics approaches exploring and implementing for the analysis and visualization of PFGE fingerprinting. The approaches include PFGE band standardization, Salmonella serotype prediction, hierarchical cluster analysis, distance matrix analysis and two-way hierarchical cluster analysis. PFGE band standardization makes it possible for cross-group large dataset analysis. The Salmonella serotype prediction approach allows users to predict serotypes of Salmonella isolates based on their PFGE patterns. The hierarchical cluster analysis approach could be used to clarify subtypes and phylogenetic relationships among groups of PFGE patterns. The distance matrix and two-way hierarchical cluster analysis tools allow users to directly visualize the similarities/dissimilarities of any two individual patterns and the inter- and intra-serotype relationships of two or more serotypes, and provide a summary of the overall relationships between user-selected serotypes as well as the distinguishable band markers of these serotypes. The functionalities of these tools were illustrated on PFGE fingerprinting data from PulseNet of CDC.
The bioinformatics approaches included in the software package developed in this study were integrated with the PFGE database to enhance the data mining of PFGE fingerprints. Fast and accurate prediction makes it possible to elucidate Salmonella serotype information before conventional serological methods are pursued. The development of bioinformatics tools to distinguish the PFGE markers and serotype specific patterns will enhance PFGE data retrieval, interpretation and serotype identification and will likely accelerate source tracking to identify the Salmonella isolates implicated in foodborne diseases.
PMCID: PMC3851133  PMID: 24267777
Data mining; Salmonella; PFGE; bioinformatics tools; data analysis.
7.  Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes 
BMC Bioinformatics  2013;14(Suppl 14):S6.
An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind and sequester estrogens, thus preventing entry to the target cell and where they could otherwise induce ER-mediated endocrine activity. Recently, we reported rat AFP binding affinities for a large set of structurally diverse chemicals, including 53 binders and 72 non-binders. However, the lack of three-dimensional (3D) structures of rat AFP hinders further understanding of the structural dependence for binding. Therefore, a 3D structure of rat AFP was built using homology modeling in order to elucidate rat AFP-ligand binding modes through docking analyses and molecular dynamics (MD) simulations.
Homology modeling was first applied to build a 3D structure of rat AFP. Molecular docking and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) scoring were then used to examine potential rat AFP ligand binding modes. MD simulations and free energy calculations were performed to refine models of binding modes.
A rat AFP tertiary structure was first obtained using homology modeling and MD simulations. The rat AFP-ligand binding modes of 13 structurally diverse, representative binders were calculated using molecular docking, (MM-GBSA) ranking and MD simulations. The key residues for rat AFP-ligand binding were postulated through analyzing the binding modes.
The optimized 3D rat AFP structure and associated ligand binding modes shed light on rat AFP-ligand binding interactions that, in turn, provide a means to estimate binding affinity of unknown chemicals. Our results will assist in the evaluation of the endocrine disruption potential of chemicals.
PMCID: PMC3851483  PMID: 24266910
8.  The novel BCR-ABL and FLT3 inhibitor ponatinib is a potent inhibitor of the multidrug resistance-associated ATP-binding cassette transporter ABCG2 
Molecular cancer therapeutics  2012;11(9):2033-2044.
Ponatinib is a novel tyrosine kinase inhibitor with potent activity against BCR-ABL with mutations including T315I, and also against fms-like tyrosine kinase 3 (FLT3). We tested interactions between ponatinib at pharmacologically relevant concentrations of 50 to 200 nM and the multidrug resistance-associated ATP-binding cassette (ABC) proteins ABCB1, ABCC1 and ABCG2. Ponatinib enhanced uptake of substrates of ABCG2 and ABCB1, but not ABCC1, in cells overexpressing these proteins, with a greater effect on ABCG2 than on ABCB1. Ponatinib potently inhibited [125I]-IAAP binding to ABCG2 and ABCB1, indicating binding to their drug substrate sites, with IC50s of 0.04 μM and 0.63 μM, respectively. Ponatinib stimulated ABCG2 ATPase activity in a concentration-dependent manner and stimulated ABCB1 ATPase activity at low concentrations, consistent with it being a substrate of both proteins at pharmacologically relevant concentrations. The ponatinib IC50s of BCR-ABL-expressing K562 cells transfected with ABCB1 and ABCG2 were approximately the same as and 2-fold higher than that of K562, respectively, consistent with ponatinib being a substrate of both proteins, but inhibiting its own transport, and resistance was also attenuated to a small degree by ponatinib-induced downregulation of ABCB1 and ABCG2 cell surface expression on resistant K562 cells. Ponatinib at pharmacologically relevant concentrations produced synergistic cytotoxicity with ABCB1 and ABCG2 substrate chemotherapy drugs and enhanced apoptosis induced by these drugs, including daunorubicin, mitoxantrone, topotecan and flavopiridol, in cells overexpressing these transport proteins. Combinations of ponatinib and chemotherapy drugs warrant further testing.
PMCID: PMC3683995  PMID: 22778153
Ponatinib; ABCG2; ABCB1; multidrug resistance; leukemia
9.  Iron-catalyzed decarboxylative alkenylation of cycloalkanes with arylvinyl carboxylic acids via a radical process 
A Fe(acac)3-catalyzed decarboxylative coupling of 2-(aryl)vinyl carboxylic acids with cycloalkanes was developed by using DTBP as an oxidant through a radical process. This reaction tolerates a wide range of substrates, and products are obtained in good to excellent yields (71–95%). The reaction also shows excellent stereoselectivity, and only trans-isomers are obtained.
PMCID: PMC3778410  PMID: 24062833
alkenylation; cycloalkanes; decarboxylative; Fe(acac)3; free radical; sp3 C–H bonds
10.  Flame figures associated with eosinophilic dermatosis of hematologic malignancy: is it possible to distinguish the condition from eosinophilic cellulitis in patients with hematoproliferative disease? 
Eosinophilic dermatosis of hematologic malignancy is a multifaceted dermatosis with a wide morphological spectrum, presenting as pruritic, erythematous, papular and occasionally vesicular, urticarial, nodular eruptions. Histopathologically eosinophil infiltration in the super and deep dermis was found. We reported a case of eosinophilic dermatosis of hematologic malignancy presented as urticarial and vesicular lesions in a patient with chronic lymphocytic leukemia. A skin biopsy revealed a prominent subepidermal blister and a diffuse infiltrate of eosinophils with flame figures in the dermis and subcutaneous tissue. Although flame figures associated with eosinophilic dermatosis of hematologic malignancy is rarely reported, we believe that it would not seem unusual to find them in this skin disease. Eosinophilic cellulitis, which share clinical and histological features with eosinophilic dermatosis of hematologic malignancy, has also been described as showing an association with hematoproliferative diseases. In order to clearly describe eosinophilic dermatosis in patients with hematologic malignancies, the terminology eosinophilic dermatosis of hematologic malignancy, instead of eosinophilic cellulitis, would be a more suitable term in patients with eosinophilic dermatosis.
PMCID: PMC3726987  PMID: 23923089
Eosinophilic dermatosis; hematologic malignancy; flame figures; chronic lymphocytic leukemia
11.  TGF-β1 Regulation of Estrogen Production in Mature Rat Leydig Cells 
PLoS ONE  2013;8(3):e60197.
Besides androgens, estrogens produced in Leydig cells are also crucial for mammalian germ cell differentiation. Transforming growth factor-β1 (TGF-β1) is now known to have multiple effects on regulation of Leydig cell function. The objective of the present study is to determine whether TGF-β1 regulates estradiol (E2) synthesis in adult rat Leydig cells and then to assess the impact of TGF-β1 on Cx43-based gap junctional intercellular communication (GJIC) between Leydig cells.
Methodology/Principal Findings
Primary cultured Leydig cells were incubated in the presence of recombinant TGF-β1 and the production of E2 as well as testosterone (T) were measured by RIA. The activity of P450arom was addressed by the tritiated water release assay and the expression of Cyp19 gene was evaluated by Western blotting and real time RT-PCR. The expression of Cx43 and GJIC were investigated with immunofluorescence and fluorescence recovery after photo-bleaching (FRAP), respectively. Results from this study show that TGF-β1 down-regulates the level of E2 secretion and the activity of P450arom in a dose-dependent manner in adult Leydig cells. In addition, the expression of Cx43 and GJIC was closely related to the regulation of E2 and TGF-β1, and E2 treatment in turn restored the inhibition of TGF-β1 on GJIC.
Our results indicate, for the first time in adult rat Leydig cells, that TGF-β1 suppresses P450arom activity, as well as the expression of the Cyp19 gene, and that depression of E2 secretion leads to down-regulation of Cx43-based GJIC between Leydig cells.
PMCID: PMC3612063  PMID: 23555924
12.  Urinary Vascular Cell Adhesion Molecule, But Not Neutrophil Gelatinase-associated Lipocalin, Is Associated with Lupus Nephritis 
The Journal of rheumatology  2012;39(6):1231-1237.
Vascular cell adhesion molecule-1 (VCAM-1), an adhesion molecule, is involved in the progression of glomerular and tubulointerstitial injury. Neutrophil gelatinase-associated lipocalin (NGAL), a member of the lipocalin superfamily, has been shown to rise in both acute and chronic kidney damage. Both VCAM-1 and NGAL have been found at high levels in the urine of patients with active lupus nephritis. We investigated both as potential biomarkers for lupus nephritis.
VCAM-1 and NGAL were measured by ELISA during 1 to 8 clinic visits in 107 patients with systemic lupus erythematosus (SLE; 91% women, 51% black, 36% white, 4% Asian, 4% Hispanic, and 5% others) for a total of 190 visits. Patients’ mean age was 41 years. We analyzed the relationship between these potential urine biomarkers and the urine protein/creatinine ratio (urine Pr/Cr), the Systemic Lupus International Collaborating Clinics (SLICC) renal activity score, SLE Disease Activity Index renal descriptors, and other clinical variables.
VCAM-1 levels were strongly associated with the physician’s global estimate of disease activity (p = 0.0002), the renal visual analog scale (p < 0.0001), the urine Pr/Cr (p < 0.0001), and SLICC renal activity score (p < 0.0001). VCAM-1 levels were also associated with a urine Pr/Cr ≥ 0.5 (p < 0.0001). NGAL was not associated with any measure of disease activity or with lupus serologies.
Urine VCAM-1 had a strong association with measures of disease activity, including multiple renal activity descriptors. In contrast to previous SLE studies, NGAL failed to show any association with lupus nephritis.
PMCID: PMC3607283  PMID: 22505707
13.  Differences between Male and Female Systemic Lupus Erythematosus in a Multiethnic Population 
The Journal of rheumatology  2012;39(4):759-769.
Male patients with systemic lupus erythematosus (SLE) are thought to be similar to female patients with SLE, but key clinical characteristics may differ. Comparisons were made between male and female patients with SLE in the Hopkins Lupus Cohort.
A total of 1979 patients in the Hopkins Lupus Cohort were included in the analysis.
The cohort consisted of 157 men (66.2% white, 33.8% African American) and 1822 women (59.8% white, 40.2% African American). The mean followup was 6.02 years (range 0–23.73). Men were more likely than women to have disability, hypertension, thrombosis, and renal, hematological, and serological manifestations. Men were more likely to be diagnosed at an older age and to have a lower education level. Women were more likely to have malar rash, photosensitivity, oral ulcers, alopecia, Raynaud’s phenomenon, or arthralgia. Men were more likely than women to have experienced end organ damage including neuropsychiatric, renal, cardiovascular, peripheral vascular disease, and myocardial infarction, and to have died. In general, differences between males and females were more numerous and striking in whites, especially with respect to lupus nephritis, abnormal serologies, and thrombosis.
Our study suggests that there are major clinical differences between male and female patients with SLE. Differences between male and female patients also depend on ethnicity. Future SLE studies will need to consider both ethnicity and gender to understand these differences.
PMCID: PMC3605704  PMID: 22382348
14.  Utility of Antiphosphatidylserine/Prothrombin and IgA Antiphospholipid Assays in Systemic Lupus Erythematosus 
The Journal of rheumatology  2013;40(3):282-286.
Currently, 3 antiphospholipid assays are widely used clinically [lupus anticoagulant (LAC), anticardiolipin (aCL), and anti-β2-glycoprotein I (anti-β2-GPI)]. LAC is the most specific assay, conferring the highest risk of thrombosis and pregnancy loss, but it cannot be validly performed in an anticoagulated patient. We investigated the usefulness of antiphosphatidyl-serine/prothrombin (anti-PS/PT) and its association with thrombosis. Anti-PS/PT is strongly associated with the presence of LAC. We also studied the association of IgA antiphospholipid isotypes and specific domains of β2-GPI with thrombosis in systemic lupus erythematosus (SLE).
Stored samples from patients with SLE, with and without past thrombosis, were assayed for antibodies to the whole β2-GPI protein (IgG/IgM/IgA), to β2-GPI domain 1 (IgG), to β2-GPI domain 4/5 (IgA), aCL (IgG/IgM/IgA), and anti-PS/PT (IgG, IgM, and IgG/M). LAC was detected using the dilute Russell’s viper venom time (dRVVT) with confirmatory testing.
Anti-PS/PT IgG and IgG/M and anti-β2-GPI IgG, IgM, and IgA were highly associated with a history of LAC by dRVVT (p < 0.0001). For all thrombosis, of the traditional ELISA assays, anti-β2-GPI IgA, IgG, and aCL IgA were most associated. Anti-PS/PT IgG and IgG/M had a similar magnitude of association to the traditional ELISA. For venous thrombosis, of the traditional ELISA, anti-β2-GPI (IgG and IgA), anti-PS/PT (IgG and IgG/M), and aCL IgA were associated. Again, anti-PS/PT (IgG and IgG/M) had the same magnitude of association as the traditional ELISA. For stroke, significant association was seen with anti-β2-GPI IgA D4/5.
In anticoagulated patients, where LAC testing is not valid, anti-PS/PT, either IgG or IgG/IgM, might serve as useful alternative tests to predict a higher risk of thrombosis. Anti-PS/PT antibodies were associated with all thrombosis and with venous thrombosis. IgA isotypes in secondary antiphospholipid syndrome are associated with thrombosis. Anti-β2-glycoprotein domain 1 was not shown to be associated with thrombosis in SLE.
PMCID: PMC3605900  PMID: 23378459
15.  Seasonal Variation in the Activity of Systemic Lupus Erythematosus 
The Journal of rheumatology  2012;39(7):1392-1398.
To determine whether there is any seasonal variation in the activity of systemic lupus erythematosus (SLE) overall and by individual organs.
The study group comprised 2102 patients with SLE who were followed in a prospective longitudinal cohort study. In this cohort, 92.3% of the patients were women. The mean ± SD age of the patients was 47.9 ± 13.9 years, 56.3% were white, 37.1% were African American, and 3.1% were Asian. Global disease activity was recorded by the Safety of Estrogens in Lupus Erythematosus National Assessment – Systemic Lupus Erythematosus Disease Activity Index (SELENA-SLEDAI) and the physician's global assessment. Activity of each organ was also recorded using SLEDAI terms and a visual analog scale (VAS; 0 to 3).
There was significant seasonal variation in photosensitive rash (p < 0.0001), which was more frequent in the spring and summer months (p < 0.0001). There was significantly more arthritis activity in spring and summer, as measured by both SELENA-SLEDAI (p = 0.0057) and the joint VAS (p = 0.0047). A decrease in renal activity was found in the summer months compared to the rest of the year (p = 0.0397). Serositis recorded by VAS had higher activity from August to October (p = 0.0392). Anti-dsDNA levels were significantly higher during October and November (p < 0.0001). There was significant seasonal variation in antiphospholipid antibody levels (p < 0.0001) and lupus anticoagulant (p = 0.0003). We found a significant variation in activity through the year in global disease activity as measured by SELENA-SLEDAI (p = 0.048).
In the Hopkins Lupus Cohort, skin and joint activity is increased during the spring and summer, but other organs have different patterns. These seasonal variations likely reflect environmental factors that influence disease activity, including ultraviolet light and infections.
PMCID: PMC3597113  PMID: 22660806
16.  Low Socioeconomic Status Is Associated with Cardiovascular Risk Factors and Outcomes in Systemic Lupus Erythematosus 
The Journal of rheumatology  2012;39(4):777-783.
Accelerated atherosclerosis is a major cause of death in systemic lupus erythematosus (SLE), yet little is known about the effect of socioeconomic status. We investigated whether education or income levels are associated with cardiovascular risk factors and outcomes in SLE.
Our study involved a longitudinal cohort of all patients with SLE enrolled in the Hopkins Lupus Cohort from 1987 through September 2011. Socioeconomic status was measured by education level (≥ 12 years or < 12) and income tertiles (> $60,000, $25,000–$60,000, or < $25,000).
A total of 1752 patients with SLE were followed prospectively every 3 months. There were 1052 whites and 700 African Americans. Current smoking, obesity, hypertension, and diabetes mellitus were more common in African Americans (p < 0.01 for all), but there was no statistical difference in the frequency of myocardial infarction or stroke. In multivariate analyses stratified by ethnicity, low income was strongly associated with most traditional cardiovascular risk factors in whites, but only with smoking and diabetes in African Americans. In whites, low income increased the risk of both myocardial infarction (OR 3.24, 95% CI 1.41–7.45, p = 0.006) and stroke (OR 2.85, 95% CI 1.56–5.21, p = 0.001); in African Americans, these relationships were not seen. Low education, in contrast, was associated with smoking in both ethnic groups.
Low income, not low education, is the socioeconomic status variable associated with cardiovascular risk factors and events. This association is most clearly demonstrable in whites.
PMCID: PMC3597116  PMID: 22382345
17.  Meta-Analysis of Pulsed-Field Gel Electrophoresis Fingerprints Based on a Constructed Salmonella Database 
PLoS ONE  2013;8(3):e59224.
A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE) patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13−15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.
PMCID: PMC3597626  PMID: 23516614
18.  Lentiviral miR30-based RNA Interference against Heparanase Suppresses Melanoma Metastasis with Lower Liver and Lung Toxicity 
Aim: To construct short hairpin RNAs (shRNAs) and miR30-based shRNAs against heparanase (HPSE) to compare their safety and their effects on HPSE down-modulation in vitro and in vivo to develop a more ideal therapeutic RNA interference (RNAi) vector targeting HPSE.
Methods: First, we constructed shRNAs and miR30-based shRNAs against HPSE (HPSE-shRNAs and HPSE-miRNAs) and packed them into lentiviral vectors. Next, we observed the effects of the shRNAs on knockdown for HPSE expression, adhesion, migration and invasion abilities in human malignant melanoma A375 cells in vitro. Furthermore, we compared the effects of the shRNAs on melanoma growth, metastasis and safety in xenograft models.
Results: Our data showed that these artificial miRNAs targeting HPSE could be effective RNAi agents mediated by Pol II promoters in vitro and in vivo, although these miRNAs were not more potent than the HPSE-shRNAs. It was noted that obvious lung injuries, rarely revealed previously, as well as hepatotoxicity could be caused by lentivirus-mediated shRNAs (LV shRNAs) rather than lentivirus-mediated miRNAs (LV miRNAs) in vivo. Furthermore, enhanced expression of pro-inflammatory cytokines IL-6 and TGF-β1 and endogenous mmu-miR-21a-5p were detected in lung tissues of shRNAs groups, whereas the expression of mmu-let-7a-5p, mmu-let-7b-5p and mmu-let-7c-5p were down-regulated.
Conclusion: These findings suggest that artificial miRNAs display an improved safety profile of lowered lung injury or hepatotoxicity relative to shRNAs in vivo. The mechanism of lung injuries caused by shRNAs may be correlated with changes of endogenous miRNAs in the lung. Our data here increase the flexibility of a miRNA-based RNAi system for functional genomic and gene therapy applications.
PMCID: PMC3708037  PMID: 23847439
RNA interference; microRNA(miRNA); heparanase; metastasis; safety
19.  Amyloidosis cutis dyschromica 
Amyloidosis cutis dyschromica is a rarely documented variant of cutaneous amyloidosis. To date, only 26 cases have been reported.
The purpose of this study was to improve the clinical and histopathological data for this variant of amyloidosis and to highlight the immunohistochemical features of the disease. The published cases were also reviewed.
We performed a retrospective review of patients with amyloidosis cutis dyschromica in a single centre. The clinical, histopathological and immunohistochemical features were documented and analysed.
We described 10 cases of amyloidosis cutis dyschromica. Six of them were female. Five patients were from the same family, and the other 5 were sporadic. The distinguishing features of the clinical presentation included generalised mottled hyper- and hypopigmented macules, which were asymptomatic or mild pruritic. The typical onset of the lesions occurred in childhood (n = 7) and occasionally after puberty (n = 3). No evidence of systemic amyloidosis deposition was observed in these cases of amyloidosis cutis dyschromica. Amyloid deposits were observed in the papillary dermis and were positive for the Congo red stain. An immunohistochemical study showed that the amyloid expresses cytokeratins CK34βE12 and CK5/6.
We described the largest series of amyloidosis cutis dyschromica to date and reviewed the published patients. This rare disease is featured by generalised mottled hyper- and hypopigmented lesions, and it is a rare variant of primary cutaneous amyloidosis without evidence of systemic amyloid deposition. Positive staining for the cytokeratins CK34βE12 and CK5/6 in amyloidosis cutis dyschromica suggests that the amyloid is derived from keratinocytes.
PMCID: PMC3554482  PMID: 23234252
Amyloidosis cutis dyschromica; Amyloid; Pigmentation disorder; Cytokeratin; Congo red; Hereditary disease
20.  Atrophic dermatofibrosarcoma protuberans: report of a case demonstrated by detecting COL1A1-PDGFB rearrangement 
Diagnostic Pathology  2012;7:166.
Dermatofibrosarcoma protuberans is a locally aggressive mesenchymal neoplasm. It usually presents as an indurated plaque that protrudes above the surface of the skin. Some patients have clinically persistent plaques that might be atrophic. The atrophic variant of dermatofibrosarcoma protuberans may be confused with some common skin diseases with atrophic appearance. We reported a 40-year-old woman who had a 10-year history of an atrophic dermatofibrosarcoma protuberans. Molecular analysis showed a fusion between COL1A1 exon 31 to exon 2 of PDGFB. The lesion was totally excised, with negative margins of the resection demonstrated by CD34 immunostaining. To our knowledge, this is the second case of atrophic dermatofibrosarcoma protuberans confirmed by detection of COL1A1-PDGFB fusion gene. This appears to be the first report of a fusion between COL1A1 exon 31 to exon 2 of PDGFB in atrophic dermatofibrosarcoma protuberans.
Virtual slides
The virtual slides for this article can be found here:
PMCID: PMC3539889  PMID: 23199263
Dermatofibrosarcoma protuberans; COL1A1-PDGFB; CD34; Atrophic; Sarcoma
21.  PGC1α promotes tumor growth by inducing gene expression programs supporting lipogenesis 
Cancer Research  2011;71(21):6888-6898.
Despite the role of aerobic glycolysis in cancer, recent studies highlight the importance of the mitochondria and biosynthetic pathways as well. PPARγ coactivator 1α (PGC1α) is a key transcriptional regulator of several metabolic pathways including oxidative metabolism and lipogenesis. Initial studies suggested that PGC1α expression is reduced in tumors compared to adjacent normal tissue. Paradoxically, other studies show that PGC1α is associated with cancer cell proliferation. Therefore the role of PGC1α in cancer and especially carcinogenesis is unclear. Using Pgc1α-/- and Pgc1α+/+ mice we show that loss of PGC1α protects mice from azoxymethane induced colon carcinogenesis. Similarly, diethylnitrosamine induced liver carcinogenesis is reduced in Pgc1α-/- mice compared to Pgc1α+/+ mice. Xenograft studies using gain and loss of PGC1α expression demonstrated that PGC1α also promotes tumor growth. Interestingly, while PGC1α induced oxidative phosphorylation and TCA cycle gene expression, we also observed an increase in the expression of two genes required for de novo fatty acid synthesis, ACC and FASN. In addition, SLC25A1 and ACLY, which are required for the conversion of glucose in to acetyl CoA for fatty acid synthesis, were also increased by PGC1α, thus linking the oxidative and lipogenic functions of PGC1α. Indeed, using 13C stable isotope tracer analysis we show that PGC1α increased de novo lipogenesis. Importantly, inhibition of fatty acid synthesis blunted these progrowth effects of PGC1α. In conclusion, these studies show for the first time that loss of PGC1α protects against carcinogenesis and that PGC1α coordinately regulates mitochondrial and fatty acid metabolism to promote tumor growth.
PMCID: PMC3282487  PMID: 21914785
Cancer metabolism; Warburg Effect; oxidative metabolism; lipogenesis; transcriptional regulation
22.  Hand-foot syndrome related to chemotherapy 
PMCID: PMC3478376  PMID: 22508979
23.  Investigating drug repositioning opportunities in FDA drug labels through topic modeling 
BMC Bioinformatics  2012;13(Suppl 15):S6.
Drug repositioning offers an opportunity to revitalize the slowing drug discovery pipeline by finding new uses for currently existing drugs. Our hypothesis is that drugs sharing similar side effect profiles are likely to be effective for the same disease, and thus repositioning opportunities can be identified by finding drug pairs with similar side effects documented in U.S. Food and Drug Administration (FDA) approved drug labels. The safety information in the drug labels is usually obtained in the clinical trial and augmented with the observations in the post-market use of the drug. Therefore, our drug repositioning approach can take the advantage of more comprehensive safety information comparing with conventional de novo approach.
A probabilistic topic model was constructed based on the terms in the Medical Dictionary for Regulatory Activities (MedDRA) that appeared in the Boxed Warning, Warnings and Precautions, and Adverse Reactions sections of the labels of 870 drugs. Fifty-two unique topics, each containing a set of terms, were identified by using topic modeling. The resulting probabilistic topic associations were used to measure the distance (similarity) between drugs. The success of the proposed model was evaluated by comparing a drug and its nearest neighbor (i.e., a drug pair) for common indications found in the Indications and Usage Section of the drug labels.
Given a drug with more than three indications, the model yielded a 75% recall, meaning 75% of drug pairs shared one or more common indications. This is significantly higher than the 22% recall rate achieved by random selection. Additionally, the recall rate grows rapidly as the number of drug indications increases and reaches 84% for drugs with 11 indications. The analysis also demonstrated that 65 drugs with a Boxed Warning, which indicates significant risk of serious and possibly life-threatening adverse effects, might be replaced with safer alternatives that do not have a Boxed Warning. In addition, we identified two therapeutic groups of drugs (Musculo-skeletal system and Anti-infective for systemic use) where over 80% of the drugs have a potential replacement with high significance.
Topic modeling can be a powerful tool for the identification of repositioning opportunities by examining the adverse event terms in FDA approved drug labels. The proposed framework not only suggests drugs that can be repurposed, but also provides insight into the safety of repositioned drugs.
PMCID: PMC3439728  PMID: 23046522
24.  Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies 
PLoS ONE  2012;7(9):e44483.
During the last several years, high-density genotyping SNP arrays have facilitated genome-wide association studies (GWAS) that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small fraction of the underlying genetic contribution to the studied phenotypic trait. Moreover, discordance observed in results between independent GWAS indicates the potential for Type I and II errors. High reliability of genotyping technology is needed to have confidence in using SNP data and interpreting GWAS results. Therefore, reproducibility of two widely genotyping technology platforms from Affymetrix and Illumina was assessed by analyzing four technical replicates from each of the six individuals in five laboratories. Genotype concordance of 99.40% to 99.87% within a laboratory for the sample platform, 98.59% to 99.86% across laboratories for the same platform, and 98.80% across genotyping platforms was observed. Moreover, arrays with low quality data were detected when comparing genotyping data from technical replicates, but they could not be detected according to venders’ quality control (QC) suggestions. Our results demonstrated the technical reliability of currently available genotyping platforms but also indicated the importance of incorporating some technical replicates for genotyping QC in order to improve the reliability of GWAS results. The impact of discordant genotypes on association analysis results was simulated and could explain, at least in part, the irreproducibility of some GWAS findings when the effect size (i.e. the odds ratio) and the minor allele frequencies are low.
PMCID: PMC3436888  PMID: 22970228
25.  Convergent Genomic Studies Identify Association of GRIK2 and NPAS2 with Chronic Fatigue Syndrome 
Neuropsychobiology  2011;64(4):183-194.
There is no consistent evidence of specific gene(s) or molecular pathways that contribute to the pathogenesis, therapeutic intervention or diagnosis of chronic fatigue syndrome (CFS). While multiple studies support a role for genetic variation in CFS, genome-wide efforts to identify associated loci remain unexplored. We employed a novel convergent functional genomics approach that incorporates the findings from single-nucleotide polymorphism (SNP) and mRNA expression studies to identify associations between CFS and novel candidate genes for further investigation.
We evaluated 116,204 SNPs in 40 CFS and 40 nonfatigued control subjects along with mRNA expression of 20,160 genes in a subset of these subjects (35 CFS subjects and 27 controls) derived from a population-based study.
Sixty-five SNPs were nominally associated with CFS (p < 0.001), and 165 genes were differentially expressed (≥4-fold; p ≤ 0.05) in peripheral blood mononuclear cells of CFS subjects. Two genes, glutamate receptor, ionotropic, kinase 2 (GRIK2) and neuronal PAS domain protein 2 (NPAS2), were identified by both SNP and gene expression analyses. Subjects with the G allele of rs2247215 (GRIK2) were more likely to have CFS (p = 0.0005), and CFS subjects showed decreased GRIK2 expression (10-fold; p = 0.015). Subjects with the T allele of rs356653 (NPAS2) were more likely to have CFS (p = 0.0007), and NPAS2 expression was increased (10-fold; p = 0.027) in those with CFS.
Using an integrated genomic strategy, this study suggests a possible role for genes involved in glutamatergic neurotransmission and circadian rhythm in CFS and supports further study of novel candidate genes in independent populations of CFS subjects.
PMCID: PMC3701888  PMID: 21912186
Chronic fatigue syndrome; Genome-wide association; Gene expression; GRIK2; NPAS2; Glutamatergic neurotransmission; Circadian rhythm; Orexin signaling

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