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Batty J, Qiu W, Gu S, Sinclair H, Veerasamy M, Beska B, Neely D, Ford G, Kunadian V. One-year clinical outcomes in older patients with non-ST elevation acute coronary syndrome undergoing coronary angiography: An analysis of the ICON1 study. Int J Cardiol 2019; 274:45-51. [DOI: 10.1016/j.ijcard.2018.09.086] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/05/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022]
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Qiu W, Kuang H, Nair J, Assis Z, Najm M, McDougall C, McDougall B, Chung K, Wilson AT, Goyal M, Hill MD, Demchuk AM, Menon BK. Radiomics-Based Intracranial Thrombus Features on CT and CTA Predict Recanalization with Intravenous Alteplase in Patients with Acute Ischemic Stroke. AJNR Am J Neuroradiol 2018; 40:39-44. [PMID: 30573458 DOI: 10.3174/ajnr.a5918] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/21/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Thrombus characteristics identified on non-contrast CT (NCCT) are potentially associated with recanalization with intravenous (IV) alteplase in patients with acute ischemic stroke (AIS). Our aim was to determine the best radiomics-based features of thrombus on NCCT and CT angiography associated with recanalization with IV alteplase in AIS patients and proximal intracranial thrombi. MATERIALS AND METHODS With a nested case-control design, 67 patients with ICA/M1 MCA segment thrombus treated with IV alteplase were included in this analysis. Three hundred twenty-six radiomics features were extracted from each thrombus on both NCCT and CTA images. Linear discriminative analysis was applied to select features most strongly associated with early recanalization with IV alteplase. These features were then used to train a linear support vector machine classifier. Ten times 5-fold cross-validation was used to evaluate the accuracy of the trained classifier and the stability of the selected features. RESULTS Receiver operating characteristic curves showed that thrombus radiomics features are predictive of early recanalization with IV alteplase. The combination of radiomics features from NCCT, CTA, and radiomics changes is best associated with early recanalization with IV alteplase (area under the curve = 0.85) and was significantly better than any single feature such as thrombus length (P < .001), volume (P < .001), and permeability as measured by mean attenuation increase (P < .001), maximum attenuation in CTA (P < .001), maximum attenuation increase (P < .001), and assessment of residual flow grade (P < .001). CONCLUSIONS Thrombus radiomics features derived from NCCT and CTA are more predictive of recanalization with IV alteplase in patients with acute ischemic stroke with proximal occlusion than previously known thrombus imaging features such as length, volume, and permeability.
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Seo M, Qiu W, Bailey W, Criner GJ, Dransfield MT, Fuhlbrigge AL, Reilly JJ, Scholand MB, Castaldi P, Chase R, Parker M, Saferali A, Yun JH, Crapo JD, Cho MH, Beaty TH, Silverman EK, Hersh CP. Genomics and response to long-term oxygen therapy in chronic obstructive pulmonary disease. J Mol Med (Berl) 2018; 96:1375-1385. [PMID: 30353303 DOI: 10.1007/s00109-018-1708-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 12/19/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, and long-term oxygen therapy has been shown to reduce mortality in COPD patients with severe hypoxemia. However, the Long-term Oxygen Treatment Trial (LOTT), a large randomized trial, found no benefit of oxygen therapy in COPD patients with moderate hypoxemia. We hypothesized that there may be differences in response to oxygen which depend on genotype or gene expression. In a genome-wide time-to-event analysis of the primary outcome of death or hospitalization in 331 subjects, 97 single nucleotide polymorphisms (SNPs) showed evidence of interaction with oxygen therapy at P < 1e-5, including 7 SNPs near arylsulfatase B (ARSB; P = 6e-6). In microarray expression profiling on 51 whole blood samples from 37 individuals, at screening and/or at 12-month follow-up, ARSB expression was associated with the primary outcome depending on oxygen treatment. The significant SNPs were conditional expression quantitative trait loci for ARSB expression. In a network analysis of genes affected by long-term oxygen, two observed clusters including 26 co-expressed genes were enriched in mitochondrial function. Using data from the observational COPDGene Study, we validated the expression of 25 of these 26 genes, plus ARSB. The effect of long-term oxygen therapy in COPD varied based on ARSB expression and genotype. ARSB has previously been shown to be associated with hypoxemia in human bronchial and colonic epithelial cells and in a mouse model. In peripheral blood, long-term oxygen treatment affected expression of mitochondrial-related genes, a biologically relevant pathway in COPD. SNPs and expression of ARSB are associated with response to long-term oxygen in COPD. The ARSB SNPs were expression quantitative trait loci depending on oxygen therapy. Genes differentially expressed by long-term oxygen were enriched in mitochondrial functions. This suggests a potential biomarker to personalize use of long-term oxygen in COPD.
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Xu C, Ye H, Qiu W, Lin H, Chen Y, Zhang H, Liao M. Phylogenetic classification of hemagglutinin gene of H9N2 avian influenza viruses isolated in China during 2012-2016 and evaluation of selected candidate vaccine strains. Poult Sci 2018; 97:3023-3030. [PMID: 29931183 DOI: 10.3382/ps/pey154] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022] Open
Abstract
H9N2 subtype avian influenza virus (AIV) was the highly contagious pathogen which has caused severe losses in the poultry industry throughout China in recent years. Using current epidemic viruses as vaccine was an effective way to prevent infection of H9N2 subtype AIV. In this study, a total of 23 H9N2 subtype AIV strains were isolated in 200 samples from 13 provinces of China during 2012-2016. The sequencing and phylogenetic analysis of the hemagglutinin gene sequence of the isolation strains showed that 22 isolation strains were clustered to h9.4.2.5 lineage, while only 1 belonged to h9.4.2.6. The data of cross-HI, neutralization and cross-immune protection shown that the A/chicken/Hunan/HN/2015 (HN) and A/chicken/Shandong/SD/2014 (SD) strains as vaccine could effectively protect present viruses infection compared with other strains. These results indicated that current epidemic viruses were mainly belong to h9.4.2.5 lineage and HN and SD strains as candidate vaccine strains were potentiality for the protection of present H9N2 subtype AIV infection.
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Zhou Y, Jia X, Yang H, Chen C, Sun X, Peng L, Kermode AG, Qiu W. Myelin oligodendrocyte glycoprotein antibody-associated demyelination: comparison between onset phenotypes. Eur J Neurol 2018; 26:175-183. [PMID: 30153357 DOI: 10.1111/ene.13791] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/17/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND PURPOSE The aim of this study was to analyse the clinical and prognostic features of myelin oligodendrocyte glycoprotein (MOG) antibody-associated demyelination with different onset phenotypes. METHODS A total of 52 MOG-IgG-seropositive patients were divided into four groups: (i) optic neuritis (ON) at onset (MOG-ON+ , n = 23), (ii) transverse myelitis (TM) at onset (MOG-TM+ , n = 12), (iii) pure brain symptoms at onset (MOG-ON- -TM- , n = 14) and (iv) both ON and TM at onset (n = 3). This final group was not included in further analyses. Data were collected through medical records and regular follow-up. RESULTS Median age at presentation was 24 (range, 3-63) years in the whole cohort (50% female). MOG-ON- -TM- patients had the youngest age of onset across the three groups. Patients with MOG-TM+ tended to relapse more frequently and had a longer interval to first relapse than was observed in MOG-ON+ and MOG-ON- -TM- patients. High MOG-IgG titres were associated with increased cerebrospinal fluid leukocytes. The likelihood of harbouring transient, low MOG-IgG titres was higher in the MOG-TM+ group than in the other groups. After a median disease duration of 20 months, most but not all cases had a favourable outcome, with 8% developing severe visual deficit, 2% becoming wheelchair-dependent and 6% developing cognitive impairment. The onset phenotype appeared to be an important predictor of disability type. Having high MOG-IgG titres (odds ratio, 0.168, P = 0.027) or female gender (odds ratio, 0.270, P = 0.067) was associated with a lower likelihood of complete recovery. CONCLUSIONS Onset phenotype may influence long-term presentation, MOG-IgG status as well as outcome. Further large and prospective studies are needed to better clarify the clinical implications of the first demyelinating event.
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Glass K, Thibault D, Guo F, Mitchel JA, Pham B, Qiu W, Li Y, Jiang Z, Castaldi PJ, Silverman EK, Raby B, Park JA, Yuan GC, Zhou X. Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke. Sci Rep 2018; 8:12750. [PMID: 30143676 PMCID: PMC6109173 DOI: 10.1038/s41598-018-30781-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
Cigarette smoke (CS) is one of the major risk factors for many pulmonary diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. The first line of defense for CS exposure is the bronchial epithelial cells. Elucidation of the epigenetic changes during CS exposure is key to gaining a mechanistic understanding into how mature and differentiated bronchial epithelial cells respond to CS. Therefore, we performed epigenomic profiling in conjunction with transcriptional profiling in well-differentiated human bronchial epithelial (HBE) cells cultured in air-liquid interface (ALI) exposed to the vapor phase of CS. The genome-wide enrichment of histone 3 lysine 27 acetylation was detected by chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) in HBE cells and suggested the plausible binding of specific transcription factors related to CS exposure. Additionally, interrogation of ChIP-Seq data with gene expression profiling of HBE cells after CS exposure for different durations (3 hours, 2 days, 4 days) suggested that earlier epigenetic changes (3 hours after CS exposure) may be associated with later gene expression changes induced by CS exposure (4 days). The integration of epigenetics and gene expression data revealed signaling pathways related to CS-induced epigenetic changes in HBE cells that may identify novel regulatory pathways related to CS-induced COPD.
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Huang Q, Xu Z, Li R, Wang YG, Shu YQ, Yang Y, Hu XQ, Chu L, Qiu W. [Analysis of clinical characteristics and prognosis of neuromyelitis optic spectrum disease complicated with malignant tumor]. ZHONGHUA YI XUE ZA ZHI 2018; 98:2496-2500. [PMID: 30139002 DOI: 10.3760/cma.j.issn.0376-2491.2018.31.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the clinical features of patients involved with both malignant tumors and neuromyelitis optica spectrum disorders (NMOSD). Methods: The clinical data of 473 patients with NMOSD admitted into the Third Affiliated Hospital of Sun Yat-sen University and the Department of Neurology, Affiliated Hospital of Guizhou Medical University from June 2012 to March 2017 were retrospectively analyzed. Eleven NMOSD patients complicated with malignant tumors were screened out (3 with breast cancer, 2 with cervical cancer, 2 with rectal cancer, 2 with leukemia, 1 with nasopharyngeal carcinoma, 1 with thyroid cancer). Fifty patients without NMOSD were included as controls. Results: Most of the NMOSD patients were complicated by low-moderately differentiated squamous cell carcinoma/adenocarcinoma, mainly seen in breast, reproductive system, digestive system and hematological system. In terms of sex ratio and autoantibodies, the NMOSD patients with and without malignant tumors showed no significant difference. However, comparing to the patients without malignant tumor, the ones with malignant tumor showed a tendency of lower rate of initial brain symptoms and relapse rate, while with older onset age, higher initial EDSS score, protein content in cerebrospinal fluid (CSF), higher rates of initial symptom resulted from the focus of posterior region of the medulla and of significant image focus. Of the 8 NMOSD patients who diagnosed as malignant tumors in our hospital, 2 with breast cancer and 1 with cervical cancer had a good prognosis (follow-up EDSS score <3). All the 3 patients received aggressive surgery and chemotherapy treatment. However, the other 5 patients had poor prognosis (follow-up EDSS score ≥3 points). All the 11 patients received anti-tumor therapy, 4 patients had first NMOSD attack after anti-tumor treatment and no relapse. Only one case from the remaining 7 patients had relapse; Among the 9 patients received immunosuppressive therapy, 7 patients had no relapse, and 8 cases maintained stable; while, among all the 9 patients received immunosuppressive agents and anti-tumor therapy, only one case had relapse. Conclusions: There are some differences in the clinical features between the NMOSD patients with malignant tumors and the NMOSD patients without malignant tumors. Immunosuppressive therapy can improve the prognosis of patients with NMOSD and tumor, without increasing the risk of malignant tumor. The pathological type, staging and antitumor therapy may influence the prognosis of NMOSD. NMOSD patients with malignant tumor could be treated with anti-tumor and immunosuppressive agents if needed.
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Gu SZ, Sinclair H, Batty J, Veerasamy M, Qiu W, Brugaletta S, Das R, Bagnall A, Zaman A, Edwards R, Egred M, Purcell I, Calvert P, Mintz G, Kunadian V. P4636Coronary artery lesion phenotype in frail older patients with non-ST elevation acute coronary syndrome undergoing invasive care - ICON1 invasive study. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy563.p4636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Qiu W, Sandberg MA, Rosner B. Application of empirical Bayes methods to predict the rate of decline in ERG at the individual level among patients with retinitis pigmentosa. Stat Med 2018; 37:2586-2598. [PMID: 29855067 DOI: 10.1002/sim.7662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 11/10/2022]
Abstract
Retinitis pigmentosa is one of the most common forms of inherited retinal degeneration. The electroretinogram (ERG) can be used to determine the severity of retinitis pigmentosa-the lower the ERG amplitude, the more severe the disease is. In practice for career, lifestyle, and treatment counseling, it is of interest to predict the ERG amplitude of a patient at a future time. One approach is prediction based on the average rate of decline for individual patients. However, there is considerable variation both in initial amplitude and in rate of decline. In this article, we propose an empirical Bayes (EB) approach to incorporate the variations in initial amplitude and rate of decline for the prediction of ERG amplitude at the individual level. We applied the EB method to a collection of ERGs from 898 patients with 3 or more visits over 5 or more years of follow-up tested in the Berman-Gund Laboratory and observed that the predicted values at the last (kth) visit obtained by using the proposed method based on data for the first k-1 visits are highly correlated with the observed values at the kth visit (Spearman correlation =0.93) and have a higher correlation with the observed values than those obtained based on either the population average decline rate or those obtained based on the individual decline rate. The mean square errors for predicted values obtained by the EB method are also smaller than those predicted by the other methods.
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Huang Q, Wang YG, Shu YQ, Yang H, Wang ZH, Yan ZW, Long YM, Yin J, Feng HY, Li CX, Lu ZZ, Hu XQ, Qiu W. [Efficacy and safety of mycophenolate mofetil in treating neuromyelitis optica spectrum disorder: a multicenter, prospective, self-control study in Guangzhou City]. ZHONGHUA YI XUE ZA ZHI 2018; 98:1664-1668. [PMID: 29925143 DOI: 10.3760/cma.j.issn.0376-2491.2018.21.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Objective: To evaluate the efficacy and safety of mycophenolate mofetil (MMF) in neuromyelitis optica spectrum disorder (NMOSD). Method: From September 2014 to February 2017, NMOSD patients with seropositive aquaporin4-IgG was enrolled through a multicenter, prospective study, and the annual recurrence rate (ARR), Expanded Disability Status Scale (EDSS) and MMF-related side effects before and after MMF treatment were compared. Results: Ninety patients were enrolled in the study. After being treated for a median of 12 months (1-30 months), the median ARR decreased from 1.1 pre-MMF to 0 post-MMF (P<0.001), and the median EDSS score decreased from 4.0 pre-MMF to 3.0 post-MMF (P<0.001). The EDSS score reduced significantly after 90 days' treatment (P<0.05). The main adverse events included the deranged liver enzymes (19%, 17/90), respiratory infection (11%, 10/90), urinary tract infection (6%, 5/90), varicella-zoster infection (6%, 5/90), anemia (6%, 5/90), leucopenia (6%, 5/90), diarrhea (2%, 2/90), hair loss (1%, 1/90); 11% (10/90) patients experienced severe adverse events, and 6% (5/90) patients discontinued MMF. Conclusions: MMF could significantly reduce the ARR and EDSS score of NMOSD. However, awareness on side effects should be raised.
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Li X, Fu Y, Wang X, Qiu W. Robust joint score tests in the application of DNA methylation data analysis. BMC Bioinformatics 2018; 19:174. [PMID: 29776330 PMCID: PMC5960098 DOI: 10.1186/s12859-018-2185-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
Background Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW’s method seems to be quite conservative and has not been fully compared with existing joint tests. Results We proposed three improved joint score tests, namely iAW.Lev, iAW.BF, and iAW.TM, and have made extensive comparisons with the joint likelihood ratio test (jointLRT), the Kolmogorov-Smirnov (KS) test, and the AW test. Systematic simulation studies showed that: 1) the three improved tests performed better (i.e., having larger power, while keeping nominal Type I error rates) than the other three tests for data with outliers and having different variances between cases and controls; 2) for data from normal distributions, the three improved tests had slightly lower power than jointLRT and AW. The analyses of two Illumina HumanMethylation27 data sets GSE37020 and GSE20080 and one Illumina Infinium MethylationEPIC data set GSE107080 demonstrated that three improved tests had higher true validation rates than those from jointLRT, KS, and AW. Conclusions The three proposed joint score tests are robust against the violation of normality assumption and presence of outlying observations in comparison with other three existing tests. Among the three proposed tests, iAW.BF seems to be the most robust and effective one for all simulated scenarios and also in real data analyses. Electronic supplementary material The online version of this article (10.1186/s12859-018-2185-3) contains supplementary material, which is available to authorized users.
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Shu Y, Zhang L, Chang Y, Li R, Sun X, Li J, Wu H, Yang Y, Peng L, Lu Z, Kermode AG, Qiu W. Association of serum Cystatin C with neuromyelitis optica spectrum disorders. Eur J Neurol 2018; 25:999-1002. [PMID: 29603501 DOI: 10.1111/ene.13646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/22/2018] [Indexed: 11/29/2022]
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Shu Y, Chang Y, Wu H, Li J, Cao B, Sun X, Wang J, Peng L, Hu X, Yu X, Qiu W. Serum cystatin C and anti-N-methyl-D-aspartate receptor encephalitis. Acta Neurol Scand 2018; 137:515-522. [PMID: 29315460 DOI: 10.1111/ane.12894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Cystatin C (CysC) is associated with many neurodegenerative disorders and autoimmune diseases, but its relationship with anti-N-Methyl-D-aspartate receptor (anti-NMDAR) encephalitis is unknown. METHODS Serum levels of CysC were determined in 66 patients with anti-NMDAR encephalitis and 115 healthy controls. Of the 66 patients, 30 had a follow-up evaluation at 3 months after admission. Association of CysC with anti-NMDAR encephalitis and its clinical parameters were evaluated in the patients. RESULTS The serum levels of CysC were significantly lower in patients with anti-NMDAR encephalitis than in controls (0.70 ± 0.13 vs 0.83 ± 0.17 mg/mL, P < .001). Disease severity and disease duration were significantly associated with CysC levels. Furthermore, a follow-up evaluation revealed that after treatment anti-NMDAR encephalitis patients had significantly increased serum CysC levels (P < .001) and significantly decreased modified Rankin Scale (mRS) scores (P < .001) compared with before treatment. In addition, a significant negative correlation was observed between the change in CysC levels and the change in mRS scores (r = -.700, P < .001). CONCLUSION Our results show that the serum levels of CysC are associated with anti-NMDAR encephalitis and its clinical parameters and that the changes in CysC levels correlate with therapeutic effect. Therefore, our findings provide new insights into the association between serum CysC and anti-NMDAR encephalitis.
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Li J, Wang Z, Qiu W, Yang JJ, Wang Q, Chen S, Pan H. The effect of interaction between EtOH dosage and exposure time on gene expression in DPSC. Genomics 2018; 111:500-507. [PMID: 29596963 DOI: 10.1016/j.ygeno.2018.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/11/2018] [Accepted: 03/07/2018] [Indexed: 12/17/2022]
Abstract
Alcohol (EtOH) dosage and exposure time can affect gene expression. However, whether there exists synergistic effect is unknown. Here, we analyzed the hDPSC gene microarray dataset GSE57255 downloaded from Gene Expression Omnibus and found that the interaction between EtOH dosage and exposure time on gene expression are statistically significant for two probes: 201917_s_at near gene SLC25A36 and 217649_at near gene ZFAND5. GeneMania showed that SLC25A36 and ZFAND5 were related to 20 genes, three of which had alcohol-related functions. WebGestalt revealed that the 22 genes were enriched in 10 KEGG pathways, four of which are related to alcoholic diseases. We explored the possible nonlinear interaction effect and got 172 gene probes with significant p-values. However, no significantly enriched pathways based on the 172 probes were detected. Our analyses indicated a possible molecular mechanism that could help explain why alcohol consumption has both deleterious and beneficial effects on human health.
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Lei ZK, Qin FY, Fang QC, Bai RX, Qiu W, Chen X. Full-field fabric stress mapping by micro Raman spectroscopy in a yarn push-out test. APPLIED OPTICS 2018; 57:924-930. [PMID: 29400768 DOI: 10.1364/ao.57.000924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
The full-field stress distribution of a two-dimensional plain fabric was mapped using micro Raman spectroscopy (MRS) through a novel yarn push-out test, simulating a quasi-static projectile impact on the fabric. The stress-strain relationship for a single yarn was established using a digital image correlation method in a single-yarn tensile test. The relationship between Raman peak shift and aramid Kevlar 49 yarn stress was established using MRS in a single-yarn tensile test. An out-of-plane loading test was conducted on an aramid Kevlar 49 plain fabric, and the yarn stress was measured using MRS. From the full-field fabric stress distribution, it can be observed that there is a cross-shaped distribution of high yarn stress; this result would be helpful in further studies on load transfer on a fabric during a projectile impact.
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Kothari PH, Qiu W, Croteau-Chonka DC, Martinez FD, Liu AH, Lemanske RF, Ober C, Krishnan JA, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, White SR, Naureckas ET, Millstein J, Gauderman WJ, Gilliland FD, Carey VJ, Weiss ST, Raby BA. Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locus. J Allergy Clin Immunol 2018; 141:2282-2286.e6. [PMID: 29374573 DOI: 10.1016/j.jaci.2017.11.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022]
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Long Y, Liang J, Xu H, Huang Q, Yang J, Gao C, Qiu W, Lin S, Chen X. Autoimmune glial fibrillary acidic protein astrocytopathy in Chinese patients: a retrospective study. Eur J Neurol 2018; 25:477-483. [PMID: 29193473 DOI: 10.1111/ene.13531] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 12/17/2022]
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Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018; 12:1. [PMID: 29335020 PMCID: PMC5769240 DOI: 10.1186/s40246-018-0132-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
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Dahlin A, Qiu W, Litonjua AA, Lima JJ, Tamari M, Kubo M, Irvin CG, Peters SP, Wu AC, Weiss ST, Tantisira KG. The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma. THE PHARMACOGENOMICS JOURNAL 2018; 18:665-677. [PMID: 29298996 PMCID: PMC6150906 DOI: 10.1038/s41397-017-0006-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/18/2017] [Indexed: 12/31/2022]
Abstract
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control). We identified 1060 QTLs jointly associated with zileuton-related differential LTB4 production in LCLs and lung function change in patients taking zileuton, of which eight QTLs were also significantly associated with persistent LTB4 production in LCLs following zileuton treatment (i.e., ‘poor’ responders). Four nominally significant trans-eQTLs were predicted to regulate three candidate genes (SELL, MTF2, and GAL), the expression of which was significantly reduced in LCLs following zileuton treatment. Gene and pathway enrichment analyses of QTL associations identified multiple genes and pathways, predominantly related to phosphatidyl inositol signaling via PI3K. We validated the PI3K pathway activation status in a subset of LCLs demonstrating variable zileuton-related LTB4 production, and show that in contrast to LCLs that responded to zileuton, the PI3K pathway was activated in poor responder LCLs. Collectively, these findings demonstrate a role for the PIK3 pathway and its targets as important determinants of differential responsiveness to zileuton.
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Wu Q, Boueiz A, Bozkurt A, Masoomi A, Wang A, DeMeo DL, Weiss ST, Qiu W. Deep Learning Methods for Predicting Disease Status Using Genomic Data. JOURNAL OF BIOMETRICS & BIOSTATISTICS 2018; 9:417. [PMID: 31131151 PMCID: PMC6530791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art machine learning algorithms. A major recent advance in machine learning is the rapid development of deep learning algorithms that can efficiently extract meaningful features from high-dimensional and complex datasets through a stacked and hierarchical learning process. Deep learning has shown breakthrough performance in several areas including image recognition, natural language processing, and speech recognition. However, the performance of deep learning in predicting disease status using genomic datasets is still not well studied. In this article, we performed a review on the four relevant articles that we found through our thorough literature search. All four articles first used auto-encoders to project high-dimensional genomic data to a low dimensional space and then applied the state-of-the-art machine learning algorithms to predict disease status based on the low-dimensional representations. These deep learning approaches outperformed existing prediction methods, such as prediction based on transcript-wise screening and prediction based on principal component analysis. The limitations of the current deep learning approach and possible improvements were also discussed.
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Hayden LP, Hardin ME, Qiu W, Lynch DA, Strand MJ, van Beek EJ, Crapo JD, Silverman EK, Hersh CP. Asthma Is a Risk Factor for Respiratory Exacerbations Without Increased Rate of Lung Function Decline: Five-Year Follow-up in Adult Smokers From the COPDGene Study. Chest 2017; 153:368-377. [PMID: 29248621 DOI: 10.1016/j.chest.2017.11.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/19/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Previous investigations in adult smokers from the COPDGene Study have shown that early-life respiratory disease is associated with reduced lung function, COPD, and airway thickening. Using 5-year follow-up data, we assessed disease progression in subjects who had experienced early-life respiratory disease. We hypothesized that there are alternative pathways to reaching reduced FEV1 and that subjects who had childhood pneumonia, childhood asthma, or asthma-COPD overlap (ACO) would have less lung function decline than subjects without these conditions. METHODS Subjects returning for 5-year follow-up were assessed. Childhood pneumonia was defined by self-reported pneumonia at < 16 years. Childhood asthma was defined as self-reported asthma diagnosed by a health professional at < 16 years. ACO was defined as subjects with COPD who self-reported asthma diagnosed by a health-professional at ≤ 40 years. Smokers with and those without these early-life respiratory diseases were compared on measures of disease progression. RESULTS Follow-up data from 4,915 subjects were examined, including 407 subjects who had childhood pneumonia, 323 subjects who had childhood asthma, and 242 subjects with ACO. History of childhood asthma or ACO was associated with an increased exacerbation frequency (childhood asthma, P < .001; ACO, P = .006) and odds of severe exacerbations (childhood asthma, OR, 1.41; ACO, OR, 1.42). History of childhood pneumonia was associated with increased exacerbations in subjects with COPD (absolute difference [β], 0.17; P = .04). None of these early-life respiratory diseases were associated with an increased rate of lung function decline or progression on CT scans. CONCLUSIONS Subjects who had early-life asthma are at increased risk of developing COPD and of having more active disease with more frequent and severe respiratory exacerbations without an increased rate of lung function decline over a 5-year period. TRIAL REGISTRY ClinicalTrials.gov; No. NCT00608764; https://clinicaltrials.gov.
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Shu Y, Chen C, Chen Y, Xu Y, Chang Y, Li R, Sun X, Peng L, Lu Z, Qiu W. Serum complement levels in anti-N
-methyl-d
-aspartate receptor encephalitis. Eur J Neurol 2017; 25:178-184. [PMID: 29053906 DOI: 10.1111/ene.13495] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
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Zhao S, Zhan X, Wang Y, Ye J, Han L, Qiu W, Gao X, Gu X, Zhang H. Large-scale study of clinical and biochemical characteristics of Chinese patients diagnosed with Krabbe disease. Clin Genet 2017; 93:248-254. [PMID: 28598007 DOI: 10.1111/cge.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 05/11/2017] [Accepted: 06/05/2017] [Indexed: 11/27/2022]
Abstract
Krabbe disease (KD) is a rare disease caused by the deficiency of β-galactocerebrosidase. This study investigated 22 unrelated Chinese patients, including their clinical presentations, plasma psychosine levels and β-galactocerebrosidase gene mutations. We found the late-onset form of KD present in 82% of the patients in our study, which was more prevalent than in patients from other populations. Plasma psychosine levels were elevated in KD, which were correlated with the severity of clinical presentations. Sanger sequencing identified 8 novel mutations, including 7 missense mutations, p.H253Y, p.S259L, p.P318L, p.F350V, p.T428A, p.L530P, p.G586D, and 1 splicing mutation, c.1251+1G>A. Quantitative real-time polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification identified a novel exon 12 and 14 deletion, separately. Next generation sequencing, applied at the final step, revealed 2 missense mutant alleles missed using Sanger sequencing. The most common mutation in Chinese population is p.P154H, which accounts for 20.5% of alleles. Consistent with the higher prevalence of the late-onset form of KD, missense mutations predominated in our study, different with the common mutation types in Europe and Japan. This work was the first large-scale study of Chinese KD patients describing their clinical, biochemical and genetic characteristics, which furthered our understanding of this classical neurological lysosomal storage disease.
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Li XM, Jiang HY, Wang YF, Qiu W, Wang Y, Wu HT. [Ovarian tumor associated with anti-N-methyl-D-aspartate receptor encephalitis: a report of 15 cases]. ZHONGHUA YI XUE ZA ZHI 2017; 97:2932-2935. [PMID: 29050165 DOI: 10.3760/cma.j.issn.0376-2491.2017.37.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To summarize the clinical features of patients with ovarian tumor and anti-N-methyl-D-aspartate receptor(NMDAR) encephalitis, and to explore the influence of operation patterns on the prognosis. Methods: The clinical information of patients with ovarian tumor and anti-NMDAR encephalitis in The 3rd Affiliated Hospital of Sun Yat-Sen University and The Zhujiang Hospital of Southern Medical University were collected and analyzed. Results: There were 15 patients were enrolled in this study, with the average age of 24.5±5.0 years old. The most frequent first symptom was psychosis. The main clinical features were psychosis, seizures, conscious disturbance, autonomic dysfunction, dyskinesia, central hypoventilation and impaired memory. Most patients' symptoms were relieved after immunotherapy and surgery. The number of favorable prognosis of patients (mRS score 0-2) with ovariectomy was higher than that of the patients with ovarian cystectomy (5 vs 3). But the difference had no statistical significance (P=0.529). Conclusions: For young female patients with psychosis, we should be alert to the possibility of anti-NMDAR encephalitis and screen for tumor. Treated with immunotherapy and operation, most patients can get a favorable prognosis.
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Qiu W, Sun B, He F, Zhang Y. MTA-induced Notch activation enhances the proliferation of human dental pulp cells by inhibiting autophagic flux. Int Endod J 2017; 50 Suppl 2:e52-e62. [DOI: 10.1111/iej.12811] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 06/27/2017] [Indexed: 12/26/2022]
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