Publications by authors named "Anqi Cheng"

24 Publications

  • Page 1 of 1

Adherence and Efficacy of Smoking Cessation Treatment Among Patients with COPD in China.

Int J Chron Obstruct Pulmon Dis 2021 30;16:1203-1214. Epub 2021 Apr 30.

Tobacco Medicine and Tobacco Cessation Centre, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.

Background: Smoking cessation is a key intervention for all smokers with chronic obstructive pulmonary disease (COPD). Poor treatment adherence is a challenge in clinical practice that might contribute to the lower efficacy of medication (eg, oral drug). However, it is unclear what factors will influence adherence among smokers with COPD.

Methods: This study was based on an open-label randomized controlled trial (RCT) of varenicline and bupropion for smoking cessation among patients with COPD in China. The medication was given for 12 weeks, and visits and assessments were conducted at weeks 0, 1, 2, 4, 6, 9, 12, and 24. We assessed whether the adherence to smoking cessation treatment affects the smoking cessation efficacy and evaluated predictors of adherence.

Results: A total of 136 participants were recruited from February 2019 to June 2020, and analyzed using the intention-to-treat (ITT) method. In this study, 48.5% (66/136) of the total participants had good adherence to smoking cessation, and good adherence significantly improved the efficacy of smoking cessation (OR=9.60, 95% CI 4.02-22.96, P < 0.001). After adjusting for age, gender, nationality, education, and marital status, we found older age, higher education level, having more previous quitting attempts, stronger self-efficacy and preparation in quitting smoking, recognizing hazards of smoking, longer duration of COPD, and higher St. George's Respiratory Questionnaire (SGRQ) scores were relevant to good adherence (P < 0.05).

Conclusion: To our best knowledge, this is the first study to evaluate adherence to smoking cessation treatment among patients with COPD in China. Our study found that good adherence to smoking cessation treatment significantly improved the smoking cessation efficacy, and predictors of adherence were evaluated. We call on the medical community to pay attention to the adherence to smoking cessation among patients with COPD.
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http://dx.doi.org/10.2147/COPD.S301579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096422PMC
April 2021

Clinical characteristics and outcome of influenza virus infection among adults hospitalized with severe COVID-19: a retrospective cohort study from Wuhan, China.

BMC Infect Dis 2021 Apr 12;21(1):341. Epub 2021 Apr 12.

Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, the Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.

Background: Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that rapidly spreads worldwide and co-infection of COVID-19 and influenza may occur in some cases. We aimed to describe clinical features and outcomes of severe COVID-19 patients with co-infection of influenza virus.

Methods: Retrospective cohort study was performed and a total of 140 patients with severe COVID-19 were enrolled in designated wards of Sino-French New City Branch of Tongji Hospital between Feb 8th and March 15th in Wuhan city, Hubei province, China. The demographic, clinical features, laboratory indices, treatment and outcomes of these patients were collected.

Results: Of 140 severe COVID-19 hospitalized patients, including 73 patients (52.14%) with median age 62 years were influenza virus IgM-positive and 67 patients (47.86%) with median age 66 years were influenza virus IgM-negative. 76 (54.4%) of severe COVID-19 patients were males. Chronic comorbidities consisting mainly of hypertension (45.3%), diabetes (15.8%), chronic respiratory disease (7.2%), cardiovascular disease (5.8%), malignancy (4.3%) and chronic kidney disease (2.2%). Clinical features, including fever (≥38 °C), chill, cough, chest pain, dyspnea, diarrhea and fatigue or myalgia were collected. Fatigue or myalgia was less found in COVID-19 patients with IgM-positive (33.3% vs 50/7%, P = 0.0375). Higher proportion of prolonged activated partial thromboplastin time (APTT) > 42 s was observed in COVID-19 patients with influenza virus IgM-negative (43.8% vs 23.6%, P = 0.0127). Severe COVID-19 Patients with influenza virus IgM positive have a higher cumulative survivor rate than that of patients with influenza virus IgM negative (Log-rank P = 0.0308). Considering age is a potential confounding variable, difference in age was adjusted between different influenza virus IgM status groups, the HR was 0.29 (95% CI, 0.081-1.100). Similarly, difference in gender was adjusted as above, the HR was 0.262 (95% CI, 0.072-0.952) in the COX regression model.

Conclusions: Influenza virus IgM positive may be associated with decreasing in-hospital death.
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http://dx.doi.org/10.1186/s12879-021-05975-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040362PMC
April 2021

Upregulation of ZHX2 predicts poor prognosis and is correlated with immune infiltration in gastric cancer.

FEBS Open Bio 2021 Apr 10. Epub 2021 Apr 10.

Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.

The transcriptional repressor Zinc-finger and homeoboxes 2 (ZHX2) is reported to regulate tumor progression in several human cancers, but little is known about its role in gastric cancer (GC). In this study, we examined the expression of ZHX2 and its relationship with clinicopathological characteristics and prognosis of GC patients, and examined the effect of ZHX2 overexpression in GC cell lines. We used UALCAN and Tumor Immune Estimation Resource (TIMER) to examine ZHX2 mRNA expression, and used Kaplan-Meier plotter to determine whether ZHX2 expression was related to GC prognosis. Expression of ZHX2 protein was detected using immunohistochemical (IHC) staining assays. Cell proliferation was evaluated using CCK-8 assay and colony formation assay while apoptosis was examined by flow cytometry. Wound healing assay and transwell assay were used to detect cell migration and invasion. We also performed gene set enrichment analysis (GSEA) and used The Cancer Genome Atlas (TCGA) database to examine correlation of ZHX2 with immune infiltration. We report that ZHX2 is highly expressed in GC tissues and significantly associated with clinical characteristics. Upregulation of ZHX2 predicted poor prognosis in GC. Furthermore, ZHX2 overexpression can promote proliferation, invasion, and migration, but inhibit apoptosis of GC cells. High expression of ZHX2 in GC is correlated with the presence of infiltrating immune cells, including B cells, CD4 T cells, macrophages and dendritic cells. Our data suggest that high expression of ZHX2 in GC predicts poor prognosis. In addition, ZHX2 may promotes malignant behaviors of GC cells, and immune infiltration might be related to the oncogenic role of ZHX2 in GC.
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http://dx.doi.org/10.1002/2211-5463.13160DOI Listing
April 2021

Association of Uncommon, Noncoding Variants in the APOE Region With Risk of Alzheimer Disease in Adults of European Ancestry.

JAMA Netw Open 2020 10 1;3(10):e2017666. Epub 2020 Oct 1.

Geriatric Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington.

Importance: The ε2 and ε4 alleles of the apolipoprotein E (APOE) gene are associated with Alzheimer disease (AD) risk. Although nearby genetic variants have also been shown to be associated with AD, including rs2075650 in the TOMM40 gene and rs4420638 near the APOC1 gene, it is unknown whether these associations are independent of the ε2 and ε4 alleles.

Objective: To assess whether variants near APOE are associated with AD independently of the ε2/ε3/ε4 genotype.

Design, Setting, And Participants: In this genetic association study of the Alzheimer's Disease Genetics Consortium imputed genotype at data, 14 415 variants near APOE (±500 kilobase) for 18 795 individuals with European ancestry were tested for association with AD using 4 logistic mixed models adjusting for sex, cohort, population structure, and relatedness. Model 1 had no APOE adjustment, and model 2 adjusted for the count of ε2 and ε4 alleles. Model 3 was restricted to ε3 homozygotes, and model 4 was restricted to ε4 homozygotes. Data were downloaded from May 31, 2018, to June 3, 2018, and analyzed from November 1, 2018, to June 24, 2020.

Main Outcomes And Measures: Alzheimer disease affectation status was defined by clinicians using standard National Institute of Neurological and Communicative Disorders and Stroke and Alzheimer Disease and Related Disorders Association criteria. Association was evaluated using Score tests; results with P < .05 divided by the number of independent tests per model were considered statistically significant.

Results: Among the 18 795 individuals in the study, 9704 were affected by AD and 9066 were control individuals; the median age at onset/evaluation was 76 (interquartile range, 70-82) years; and 11 167 were female (59.4%). Associations with AD were found for rs2075650 (odds ratio [OR], 2.59; 95% CI, 2.45-2.75; P = 3.19 × 10-228) and rs4420638 (OR, 2.77; 95% CI, 2.62-2.94; P = 2.99 × 10-254) without APOE adjustment. Although rs2075650 was nominally associated with AD among the ε4 homozygotes (OR, 1.33; 95% CI, 1.00-1.77; P = .047), the association between rs4420638 and AD was eliminated by APOE adjustment (model 2 OR, 1.06 [95% CI, 0.96-1.18; P = .24]; model 3 OR, 1.13 [95% CI, 0.95-1.34; P = .18]; model 4 OR, 0.90 [95% CI, 0.56-1.45; P = .66]). There was a significant association between rs192879175 and AD among ε3 homozygotes (OR, 0.50; 95% CI, 0.37-0.68; P = 8.30 × 10-6).

Conclusions And Relevance: The results of this genetic association study suggest that ε2/ε3/ε4 alleles are not the only variants in the APOE region that are associated with AD risk. Additional work with independent data is needed to replicate these results.
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http://dx.doi.org/10.1001/jamanetworkopen.2020.17666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7582128PMC
October 2020

Identification of the Prognostic Value of Immune-Related Genes in Esophageal Cancer.

Front Genet 2020 21;11:989. Epub 2020 Aug 21.

Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.

Esophageal cancer (EC) is a serious malignant tumor, both in terms of mortality and prognosis, and immune-related genes (IRGs) are key contributors to its development. In recent years, immunotherapy for tumors has been widely studied, but a practical prognostic model based on immune-related genes (IRGs) in EC has not been established and reported. This study aimed to develop an immunogenomic risk score for predicting survival outcomes among EC patients. In this study, we downloaded the transcriptome profiling data and matched clinical data of EC patients from The Cancer Genome Atlas (TCGA) database and found 4,094 differentially expressed genes (DEGs) between EC and normal esophageal tissue ( < 0.05 and fold change >2). Then, the intersection of DEGs and the immune genes in the "ImmPort" database resulted in 303 differentially expressed immune-related genes (DEIRGs). Next, through univariate Cox regression analysis of DEIRGs, we obtained 17 immune genes related to prognosis. We detected nine optimal survival-associated IRGs () by using Lasso regression and multivariate Cox regression analyses. Finally, we used those survival-associated IRGs to construct a risk model to predict the prognosis of EC patients. This model could accurately predict overall survival in EC and could be used as a classifier for the evaluation of low-risk and high-risk groups. In conclusion, we identified a practical and robust nine-gene prognostic model based on immune gene dataset. These genes may provide valuable biomarkers and prognostic predictors for EC patients and could be further studied to help understand the mechanism of EC occurrence and development.
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http://dx.doi.org/10.3389/fgene.2020.00989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472890PMC
August 2020

Circular RNA circREPS2 Acts as a Sponge of miR-558 to Suppress Gastric Cancer Progression by Regulating RUNX3/β-catenin Signaling.

Mol Ther Nucleic Acids 2020 Sep 27;21:577-591. Epub 2020 Jun 27.

Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China. Electronic address:

Circular RNAs (circRNAs) play an essential regulatory role in multiple cancers. However, the role of a large number of circRNAs in gastric cancer (GC) is still unknown. Here, hsa_circ_0139996 (circREPS2), a novel circRNA that was significantly downregulated in GC, was selected for further investigation. circREPS2 was validated and analyzed by DNA sequencing and quantitative real-time PCR. The roles of circREPS2 in GC cells were verified by gain- and loss-of-function experiments. Bioinformatics analysis, luciferase reporter, RNA pull-down, and RNA immunoprecipitation assays were performed to evaluate the functional mechanism of circREPS2 on microRNA-558 (miR-558)/RUNX3/β-catenin axis in GC cells. In the present study, we found that circREPS2 was downregulated in GC tissues and cell lines. Low expression of circREPS2 was associated with a higher tumor-node-metastasis (TNM) stage, poor tumor differentiation, and larger tumor size in GC patients. Functionally, circREPS2 significantly inhibited GC cell proliferation, migration, invasion, and epithelial-mesenchymal transformation (EMT) in vitro and tumorigenesis in vivo. Furthermore, our data demonstrated that circREPS2 acted as a miR-558 sponge and upregulated RUNX3 expression to inactivate β-catenin signaling in GC cells. In conclusion, circREPS2 suppresses the progression of GC via miR-558/RUNX3/β-catenin signaling and is a novel promising biomarker and target for GC treatment.
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http://dx.doi.org/10.1016/j.omtn.2020.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390859PMC
September 2020

Circular RNA circFGD4 suppresses gastric cancer progression via modulating miR-532-3p/APC/β-catenin signalling pathway.

Clin Sci (Lond) 2020 07;134(13):1821-1839

Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China.

Background: Mounting evidence has displayed critical roles of circular RNAs (circRNAs) in multiple cancers. The underlying mechanisms by which circFGD4 contributed to gastric cancer (GC) are still unclear.

Methods: The levels and clinical values of circFGD4 in GC patients were detected and analysed by quantitative real-time PCR. The biological roles of circFGD4 in GC were assessed in vitro and in vivo experiments. Dual-luciferase reporter, fluorescence in situ hybridization, RNA immunoprecipitation, biotin-coupled RNA pull-down, and TOP/Flash and FOP/Flash reporter gene assays were employed to evaluate the effects of circFGD4 on miR-532-3p-mediated adenomatous polyposis coli (APC)/β-catenin signalling in GC cells.

Results: circFGD4 expression was down-regulated the most in human GC tissues and cell lines. Low expression of circFGD4 was correlated with poor tumour differentiation, lymphatic metastasis, and poor prognosis of GC patients. circFGD4 suppressed GC cell viability, colony formation, migration, induced epithelial-mesenchymal transition (EMT), and tumorigenesis and metastasis in vivo. Next, we validated that circFGD4 acted as a sponge of miR-532-3p to relieve the tumour-promoting effects of miR-532-3p on its target APC. The mechanistic analysis demonstrated that the circFGD4 suppressed GC cell viability, migration, and EMT by modulating the miR-532-3p/APC axis to inactivate the β-catenin signalling.

Conclusion: circFGD4 suppressed GC progression through sponging miR-532-3p and enhancing APC expression to inactivate the β-catenin signalling. Thus circFGD4 provides a novel potential biomarker and valuable therapeutic strategy for GC.
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http://dx.doi.org/10.1042/CS20191043DOI Listing
July 2020

Prevalence and risk factors of small airway dysfunction, and association with smoking, in China: findings from a national cross-sectional study.

Lancet Respir Med 2020 11 26;8(11):1081-1093. Epub 2020 Jun 26.

State Key Laboratory of Biotherapy of China and Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China.

Background: Small airway dysfunction is a common but neglected respiratory abnormality. Little is known about its prevalence, risk factors, and prognostic factors in China or anywhere else in the world. We aimed to estimate the prevalence of small airway dysfunction using spirometry before and after bronchodilation, both overall and in specific population subgroups; assess its association with a range of lifestyle and environmental factors (particularly smoking); and estimate the burden of small airway dysfunction in China.

Methods: From June, 2012, to May, 2015, the nationally representative China Pulmonary Health study invited 57 779 adults to participate using a multistage stratified sampling method from ten provinces (or equivalent), and 50 479 patients with valid lung function testing results were included in the analysis. We diagnosed small airway dysfunction on the basis of at least two of the following three indicators of lung function being less than 65% of predicted: maximal mid-expiratory flow, forced expiratory flow (FEF) 50%, and FEF 75%. Small airway dysfunction was further categorised into pre-small airway dysfunction (defined as having normal FEV and FEV/forced vital capacity [FVC] ratio before bronchodilator inhalation), and post-small airway dysfunction (defined as having normal FEV and FEV/FVC ratio both before and after bronchodilator inhalation). Logistic regression yielded adjusted odds ratios (ORs) for small airway dysfunction associated with smoking and other lifestyle and environmental factors. We further estimated the total number of cases of small airway dysfunction in China by applying present study findings to national census data.

Findings: Overall the prevalence of small airway dysfunction was 43·5% (95% CI 40·7-46·3), pre-small airway dysfunction was 25·5% (23·6-27·5), and post-small airway dysfunction was 11·3% (10·3-12·5). After multifactor regression analysis, the risk of small airway dysfunction was significantly associated with age, gender, urbanisation, education level, cigarette smoking, passive smoking, biomass use, exposure to high particulate matter with a diameter less than 2·5 μm (PM) concentrations, history of chronic cough during childhood, history of childhood pneumonia or bronchitis, parental history of respiratory diseases, and increase of body-mass index (BMI) by 5 kg/m. The ORs for small airway dysfunction and pre-small airway dysfunction were similar, whereas larger effect sizes were generally seen for post-small airway dysfunction than for either small airway dysfunction or pre-small airway dysfunction. For post-small airway dysfunction, cigarette smoking, exposure to PM, and increase of BMI by 5 kg/m were significantly associated with increased risk, among preventable risk factors. There was also a dose-response association between cigarette smoking and post-small airway dysfunction among men, but not among women. We estimate that, in 2015, 426 (95% CI 411-468) million adults had small airway dysfunction, 253 (238-278) million had pre-small airway dysfunction, and 111 (104-126) million had post-small airway dysfunction in China.

Interpretation: In China, spirometry-defined small airway dysfunction is highly prevalent, with cigarette smoking being a major modifiable risk factor, along with PM exposure and increase of BMI by 5 kg/m. Our findings emphasise the urgent need to develop and implement effective primary and secondary prevention strategies to reduce the burden of this condition in the general population.

Funding: Ministry of Science and Technology of China; National Natural Science Foundation of China; National Health Commission of China.
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http://dx.doi.org/10.1016/S2213-2600(20)30155-7DOI Listing
November 2020

Circ-OXCT1 Suppresses Gastric Cancer EMT and Metastasis by Attenuating TGF-β Pathway Through the Circ-OXCT1/miR-136/SMAD4 Axis.

Onco Targets Ther 2020 11;13:3987-3998. Epub 2020 May 11.

Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, People's Republic of China.

Background: Circular RNAs (circRNAs) have been proven to play important roles in tumorigenesis. However, the mechanism by which circRNAs act on gastric cancer (GC) through epithelial-to-mesenchymal transition (EMT) is unclear. In this study, we identified circ-OXCT1 and elucidated its function on EMT in GC.

Methods: Tissue circRNA microarray analysis and qRT-PCR were utilized to determine the expression level of circ-OXCT1 in GC. Luciferase reporter assay and FISH were employed to confirm the interaction between circ-OXCT1 and miR-136. CCK-8, cloning formation, transwell, wound healing, nude mice experiment, circ-OXCT1 overexpression and silencing were conducted to elucidate the function of circ-OXCT1 in vivo and in vitro. Western blot and rescue experiment were carried out to evaluate the changes of EMT-related proteins induced by circ-OXCT1 overexpression or silencing.

Results: Circ-OXCT1 was downregulated in GC tissues and cell lines. Its expression level was significantly associated with lymph node metastasis, pathologic stage and overall survival rate through clinicopathologic data analysis. Circ-OXCT1 silencing downregulated SMAD4 expression and accordingly regulated expression of E-cadherin, N-cadherin and vimentin through the transforming growth factor-beta (TGF-β)/Smad signaling pathway by a circ-OXCT1/miR-136/SMAD4 axis, resulting in enhancement of EMT and subsequent boost of cell migration, invasion and nude mice lung metastasis.

Conclusion: Our data showed that circ-OXCT1 suppresses gastric cancer EMT and metastasis through TGF-β/Smad signaling pathway. The clinicopathologic data analysis revealed that circ-OXCT1 overexpression could be a novel treatment for advanced GC especially with distant metastasis by targeting the circ-OXCT1/miR-136/SMAD4 axis.
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http://dx.doi.org/10.2147/OTT.S239789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236241PMC
May 2020

Circular RNA circGRAMD1B inhibits gastric cancer progression by sponging miR-130a-3p and regulating PTEN and p21 expression.

Aging (Albany NY) 2019 11 13;11(21):9689-9708. Epub 2019 Nov 13.

Department of Gastrointestinal Surgery, Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.

Circular RNAs (circRNAs) have emerged as essential regulators and biomarkers of various cancers. However, the effects of a novel circRNA termed circGRAMD1B in human gastric cancer (GC) remain unclear. A microarray was used to screen circRNA expression in GC. Quantitative real-time PCR was used to detect the expression of circGRAMD1B. Gain- and loss- of-function experiments were performed to investigate the biological functions of circGRAMD1B in vitro and vivo. Bioinformatics analysis, fluorescence in situ hybridization, dual-luciferase reporter assay, RNA immunoprecipitation, RNA pull-down assay, and rescue experiments were conducted to confirm the underlying mechanisms of competitive endogenous RNAs (ceRNAs). We screened differentially expressed circRNAs and found that circGRAMD1B expression was downregulated in GC tissues and cell lines. Functionally, circGRAMD1B acted as an anti-oncogene and inhibited the proliferation, migration, and invasion abilities of GC cells. Then, we verified that circGRAMD1B served as a sponge that targeted miR-130a-3p in GC cells; circGRAMD1B alleviated GC cell proliferation, migration, and invasion by targeting miR-130a-3p. A mechanistic analysis showed that PTEN and p21 were involved in circGRAMD1B/miR-130a-3p axis-inhibited GC tumorigenesis. Our findings suggest that circGRAMD1B plays an important role in GC progression by regulating miR-130a-3p-PTEN/p21, which may provide a potential biomarker and therapeutic target for GC.
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http://dx.doi.org/10.18632/aging.102414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874462PMC
November 2019

A four-gene transcript score to predict metastatic-lethal progression in men treated for localized prostate cancer: Development and validation studies.

Prostate 2019 10 2;79(14):1589-1596. Epub 2019 Aug 2.

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.

Background: Molecular studies have tried to address the unmet need for prognostic biomarkers in prostate cancer (PCa). Some gene expression tests improve upon clinical factors for prediction of outcomes, but additional tools for accurate prediction of tumor aggressiveness are needed.

Methods: Based on a previously published panel of 23 gene transcripts that distinguished patients with metastatic progression, we constructed a prediction model using independent training and testing datasets. Using the validated messenger RNAs and Gleason score (GS), we performed model selection in the training set to define a final locked model to classify patients who developed metastatic-lethal events from those who remained recurrence-free. In an independent testing dataset, we compared our locked model to established clinical prognostic factors and utilized Kaplan-Meier curves and receiver operating characteristic analyses to evaluate the model's performance.

Results: Thirteen of 23 previously identified gene transcripts that stratified patients with aggressive PCa were validated in the training dataset. These biomarkers plus GS were used to develop a four-gene (CST2, FBLN1, TNFRSF19, and ZNF704) transcript (4GT) score that was significantly higher in patients who progressed to metastatic-lethal events compared to those without recurrence in the testing dataset (P = 5.7 × 10 ). The 4GT score provided higher prediction accuracy (area under the ROC curve [AUC] = 0.76; 95% confidence interval [CI] = 0.69-0.83; partial area under the ROC curve [pAUC] = 0.008) than GS alone (AUC = 0.63; 95% CI = 0.56-0.70; pAUC = 0.002), and it improved risk stratification in subgroups defined by a combination of clinicopathological features (ie, Cancer of the Prostate Risk Assessment-Surgery).

Conclusion: Our validated 4GT score has prognostic value for metastatic-lethal progression in men treated for localized PCa and warrants further evaluation for its clinical utility.
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http://dx.doi.org/10.1002/pros.23882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715522PMC
October 2019

Vigorous Physical Activity Is Associated with Lower Risk of Metastatic-Lethal Progression in Prostate Cancer and Hypomethylation in the Gene.

Cancer Epidemiol Biomarkers Prev 2019 02 21;28(2):258-264. Epub 2018 Nov 21.

Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington.

Background: There is preliminary evidence linking physical activity to better prostate cancer outcomes, though the molecular mechanisms underlying this association are not clear.

Methods: In a Seattle-based cohort of patients diagnosed with clinically localized prostate cancer and prospective follow-up for outcomes ( = 1,354), we studied the association between self-reported vigorous physical activity and prostate cancer progression to a metastatic-lethal phenotype. A subset of patients had prostate cancer tissue samples available for investigating DNA methylation (Infinium HumanMethylation450 BeadChip array) and exercise ( = 524).

Results: Patients who had vigorous physical activity at least once per week during the year before diagnosis (∼79% of the cohort) were significantly less likely to progress to metastatic-lethal prostate cancer compared with those who had vigorous physical activity less frequently (adjusted hazard ratio = 0.63; = 0.029). Among the subset of men who had radical prostatectomy as primary treatment and tumor tissue available, a differentially methylated region (DMR) was identified (family-wise error rate = 0.03, hypomethylated in the weekly exercise group), with 9 methylation probes located in the promoter region of . This gene encodes a calcium binding protein involved in innate immune response. The methylation level of the nine CpGs was inversely correlated with gene expression (average correlation coefficient = -0.35).

Conclusions: Vigorous physical activity before diagnosis is associated with epigenetic alterations of and prostate cancer metastatic-lethal progression.

Impact: This analysis provides strong evidence for the association between vigorous physical activity and a less likelihood to develop metastatic-lethal progression, and a suggestive link between exercise and DNA methylation in the gene.
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http://dx.doi.org/10.1158/1055-9965.EPI-18-0622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363836PMC
February 2019

Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans.

J Infect Dis 2019 03;219(7):1058-1066

Department of Medicine, University of Washington, Seattle, Washington.

Background: Orolabial herpes simplex virus type 1 (HSV-1) infection has a wide spectrum of severity in immunocompetent persons. To study the role of viral genotype and host immunity, we characterized oral HSV-1 shedding rates and host cellular response, and genotyped viral strains, in monozygotic (MZ) and dizygotic (DZ) twins.

Methods: A total of 29 MZ and 22 DZ HSV-1-seropositive twin pairs were evaluated for oral HSV-1 shedding for 60 days. HSV-1 strains from twins were genotyped as identical or different. CD4+ T-cell responses to HSV-1 proteins were studied.

Results: The median per person oral HSV shedding rate was 9% of days that a swab was obtained (mean, 10.2% of days). A positive correlation between shedding rates was observed within all twin pairs, and in the MZ and DZ twins. In twin subsets with sufficient HSV-1 DNA to genotype, 15 had the same strain and 14 had different strains. Viral shedding rates were correlated for those with the same but not different strains. The median number of HSV-1 open reading frames recognized per person was 16. The agreement in the CD4+ T-cell response to specific HSV-1 open reading frames was greater between MZ twins than between unrelated persons (P = .002).

Conclusion: Viral strain characteristics likely contribute to oral HSV-1 shedding rates.
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http://dx.doi.org/10.1093/infdis/jiy631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420167PMC
March 2019

Quadrivalent HPV vaccine in HIV-1-infected early adolescent girls and boys in Kenya: Month 7 and 12 post vaccine immunogenicity and correlation with immune status.

Vaccine 2018 11 5;36(46):7025-7032. Epub 2018 Oct 5.

Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Departments of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA.

Introduction: In sub-Saharan Africa, a generation of HIV-1-infected children is approaching the age of sexual debut and becoming at risk for HPV infection and its sequelae. We assessed safety and immunogenicity of the quadrivalent HPV (qHPV) vaccine in HIV-1-infected adolescents.

Methods: In an open-label trial among Kenyan, HIV-1-infected adolescents aged 9-14 years, we administered the qHPV vaccine at 0, 2 and 6 months and measured antibody titers to HPV-16, 18, 6 and 11 at month 7 and 12 post-vaccination. Measures of immunogenic response from HIV-1-negative historical cohorts from Africa and HIV-1 positive adolescent cohorts from the USA were used for comparison.

Results: We enrolled 100 girls and 80 boys with a median age of 12 years and median baseline CD4 cell count of 684 (IQR 478, 935) cells/µL. One hundred and fifty four (86%) were receiving antiretroviral therapy for a median of 4.5 (IQR 2.3, 6.3) years; 110 (71%) had <400 copies of plasma HIV-1 RNA/mL. Of 189 enrolled children, 179 received all three doses. Two hundred and eighty five (64%) of 445 adverse events were injection site reactions; none were greater than grade 2. Of 6 Serious Adverse Events (SAEs), none were considered vaccine related. Seroconversion to HPV-18, 16, 11, 6 at month 7 occurred in 93.3%, 98.3%, 97.2% and 99.6% of vaccine recipients; similar rates have been reported in historical controls. The mean log HPV antibody titer measured at month 7 increased with each log increase in CD4 by 1.4 (95% CI: 1.1-1.7) for HPV-18; 1.2 (0.9-1.4) for HPV-16; 1.1 (0.8-1.3) for HPV-11; 0.7 (0.5-1.0) for HPV-6 (all p < 0.0001).

Conclusion: Almost all Kenyan HIV-1-infected adolescents mounted an immune response comparable to other immunized populations. HPV antibody titers were higher in those with preserved CD4 cell counts. Longer term-follow up will determine sustainability of the immune response. ClinicalTrials.gov number, NCT00557245.
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http://dx.doi.org/10.1016/j.vaccine.2018.09.059DOI Listing
November 2018

A five-CpG DNA methylation score to predict metastatic-lethal outcomes in men treated with radical prostatectomy for localized prostate cancer.

Prostate 2018 Jun 28. Epub 2018 Jun 28.

Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington.

Background: Prognostic biomarkers for localized prostate cancer (PCa) could improve personalized medicine. Our group previously identified a panel of differentially methylated CpGs in primary tumor tissue that predict disease aggressiveness, and here we further validate these biomarkers.

Methods: Pyrosequencing was used to assess CpG methylation of eight biomarkers previously identified using the HumanMethylation450 array; CpGs with strongly correlated (r >0.70) results were considered technically validated. Logistic regression incorporating the validated CpGs and Gleason sum was used to define and lock a final model to stratify men with metastatic-lethal versus non-recurrent PCa in a training dataset. Coefficients from the final model were then used to construct a DNA methylation score, which was evaluated by logistic regression and Receiver Operating Characteristic (ROC) curve analyses in an independent testing dataset.

Results: Five CpGs were technically validated and all were retained (P < 0.05) in the final model. The 5-CpG and Gleason sum coefficients were used to calculate a methylation score, which was higher in men with metastatic-lethal progression (P = 6.8 × 10 ) in the testing dataset. For each unit increase in the score there was a four-fold increase in risk of metastatic-lethal events (odds ratio, OR = 4.0, 95%CI = 1.8-14.3). At 95% specificity, sensitivity was 74% for the score compared to 53% for Gleason sum alone. The score demonstrated better prediction performance (AUC = 0.91; pAUC = 0.037) compared to Gleason sum alone (AUC = 0.87; pAUC = 0.025).

Conclusions: The DNA methylation score improved upon Gleason sum for predicting metastatic-lethal progression and holds promise for risk stratification of men with aggressive tumors. This prognostic score warrants further evaluation as a tool for improving patient outcomes.
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http://dx.doi.org/10.1002/pros.23667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120526PMC
June 2018

Aspergillus fumigatus during COPD exacerbation: a pair-matched retrospective study.

BMC Pulm Med 2018 Apr 3;18(1):55. Epub 2018 Apr 3.

Department of Respiratory and Critical Care Medicine, Beijing Hospital, Beijing, 100730, People's Republic of China.

Background: Recently awareness of the importance of Aspergillus colonization in the airway of patients with chronic obstructive pulmonary disease (COPD) was rising. The aim of this study was to investigate the clinical features and short-term outcomes of COPD patients with Aspergillus colonization during acute exacerbation.

Methods: A pair-matched retrospective study on patients presenting with COPD exacerbation was conducted from January 2014 to March 2016 in Beijing Hospital, China.

Results: Twenty-three patients with Aspergillus colonization and 69 patients as controls, diagnosed of COPD exacerbation, were included in this study at a pair-matched ratio of 1:3. In stable stage, the percentage of patients with high-dose corticosteroids inhalation in the Aspergillus colonization group is higher than that of in control group (65.5% vs 33.3%, p = 0.048). Multivariate analysis showed that corticosteroids use was the risk factor for isolation of Aspergillus. In acute exacerbation stage, patients in Aspergillus colonization group received higher dose of inhaled corticosteroids and more types of antibiotics than control group. The short-time outcome hinted that the remission time and the duration of hospitalization were longer in the Aspergillus colonization group than in the control group (remission time: 11 ± 4 days vs 7 ± 4 days, p = 0.001; duration: 15 ± 5 days vs 12 ± 4 days, p = 0.011).

Conclusions: Aspergillus colonization in the lower respiratory tract of COPD patients showed typical clinical manifestations, affected their short time outcome and provided a dilemma of clinical treatment strategy.
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http://dx.doi.org/10.1186/s12890-018-0611-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883425PMC
April 2018

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U and U regions from genital swabs collected from 3 continents.

Virology 2017 10 13;510:90-98. Epub 2017 Jul 13.

Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA; Benaroya Research Institute, Seattle, WA, USA.

Introduction: Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines.

Methods: Genital lesion swabs containing ≥ 10log copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (U_U) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction.

Results: Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated UU segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids.

Conclusions: Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.
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http://dx.doi.org/10.1016/j.virol.2017.06.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5565707PMC
October 2017

Selective Expression of CCR10 and CXCR3 by Circulating Human Herpes Simplex Virus-Specific CD8 T Cells.

J Virol 2017 10 12;91(19). Epub 2017 Sep 12.

Department of Global Health, Program in Pathobiology, University of Washington, Seattle, Washington, USA

Herpes simplex virus (HSV) infection is restricted to epithelial cells and neurons and is controlled by CD8 T cells. These cells both traffic to epithelial sites of recurrent lytic infection and to ganglia and persist at the dermal-epidermal junction for up to 12 weeks after lesion resolution. We previously showed that cutaneous lymphocyte-associated antigen (CLA), a functional E-selectin ligand (ESL), is selectively expressed on circulating HSV-2-specific CD8 T cells. CLA/ESL mediates adhesion of T cells to inflamed vascular endothelium. Later stages in T-cell homing involve chemokines (Ch) and lymphocyte chemokine receptors (ChR) for vascular wall arrest and diapedesis. Several candidate ChR have been implicated in skin homing. We measured cell surface ChR on HSV-specific human peripheral blood CD8 T cells and extended our studies to HSV-1. We observed preferential cell surface expression of CCR10 and CXCR3 by HSV-specific CD8 T cells compared to CD8 T cells specific for control viruses, Epstein-Barr virus (EBV) and cytomegalovirus (CMV), and compared to bulk memory CD8 T cells. CXCR3 ligand mRNA levels were selectively increased in skin biopsy specimens from persons with recurrent HSV-2, while the mRNA levels of the CCR10 ligand CCL27 were equivalent in lesion and control skin. Our data are consistent with a model in which CCL27 drives baseline recruitment of HSV-specific CD8 T cells expressing CCR10, while interferon-responsive CXCR3 ligands recruit additional cells in response to virus-driven inflammation. HSV-2 causes very localized recurrent infections in the skin and genital mucosa. Virus-specific CD8 T cells home to the site of recurrent infection and participate in viral clearance. The exit of T cells from the blood involves the use of chemokine receptors on the T-cell surface and chemokines that are present in infected tissue. In this study, circulating HSV-2-specific CD8 T cells were identified using specific fluorescent tetramer reagents, and their expression of several candidate skin-homing-associated chemokine receptors was measured using flow cytometry. We found that two chemokine receptors, CXCR3 and CCR10, are upregulated on HSV-specific CD8 T cells in blood. The chemokines corresponding to these receptors are also expressed in infected tissues. Vaccine strategies to prime CD8 T cells to home to HSV lesions should elicit these chemokine receptors if possible to increase the homing of vaccine-primed cells to sites of infection.
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http://dx.doi.org/10.1128/JVI.00810-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599734PMC
October 2017

DIMT1 overexpression correlates with progression and prognosis in gastric carcinoma.

Hum Pathol 2017 12 7;70:35-42. Epub 2017 Jun 7.

Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China. Electronic address:

We investigated the expression of dimethyladenosine transferase 1 homolog (DIMT1) in human gastric carcinoma (GC) tissues, pericarcinoma histologically normal tissues, and normal gastric tissues and explored its clinical significance. Immunohistochemistry staining was used to detect the expression of DIMT1, and the findings were compared with clinicopathological features of patients with GC. The result also was ascertained by Western blotting. The Kaplan-Meier method and log-rank test were used to compare the overall survival rate and time in the DIMT1 low-level and high-level expression groups. Immunohistochemical staining indicated that the expression of DIMT1 in GC tissues (65/75; 86.7%) was significantly more common (P<.001) than that in pericarcinoma histologically normal tissues (14/75; 18.7%) and normal gastric tissues (2/12; 16.7%). High expression of DIMT1 correlated closely with differentiation (P=.023), invasion (P=.042), lymph node metastasis (P=.008), distant metastasis (P=.006), and TNM stage (P=.013). Western blotting showed that DIMT1 expression correlated positively with TNM stage and implied that more advanced TNM stage was accompanied by higher expression of DIMT1 (P<.001). Kaplan-Meier survival analysis showed that high DIMT1 expression correlated significantly (P<.001) with a poor prognosis. Our data suggest that DIMT1 is a useful molecular biomarker to predict tumor progression and prognosis in patients with GC.
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http://dx.doi.org/10.1016/j.humpath.2017.02.034DOI Listing
December 2017

In Situ Detection of Regulatory T Cells in Human Genital Herpes Simplex Virus Type 2 (HSV-2) Reactivation and Their Influence on Spontaneous HSV-2 Reactivation.

J Infect Dis 2016 07 25;214(1):23-31. Epub 2016 Apr 25.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Laboratory Medicine Department of Medicine.

Background: Herpes simplex virus type 2 (HSV-2) reactivation is accompanied by a sustained influx of CD4(+) and CD8(+) T cells that persist in genital tissue for extended periods. While CD4(+) T cells have long been recognized as being present in herpetic ulcerations, their role in subclinical reactivation and persistence is less well known, especially the role of CD4(+) regulatory T cells (Tregs).

Methods: We characterized the Treg (CD4(+)Foxp3(+)) population during human HSV-2 reactivation in situ in sequential genital skin biopsy specimens obtained from HSV-2-seropositive subjects at the time of lesion onset up to 8 weeks after healing.

Results: High numbers of Tregs infiltrated to the site of viral reactivation and persisted in proximity to conventional CD4(+) T cells (Tconvs) and CD8(+) T cells. Treg density peaked during the lesion stage of the reactivation. The number of Tregs from all time points (lesion, healed, 2 weeks after healing, 4 weeks after healing, and 8 weeks after healing) was significantly higher than in control biopsy specimens from unaffected skin. There was a direct correlation between HSV-2 titer and Treg density.

Conclusions: The association of a high Treg to Tconv ratio with high viral shedding suggests that the balance between regulatory and effector T cells influences human HSV-2 disease.
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http://dx.doi.org/10.1093/infdis/jiw091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907414PMC
July 2016

Digital detection of endonuclease mediated gene disruption in the HIV provirus.

Sci Rep 2016 Feb 2;6:20064. Epub 2016 Feb 2.

Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA.

Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields. Among all fields, the T7 endonuclease mismatch cleavage assay, or Surveyor assay, is the most commonly used tool to assess genomic editing by designer nucleases. This assay, while relatively easy to perform, provides only a semi-quantitative measure of mutation efficiency that lacks sensitivity and accuracy. We demonstrate a simple droplet digital PCR assay that quickly quantitates a range of indel mutations with detection as low as 0.02% mutant in a wild type background and precision (≤6%CV) and accuracy superior to either mismatch cleavage assay or clonal sequencing when compared to next-generation sequencing. The precision and simplicity of this assay will facilitate comparison of gene editing approaches and their optimization, accelerating progress in this rapidly-moving field.
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http://dx.doi.org/10.1038/srep20064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735761PMC
February 2016

Consistent viral DNA quantification after prolonged storage at ambient temperature.

J Virol Methods 2016 Feb 22;228:91-4. Epub 2015 Nov 22.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States; Department of Laboratory Medicine, University of Washington, United States; Department of Biostatistics, University of Washington, United States. Electronic address:

Long-term storage of biological specimens at low temperatures is costly and impractical in resource limited settings, where the disease burden of chronic viral infections is highest, and the need for research greatest. We examined the necessity of cold storage by comparing the quantity of HHV-8 DNA recovered from swab samples before and after 9-11 months of storage at temperatures of -20 °C, 4 °C and 37 °C. Quantitative levels of HHV-8 DNA remained consistent for laboratory or mucosal swab samples regardless of storage temperature. Freezer storage is determined to be not necessary for mucosal samples destined for HHV-8 DNA quantification.
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http://dx.doi.org/10.1016/j.jviromet.2015.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718791PMC
February 2016

Evaluating risk factors for Clostridium difficile infection in adult and pediatric hematopoietic cell transplant recipients.

Antimicrob Resist Infect Control 2015 14;4:41. Epub 2015 Oct 14.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Medicine, University of Washington, Seattle, WA USA ; Infection Prevention, Seattle, WA USA.

Background: Although hematopoietic cell transplant (HCT) recipients are routinely exposed to classic risk factors for Clostridium difficile infection (CDI), few studies have assessed CDI risk in these high-risk patients, and data are especially lacking for pediatric HCT recipients. We aimed to determine incidence and risk factors for CDI in adult and pediatric allogeneic HCT recipients.

Methods: CDI was defined as having diarrhea that tested positive for C. difficile via PCR, cytotoxin assay, or dual enzyme immunoassays. We included all patients who received an allogeneic HCT from 2008 to 2012 at the Fred Hutchinson Cancer Research Center; those <1 year old or with CDI within 8 weeks pre-HCT were excluded. Patients were categorized by transplanting hospital ("adult" or "pediatric") and followed for 100 days post-HCT.

Results: Of 1182 HCT recipients, CDI was diagnosed in 17 % (33/192) of pediatric recipients for an incidence of 20 per 10,000 patient-days, and 11 % (107/990) of adult recipients for an incidence of 12 per 10,000. Pediatric recipients were diagnosed a median of 51 days (interquartile range [IQR]: 5, 72) after HCT and adults at 16 days (IQR = 5, 49). Compared with calendar year 2008, pediatric recipients transplanted in 2012 were at increased risk for CDI (hazard ratio [HR] = 3.99, p =.02). Myeloablative conditioning increased CDI risk in adult recipients (HR = 1.81, p =.005).

Conclusions: Pediatric and adult allogeneic recipients are at high risk of CDI post-HCT, particularly adult recipients of myeloablative conditioning. Differences in CDI incidence between children and adults may have resulted from exposure differences related to age; therefore, separately evaluating these groups should be considered in future CDI studies.
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http://dx.doi.org/10.1186/s13756-015-0081-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4606905PMC
October 2015

Clinical utility of droplet digital PCR for human cytomegalovirus.

J Clin Microbiol 2014 Aug 28;52(8):2844-8. Epub 2014 May 28.

Molecular Virology Laboratory, Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA The Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

Human cytomegalovirus (CMV) has historically been the major infectious cause of morbidity and mortality among patients receiving hematopoietic cell or organ transplant. Standard care in a transplant setting involves frequent monitoring of CMV viral load over weeks to months to determine when antiviral treatment may be required. Quantitative PCR (qPCR) is the standard molecular diagnostic method for monitoring. Recently, digital PCR (dPCR) has shown promise in viral diagnostics, although current dPCR systems have lower throughput than qPCR systems. Here, we compare qPCR and droplet digital PCR (ddPCR) for CMV detection in patient plasma samples. Droplet digital PCR exhibits increased precision over qPCR at viral loads of ≥4 log10 with equivalent sensitivity. However, retrospective analysis of longitudinal samples from transplant patients with CMV viral loads near therapeutic thresholds did not provide evidence that the improved precision of ddPCR would be of clinical benefit. Given the throughput advantages of current qPCR systems, a widespread switch to dPCR for CMV monitoring would appear premature.
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http://dx.doi.org/10.1128/JCM.00803-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136144PMC
August 2014