Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Background

Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.

Patients and methods

We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes.

Results

Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016).

Conclusions

Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Detection and genetic characterization of porcine pegivirus in pigs in the United States

Using next-generation sequencing on vesicular swab and serum from swine from the USA exhibiting lameness and vesicles, porcine pegivirus (PPgV) was first identified and genetically characterized in the United States. Further screening using RT-PCR revealed that 24 of 159 (15.1%) serum samples were positive for PPgV. Future studies are needed to understand clinical impacts of the virus.

Clinical and molecular insights into Glanzmann's thrombasthenia in China

Glanzmann's thrombasthenia (GT) is a rare bleeding disorder characterized by spontaneous mucocutaneous bleeding. The disorder is caused by quantitative or qualitative defects in integrin αIIbβ3 (encoded by ITGA2B and ITGB3) on the platelet and is more common in consanguineous populations. However, the prevalence rate and clinical characteristics of GT in non-consanguineous populations have been unclear. We analyzed 97 patients from 93 families with GT in the Han population in China. This analysis showed lower consanguinity (18.3%) in Han patients than other ethnic populations in GT-prone countries. Compared with other ethnic populations, there was no significant difference in the distribution of GT types. Han females suffered more severe bleeding and had a poorer prognosis. We identified a total of 43 different ITGA2B and ITGB3 variants, including 25 previously unidentified, in 45 patients. These variants included 14 missense, 4 nonsense, 4 frameshift, and 3 splicing site variants. Patients with the same genotype generally manifested the same GT type but presented with different bleeding severities. This suggests that GT clinical phenotype does not solely depend on genotype. Our study provides an initial, yet important, clinical and molecular characterization of GT heterogeneity in China.

[The clinical assessment of regional resection in the benign tumor of parotid gland]

Objective:To evaluate the clinical assessment of regional resection and superficial lobe total resection in the treatment of benign tumors of the parotid gland. Method:One hundred and nighty-five patients operated in the First Hospital of Peking University from January 1998 to March 2017 with benign tumor of the parotid gland were retrospectively analyzed. There were 189 patients with single side tumor and 6 patients with bilateral sides, 157 cases underwent regional resection and the other 44 cases underwent superficial lobe total resection. All the results and complications were recorded and analyzed between the two groups.Result:There were total 195 patients with 201 cases. All the complications were as follows, 4 cases with recurrence, 44 cases with temporal facial paralysis, 13 cases with permanent facial paralysis, 80 cases with earlobe numbness, 49 cases with facial numbness, 44 cases with skin retraction, 26 cases with operated region effusion, 2 cases with sialosyrinx, 55 cases with Frey syndrome. There were no significant differences between the two groups in the incidences of recurrence, temporal facial paralysis, permanent facial paralysis, earlobe numbness, facial numbness, skin retraction. The incidence of Frey syndrome in the superficial lobe total resection group was significantly higher than the regional resection group(45.5%, 22.3%，P<0.05). The incidence of operated region effusion or sialosyrinx in the regional resection group was significantly higher than the superficial lobe total resection group (16.6%, 4.5%,P<0.05),further analysis showed that the operation method and the location of the tumor were the independent risk factors. Conclusion:Regional resection in the parotid gland tumor was less invasive, the incidences in the most complications were in consistent with superficial lobe total resection, and it was helpful in preventing the occurrence of Frey syndrome. Although regional resection conserved more parotid gland tissue so that the more conserved gland function and it also did not increase the incidence of sialosyrinx, the operated region effusion was significantly increased. If the operated region effusion was not discovered and handled, there would be a risk of sialosyrinx.

Distribution of ABO/Rh blood groups and their association with hepatitis B virus infection in 3.8 million Chinese adults: A population-based cross-sectional study

ABO and Rh blood groups play a vital role in blood transfusion safety and clinical practice and are thought to be linked with disease susceptibility. The results from previous studies that focused on the association between blood groups and HBV infection remain controversial. China has the world's largest burden of HBV infection. We assessed the distribution of ABO/Rh blood groups in Chinese adults and examined the association between these groups and HBV infection. We did a nationwide cross-sectional study using data from a physical check-up programme from 31 provinces examined between 2010 and 2012. ELISA was used to test for HBsAg in serologic samples. Multivariable logistic regression was used to estimate aOR of the association between ABO and Rh blood groups and HBV infection. Among 3 827 125 participants, the proportion of participants with blood group A was highest (30.54%), followed by O (30.37%), B (29.42%) and AB (9.66%). A total of 38 907 (1.02%) were Rh-D negative. The prevalence of HBsAg in blood groups O, A, B and AB were 6.34%, 5.55%, 5.18% and 5.06%, respectively. HBsAg prevalence was 5.65% in Rh-D-positive and 3.96% in Rh-D-negative participants. After controlling for other potential risk factors, multivariate models showed that participants with blood group O (adjusted OR = 1.22, 95% CI: 1.20-1.25) were at higher risk of HBV infection compared with group AB. Rh-D-positive participants (adjusted OR = 1.44, 95% CI: 1.37-1.52) were at higher risk of HBV infection than Rh-D-negative participants. The associations between ABO/Rh blood groups and HBV infection were similar in subgroup analysis. The proportions of O, A, B and AB blood groups were approximately 3:3:3:1, and nearly 1 in 100 people was Rh-D negative among Chinese adults. Blood group O and Rh-D positivity were both associated with increased HBV infection. The risk of HBV infection and blood safety should be taken into consideration in clinical practice, especially when transfusing those with blood group O. Awareness and prevention of HBV infection is of particular importance for individuals with blood group O.

Impacts of Regulations on Air Quality and Emergency Department Visits in the Atlanta Metropolitan Area, 1999-2013

INTRODUCTION

The United States and Western Europe have seen great improvements in air quality, presumably in response to various regulations curtailing emissions from the broad range of sources that have contributed to local, regional, and global pollution. Such regulations, and the ensuing controls, however, have not come without costs, which are estimated at tens of billions of dollars per year. These costs motivate accountability-related questions such as, to what extent do regulations lead to emissions changes? More important, to what degree have the regulations provided the expected human health benefits?

Here, the impacts of specific regulations on both electricity generating unit (EGU) and on-road mobile sources are examined through the classical accountability process laid out in the 2003 Health Effects Institute report linking regulations to emissions to air quality to health effects, with a focus on the 1999-2013 period. This analysis centers on regulatory actions in the southeastern United States and their effects on health outcomes in the 5-county Atlanta metropolitan area. The regulations examined are largely driven by the 1990 Clean Air Act Amendments (C). This work investigates regulatory actions and controls promulgated on EGUs: the Acid Rain Program (ARP), the NOx Budget Trading Program (NBP), and the Clean Air Interstate Rule (CAIR) - and mobile sources: Tier 2 Gasoline Vehicle Standards and the 2007 Heavy Duty Diesel Rule.

METHODS

Each step in the classic accountability process was addressed using one or more methods. Linking regulations to emissions was accomplished by identifying major federal regulations and the associated state regulations, along with analysis of individual facility emissions and control technologies and emissions modeling (e.g., using the U.S. Environmental Protection Agency's [U.S. EPA's] MOtor Vehicle Emissions Simulator [MOVES] mobile-source model). Regulators, including those from state environmental and transportation agencies, along with the public service commissions, play an important role in implementing federal rules and were involved along with other regional stakeholders in the study. We used trend analysis, air quality modeling, satellite data, and a ratio-of-ratios technique to investigate a critical current issue, a potential large bias in mobile-source oxides of nitrogen (NOx) emissions estimates.

The second link, emissions-air quality relationships, was addressed using both empirical analyses as well as chemical transport modeling employing the Community Multiscale Air Quality (CMAQ) model. Kolmogorov-Zurbenko filtering accounting for day of the year was used to separate the air quality signal into long-term, seasonal, weekday-holiday, and short-term meteorological signals. Regression modeling was then used to link emissions and meteorology to ambient concentrations for each of the species examined (ozone [O3], particulate matter ≤ 2.5 μm in aerodynamic diameter [PM2.5], nitrogen dioxide [NO2], sulfur dioxide [SO2], carbon monoxide [CO], sulfate [SO4-2], nitrate [NO3-], ammonium [NH4+], organic carbon [OC], and elemental carbon [EC]). CMAQ modeling was likewise used to link emissions changes to air quality changes, as well as to further establish the relative roles of meteorology versus emissions change impacts on air quality trends. CMAQ and empirical modeling were used to investigate aerosol acidity trends, employing the ISORROPIA II thermodynamic equilibrium model to calculate pH based on aerosol composition. The relationships between emissions and meteorology were then used to construct estimated counterfactual air quality time series of daily pollutant concentrations that would have occurred in the absence of the regulations. Uncertainties in counterfactual air quality were captured by the construction of 5,000 pollutant time series using a Monte Carlo sampling technique, accounting for uncertainties in emissions and model parameters.

Health impacts of the regulatory actions were assessed using data on cardiorespiratory emergency department (ED) visits, using patient-level data in the Atlanta area for the 1999-2013 period. Four outcome groups were chosen based on previous studies identifying associations with ambient air pollution: a combined respiratory disease (RD) category; the subgroup of RD presenting with asthma; a combined cardiovascular disease (CVD) category; and the subgroup of CVD presenting with congestive heart failure (CHF).

Models were fit to estimate the joint effects of multiple pollutants on ED visits in a time-series framework, using Poisson generalized linear models accounting for overdispersion, with a priori model formulations for temporal and meteorological covariates and lag structures. Several parameterizations were considered for the joint-effects models, including different sets of pollutants and models with nonlinear pollutant terms and first-order interactions among pollutants. Use of different periods for parameter estimates was assessed, as associations between pollutant levels and ED visits varied over the study period. A 7-pollutant, nonlinear model with pollutant interaction terms was chosen as the baseline model and fitted using pollutant and outcome data from 1999-2005 before regulations might have substantially changed the toxicity of pollutant mixtures. In separate analyses, these models were fitted using pollutant and outcome data from the entire 1999-2013 study period. Daily counterfactual time series of pollutant concentrations were then input into the health models, and the differences between the observed and counterfactual concentrations were used to estimate the impacts of the regulations on daily counts of ED visits. To account for the uncertainty in both the estimation of the counterfactual time series of ambient pollutant levels and the estimation of the health model parameters, we simulated 5,000 sets of parameter estimates using a multivariate normal distribution based on the observed variance-covariance matrix, allowing for uncertainty at each step of the chain of accountability. Sensitivity tests were conducted to assess the robustness of the results.

RESULTS

EGU NOx and SO2 emissions in the Southeast decreased by 82% and 83%, respectively, between 1999 and 2013, while mobile-source emissions controls led to estimated decreases in Atlanta-area pollutant emissions of between 61% and 93%, depending on pollutant. While EGU emissions were measured, mobile-source emissions were modeled. Our results are supportive of a potential high bias in mobile-source NOx and CO emissions estimates. Air quality benefits from regulatory actions have increased as programs have been fully implemented and have had varying impacts over different seasons. In a scenario that accounted for all emissions reductions across the period, observed Atlanta central monitoring site maximum daily 8-hour (MDA8h) O3 was estimated to have been reduced by controls in the summertime and increased in the wintertime, with a change in mean annual MDA8h O3 from 39.7 ppb (counterfactual) to 38.4 ppb (observed). PM2.5 reductions were observed year-round, with average 2013 values at 8.9 μg/m3 (observed) versus 19.1 μg/m3 (counterfactual). Empirical and CMAQ analyses found that long-term meteorological trends across the Southeast over the period examined played little role in the distribution of species concentrations, while emissions changes explained the decreases observed. Aerosol pH, which plays a key role in aerosol formation and dynamics and may have health implications, was typically very low (on the order of 1-2, but sometimes much lower), with little trend over time despite the stringent SO2 controls and SO42- reductions.

Using health models fit from 1999-2005, emissions reductions from all selected pollution-control policies led to an estimated 55,794 cardiorespiratory disease ED visits prevented (i.e., fewer observed ED visits than would have been expected under counterfactual scenarios) - 52,717 RD visits, of which 38,038 were for asthma, and 3,057 CVD visits, of which 2,104 were for CHF - among the residents of the 5-county area over the 1999-2013 period, an area with approximately 3.5 million people in 2013. During the final two years of the study (2012-2013), when pollution-control policies were most fully implemented and the associated benefits realized, these policies were estimated to prevent 5.9% of the RD ED visits that would have occurred in the absence of the policies (95% interval estimate: -0.4% to 12.3%); 16.5% of the asthma ED visits (95% interval estimate: 7.5% to 25.1%); 2.3% of the CVD ED visits (95% interval estimate: -1.8% to 6.2%); and -.6% of the CHF ED visits (95% interval estimate: 26.3% to 10.4%). Estimates of ED visits prevented were generally lower when using health models fit for the entire 1999-2013 study period.

Sensitivity analyses were conducted to show the impact of the choice of parameterization of the health models and to assess alternative definitions of the study area. When impacts were assessed for separate policy interventions, policies affecting emissions from EGUs, especially the ARP and the NBP, appeared to have had the greatest effect on prevention of RD and asthma ED visits.

CONCLUSIONS

This study demonstrates the effectiveness of regulations on improving air quality and health in the southeastern United States. It also demonstrates the complexities of accountability assessments as uncertainties are introduced in each step of the classic accountability process. While accounting for uncertainties in emissions, air quality-emissions relationships, and health models does lead to relatively large uncertainties in the estimated outcomes due to specific regulations, overall the benefits of regulations have been substantial.

Diffusion kurtosis imaging in identifying the malignancy of lymph nodes during the primary staging of rectal cancer

AIM

The aim was to assess the diagnostic value of diffusion kurtosis imaging (DKI) for discriminating between benign and malignant lymph nodes in patients with rectal carcinoma.

METHOD

ighty-five patients with rectal adenocarcinoma who underwent total mesorectal excision of the rectum were studied. A total of 273 lymph nodes were harvested and subjected to histological analysis. Quantitative parameters [apparent diffusion parameter D_app of the Gaussian distribution, apparent kurtosis coefficient K_app and apparent diffusion coefficient (ADC)] of lymph nodes were derived from DKI. Differences and the diagnostic performance of these parameters were calculated by using the independent-samples t test and receiver operating characteristic curve analyses.

RESULTS

The median D_app and ADC values of metastatic lymph nodes were significantly greater than those of benign lymph nodes, whereas the median K_app of metastatic lymph nodes was statistically less than that of normal lymph nodes. D_app had the relatively highest area under the curve of 0.774. When 1126.15 × 10^-6  mm² /s was used as a D_app threshold value, the sensitivity and specificity were 96.97% and 41.82%, respectively.

CONCLUSION

DKI can help differentiate metastatic vs benign lymph nodes during the primary staging of rectal cancer.

Effect of local scrotal heating on the expression of tight junction-associated molecule Occludin in boar testes

The aim of this study was to determine whether local scrotal heating (42°C, for 1 hr) had an effect on the expression of tight junction (TJ)-associated molecule Occludin in boar testes. Adult boars (Landrace, n = 6) were used and randomly divided into two groups (n = 3 each). Three boars were given local scrotal exposure to 42°C for approximately 1 h with a home-made electric blanket of controlled temperature as local scrotal heating group, the other three boars received no heat treatment and were left at standard room temperature as control group. After 6 hr, all boars were castrated and the testes were harvested. qRT-PCR, Western blotting and immunohistochemistry were used to explore the expression and localization of Occludin. qRT-PCR and Western blotting showed that the protein and mRNA levels of Occludin significantly decreased in local scrotal heating group as compared to the control. Furthermore, immunoreactivity staining of Occludin was localized at the sites of the blood-testis barrier (BTB) and formed an almost consecutive and strong immunoreactivity strand in the control, while Occludin was limited to Sertoli cells (SCs) and no obvious immunoreactivity strand was present in local scrotal heating group. These data indicated that local scrotal heating decreased the expression of TJ-associated molecule Occludin, which may be involved in heat-induced spermatogenesis damage.

[Clinical observation of coblation assisted transoral microsurgery for the treatment of oral and oropharygneal malignancy]

Objective:To evaluate the feasibility and effectiveness of coblation assisted transoral surgery for the treatment of oral and oropharyngeal malignancy. Method:19 patients who suffered from oral or oropharyngeal malignant tumors underwent coblation assisted transoral surgery from August 2008 to August 2017 were studied. According to the tumor sites and pathological results, there were four oral squamous cell carcinoma (SCC) (two tongue carcinoma and two mouth floor carcinoma), eleven oropharygneal SCC (five tonsillar carcinoma, four soft palate carcinoma, one tongue base cartinama and one multiple carcinoma invading both soft palatine and hypopharynx), and four lymphatic and hematopoietic malignancies (three tonsillar tumors and one tumor invading both tonsil and tongue base). According to AJCC guideline, the stages of four oral SCC were T₁N₀M₀, T₁N₂M₀, T₂N₁M₀, and T₂N₂M₀ respectively; while the stages of eleven orophygneal SCC were T₁N₀M₀ for 5 patients, T₂N₀M₀ for 4 patients, T₂N₁M₀ for one patient, and T₂N₂M₀ for one patient respectively. Result:Among the 19 patients studied, concurrent neck dissections and tracheotomies were performed in six and four patients respectively. For all the transoral procedures, the blood loss could be controlled within 20 ml, while the operative time were controlled within two hours. 13 patients started oral feeding the day they were operated on. All of the four patients who underwent the tracheotomy could be decannulated successfully after surgery. Four patients diagnosed as lymphatic and hematopoietic malignancies turned to hematology department for further treatments. For the remaining 15 SCC patients, 14 were followed up successfully with one loss to follow-up: the follow up time ranged from 6 to 108 months, during these times, one patient with multiple carcinomas invading the soft palate and hypopharynx had developed new carcinomas located in contralateral hypopharynx and esophagus and had the metastasis in cervical lymph nodes 5 months after surgery, another patient with soft palate carcinoma had the metastasis in cervical lymph nodes 18 months after surgery. Two patients died because of intracranial hemorrhage and cardiovascular event 5 and 12 months after surgery respectively. The three years' tumor free survival and overall survival rates calculated by Kaplan-Meier method were 75.0% and 77.9% respectively. All patients had no severe dysfunctions for swallow, speech and breathing related to the surgery. Conclusion:Radiofrenquency coblation assisted transoral surgery for oral and oropharygneal carcinoma has definite therapeutic effect. Most cases can avoid open surgery and tracheotomy.The advantages are blood control, simplifing surgery,shortening operational time,faster recovery, lower incidence of complications and better preservation of organ function.

Direct Observation of Dynamical Quantum Phase Transitions in an Interacting Many-Body System

The theory of phase transitions represents a central concept for the characterization of equilibrium matter. In this work we study experimentally an extension of this theory to the nonequilibrium dynamical regime termed dynamical quantum phase transitions (DQPTs). We investigate and measure DQPTs in a string of ions simulating interacting transverse-field Ising models. During the nonequilibrium dynamics induced by a quantum quench we show for strings of up to 10 ions the direct detection of DQPTs by revealing nonanalytic behavior in time. Moreover, we provide a link between DQPTs and the dynamics of other quantities such as the magnetization, and we establish a connection between DQPTs and entanglement production.

Prevalence of HBsAg/HBeAg amongst 1 936 801 couples preparing for pregnancy in rural China: An observational study

There are few extant studies on the prevalence of HBV infection in couples preparing for pregnancy. We assessed the prevalence of hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) in couples preparing for pregnancy in rural China, and the association between HBV prevalence and the statuses of HBsAg/HBeAg and ALT in the spouses. We performed a nationwide cross-sectional study, using data from a health check-up program for 1 936 801 rural couples from 31 provinces preparing for pregnancy between 2010 and 2012. ELISA was used to test serologic samples, and we defined couples who were either discordant or both positive for HBsAg as "POSITIVE COUPLES" (PC). Amongst the 1 936 801 couples, 202 816 (10.47%; 95% CI, 10.43%-10.51%) were PC. HBeAg (high infectiousness) was detected in 56 474 (27.84%; 95% CI, 27.65%-28.04%) of 202 816 HBsAg-positive couples. Multivariate models showed that the prevalence of HBV infection in wives increased along with the positive statuses for HBsAg/HBeAg and alanine aminotransferase (ALT) of their husbands (adjusted odds ratio increased from 2.31 to 4.98), after adjustment for potential confounders. Similarly, the prevalence of HBV infection in husbands was associated with the positive statuses of HBsAg/HBeAg and ALT of their wives (adjusted odds ratio increased from 2.04 to 4.93). The prevalence of POSITIVE COUPLES in couples preparing for pregnancy in rural China was high, and the prevalence of HBV infection was independently associated with the positive statuses of HBsAg/HBeAg and ALT of the spouses. Instead of solely focussing on mothers prior to becoming pregnant, POSITIVE COUPLES should be taken as an important unit of care.