Synthetic surrogates improve power for genome-wide association studies of partially missing phenotypes in population biobanks.

Within population biobanks, incomplete measurement of certain traits limits the power for genetic discovery. Machine learning is increasingly used to impute the missing values from the available data. However, performing genome-wide association studies (GWAS) on imputed traits can introduce spurious associations, identifying genetic variants that are not associated with the original trait. Here we introduce a new method, synthetic surrogate (SynSurr) analysis, which makes GWAS on imputed phenotypes robust to imputation errors. Rather than replacing missing values, SynSurr jointly analyzes the original and imputed traits. We show that SynSurr estimates the same genetic effect as standard GWAS and improves power in proportion to the quality of the imputations. SynSurr requires a commonly made missing-at-random assumption but relaxes the requirements of existing imputation methods by not requiring correct model specification. We present extensive simulations and ablation analyses to validate SynSurr and apply it to empower the GWAS of dual-energy X-ray absorptiometry traits within the UK Biobank.

Semi-supervised ROC analysis for reliable and streamlined evaluation of phenotyping algorithms.

OBJECTIVE: High-throughput phenotyping will accelerate the use of electronic health records (EHRs) for translational research. A critical roadblock is the extensive medical supervision required for phenotyping algorithm (PA) estimation and evaluation. To address this challenge, numerous weakly-supervised learning methods have been proposed. However, there is a paucity of methods for reliably evaluating the predictive performance of PAs when a very small proportion of the data is labeled. To fill this gap, we introduce a semi-supervised approach (ssROC) for estimation of the receiver operating characteristic (ROC) parameters of PAs (eg, sensitivity, specificity). MATERIALS AND METHODS: ssROC uses a small labeled dataset to nonparametrically impute missing labels. The imputations are then used for ROC parameter estimation to yield more precise estimates of PA performance relative to classical supervised ROC analysis (supROC) using only labeled data. We evaluated ssROC with synthetic, semi-synthetic, and EHR data from Mass General Brigham (MGB). RESULTS: ssROC produced ROC parameter estimates with minimal bias and significantly lower variance than supROC in the simulated and semi-synthetic data. For the 5 PAs from MGB, the estimates from ssROC are 30% to 60% less variable than supROC on average. DISCUSSION: ssROC enables precise evaluation of PA performance without demanding large volumes of labeled data. ssROC is also easily implementable in open-source R software. CONCLUSION: When used in conjunction with weakly-supervised PAs, ssROC facilitates the reliable and streamlined phenotyping necessary for EHR-based research.

Integrating variant functional annotation scores have varied abilities to improve power of genome-wide association studies.

Functional annotations have the potential to increase power of genome-wide association studies (GWAS) by prioritizing variants according to their biological function, but this potential has not been well studied. We comprehensively evaluated all 1132 traits in the UK Biobank whose SNP-heritability estimates were given "medium" or "high" labels by Neale's lab. For each trait, we integrated GWAS summary statistics of close to 8 million common variants (minor allele frequency [Formula: see text]) with either their 75 individual functional scores or their meta-scores, using three different data-integration methods. Overall, the number of new genome-wide significant findings after data-integration increases as a trait SNP-heritability estimate increases. However, there is a trade-off between new findings and loss of baseline GWAS findings, resulting in similar total numbers of significant findings between using GWAS alone and integrating GWAS with functional scores, across all 1132 traits analyzed and all three data-integration methods considered. Our findings suggest that, even with the current biobank-level sample size, more informative functional scores and/or new data-integration methods are needed to further improve the power of GWAS of common variants. For example, studying variants in coding sequence and obtaining cell-type-specific scores are potential future directions.

Effect modification of greenness on PM2.5 associated all-cause mortality in a multidrug-resistant tuberculosis cohort.

RATIONALE: Evidence for the association between fine particulate matter (PM2.5) and mortality among patients with tuberculosis (TB) is limited. Whether greenness protects air pollution-related mortality among patients with multidrug-resistant tuberculosis (MDR-TB) is completely unknown. METHODS: 2305 patients reported in Zhejiang and Ningxia were followed up from MDR-TB diagnosis until death, loss to follow-up or end of the study (31 December 2019), with an average follow-up of 1724 days per patient. 16-day averages of contemporaneous Normalised Difference Vegetation Index (NDVI) in the 500 m buffer of patient's residence, annual average PM2.5 and estimated oxidant capacity Ox were assigned to patients regarding their geocoded home addresses. Cox proportional hazards regression models were used to estimate HRs per 10 µg/m3 exposure to PM2.5 and all-cause mortality among the cohort and individuals across the three tertiles, adjusting for potential covariates. RESULTS: HRs of 1.702 (95% CI 1.680 to 1.725) and 1.169 (1.162 to 1.175) were observed for PM2.5 associated with mortality for the full cohort and individuals with the greatest tertile of NDVI. Exposures to PM2.5 were stronger in association with mortality for younger patients (HR 2.434 (2.432 to 2.435)), female (2.209 (1.874 to 2.845)), patients in rural (1.780 (1.731 to 1.829)) and from Ningxia (1.221 (1.078 to 1.385)). Cumulative exposures increased the HRs of PM2.5-related mortality, while greater greenness flattened the risk with HRs reduced in 0.188-0.194 on average. CONCLUSIONS: Individuals with MDR-TB could benefit from greenness by having attenuated associations between PM2.5 and mortality. Improving greener space and air quality may contribute to lower the risk of mortality from TB/MDR-TB and other diseases.

The E3 Ubiquitin Ligase HOIP inhibits Cancer Cell Apoptosis via modulating PTEN stability.

Chemotherapy is widely used in a variety of solid tumors, such as lung cancer, gastric cancer and breast cancer. The genotoxic drugs, such as cisplatin, suppress cancer progression either by inhibition cell proliferation or facilitating apoptosis. However, the chemotherapy resistance remains an urgent challenge in cancer therapy, especially in advanced stages. Several studies showed that the activation of pro-survival pathways, such as PI3K-AKT, participated in mediating chemotherapy resistance. The insights into the molecular mechanisms for underlying chemotherapy resistance are of great importance to improve cancer patient survival in advanced stages. The HOIP protein belongs to the RING family E3 ubiquitin ligases and modulates several atypical ubiquitination processes in cellular signaling. Previous studies showed that HOIP might be an important effector in modulating cancer cell death under genotoxic drugs. Here, we report that HOIP associates with PTEN and facilitates PTEN degradation in cancer cells. Depletion of HOIP causes cell cycle arrest and apoptosis, which effects could be rescued by PTEN silencing. Besides, the survival data from public available database show that HOIP expression correlates with poor survival in several types of chemotherapy-treated cancer patients. In conclusion, our study establishes a novel mechanism by which HOIP modulates PTEN stability and facilitates chemotherapy resistance in malignancies.

The Effect of Empathy on the Attentional Processing of Painful and Emotional Stimuli.

BACKGROUND: Empathy is shown to affect the attentional processing of painful stimuli and emotional stimuli. However, whether the attentional effects on emotional stimuli depend on emotional valence and the nature of the relationship between the attentional effects on different stimuli are still unknown. METHODS: In the present study, 25 high-empathy (HE) participants and 25 low-empathy (LE) participants were recruited to perform dot-probe tasks on painful stimuli and emotional stimuli. RESULTS: The results showed that HE individuals had weak attentional disengagement to painful pictures. More importantly, regarding emotional pictures, HE individuals showed attentional avoidance to negative emotion pictures, while LE individuals showed attentional bias to positive emotion pictures. Correlation analysis showed that the attentional bias score and attentional disengagement score were only associated with each other within the same category of stimuli (painful, positive or negative stimuli). CONCLUSION: These results revealed that HE individuals mainly showed attentional avoidance to negative stimuli, while LE individuals mainly showed attentional bias to positive stimuli.

PD-1-siRNA Delivered by Attenuated Salmonella Enhances the Antitumor Effect of Chloroquine in Colon Cancer.

The widespread appearance of drug tolerance and the low efficiency of single treatment have severely affected the survival time of the patients with colorectal cancer. Exploring new treatment options and combined treatment strategies have become the key to improving the prognosis. The combination of immunotherapy and chemotherapy have shown good clinical expectations. Here, we studied the cooperative effects of chloroquine, an anti-malarial drug that is now widely used in anti-tumor research, and RNA interference (RNAi) targeting the immune checkpoint molecule Programmed Death-1 (PD-1) delivered with attenuated Salmonella. Our results show that chloroquine can not only significantly inhibit the survival of colon cancer cells and induce apoptosis, but also effectively inhibit cell invasion and migration. The results of in vivo experiments show that chloroquine can increase the expression of PD-1 in tumor tissues. Combining chloroquine and PD-1 siRNA can further inhibit the growth and metastases of colon cancer and induce apoptosis. The mechanism underlying this phenomenon is the occurrence of chloroquine-induced apoptosis and the effective immune response caused by the attenuated Salmonella carrying PD-1 siRNA. This study suggests that the combined application of PD-1-based immunotherapy and anti-cancer drugs has become a new expectation for clinical treatment of colorectal cancer.

CD73+ Mesenchymal Stem Cells Ameliorate Myocardial Infarction by Promoting Angiogenesis.

With multipotent differentiation potential and paracrine capacity, mesenchymal stem cells (MSCs) have been widely applied in clinical practice for the treatment of ischemic heart disease. MSCs are a heterogeneous population and the specific population of MSCs may exhibit a selective ability for tissue repair. The aim of our research was to adapt the CD73+ subgroup of adipose derived MSCs (AD-MSCs) for the therapy of myocardial infarction (MI). In this research, AD-MSCs were isolated from adipose tissue surrounding the groin of mice and CD73+ AD-MSCs were sorted using flow cytometry. To investigate the therapeutic effects of CD73+ AD-MSCs, 1.2 × 106 CD73+ AD-MSCs were transplanted into rat model of MI, and CD73- AD-MSCs, normal AD-MSCs transplantation served as control. Our results revealed that CD73+ AD-MSCs played a more effective role in the acceleration function of cardiac recovery by promoting angiogenesis in a rat model of MI compared with mixed AD-MSCs and CD73- AD-MSCs. Moreover, with the expression of CD73 in AD-MSCs, the secretion of VEGF, SDF-1α, and HGF factors could be promoted. It also shows differences between CD73+ and CD73- AD-MSCs when the transcription profiles of these two subgroups were compared, especially in VEGF pathway. These findings raise an attractive outlook on CD73+ AD-MSCs as a dominant subgroup for treating MI-induced myocardial injury. CD73, a surface marker, can be used as a MSCs cell quality control for the recovery of MI by accelerating angiogenesis.

Changes in ambient temperature increase hospital outpatient visits for allergic rhinitis in Xinxiang, China.

BACKGROUND: The effect of ambient temperature on allergic rhinitis (AR) remains unclear. Accordingly, this study aimed to explore the relationship between ambient temperature and the risk of AR outpatients in Xinxiang, China. METHOD: Daily data of outpatients for AR, meteorological conditions, and ambient air pollution in Xinxiang, China were collected from 2015 to 2018. The lag-exposure-response relationship between daily mean temperature and the number of hospital outpatient visits for AR was analyzed by distributed lag non-linear model (DLNM). Humidity, long-time trends, day of the week, public holidays, and air pollutants including sulfur dioxide (SO2), and nitrogen dioxide (NO2) were controlled as covariates simultaneously. RESULTS: A total of 14,965 AR outpatient records were collected. The relationship between ambient temperature and AR outpatients was generally M-shaped. There was a higher risk of AR outpatient when the temperature was 1.6-9.3 °C, at a lag of 0-7 days. Additionally, the positive association became significant when the temperature rose to 23.5-28.5 °C, at lag 0-3 days. The effects were strongest at the 25th (7 °C) percentile, at lag of 0-7 days (RR: 1.32, 95% confidence intervals (CI): 1.05-1.67), and at the 75th (25 °C) percentile at a lag of 0-3 days (RR: 1.15, 95% CI: 1.02-1.29), respectively. Furthermore, men were more sensitive to temperature changes than women, and the younger groups appeared to be more influenced. CONCLUSIONS: Both mild cold and mild hot temperatures may significantly increase the risk of AR outpatients in Xinxiang, China. These findings could have important public health implications for the occurrence and prevention of AR.

Greenness exposure and all-cause mortality during multi-drug resistant tuberculosis treatment: A population-based cohort study.

BACKGROUND: Living closer to greenness were thought to benefit various health outcomes. We aimed to assess the association between residential greenness and mortality among patients undergoing multidrug resistant tuberculosis (MDR-TB) treatment. METHODS: We enrolled all local MDR-TB patients reported in Zhejiang, China from 2009 to 2017 and followed them throughout the treatment. We calculated the contemporaneous normalized difference vegetation index (NDVI) in the 250 and 500 m radius around patient's residence. Cox proportional hazards regression models with time-varying NDVI were used to assess the impact of greenness exposure on all-cause mortality during MDR-TB treatment, adjusting for potential individual and contextual covariates. RESULTS: We ascertained 1,621 active MDR-TB cases, which contributed 3036 person-years at risk with an average follow-up of 684 days (s.d. 149 days) per patient. Among them, there were 163 deaths during follow-up, representing a crude mortality rate of 537 deaths per 10,000 person-years. Patients exposed to the second quintile (Q2) of greenness within the 500 m buffer had around 64% reduced mortality risk over the lowest quintile of greenness with hazard ratio (HR) = 0.364 (95% CI: 0.109-1.22). In lower nighttime light (NTL) areas, the hazard ratios (HR) per quintile increase in NDVI within the 500 m buffer were Q2: 0.35 (95% CI: 0.10-1.18), Q3: 0.24 (95% CI: 0.09-0.66), Q4: 0.26 (95% CI: 0.10-0.69), and Q5: 0.26 (95% CI: 0.10-0.71) relevant to the lowest quintile Q1, with a trend of p-value ≤0.01. Patients who were female, younger (<60 years), resided in urban areas, or had high PM2.5 (i.e. particles with diagram ≤2.5 µm) exposure were more likely to benefit from greenness exposure. Associations were neither observed with NDVI in the 250 m buffer nor for patients living in higher NTL areas. There was a non-linear exposure-response relationship between greenness and deaths with p-value ≤0.05. CONCLUSION: Increasing greenness exposure along with medical treatment reduces all-cause mortality among patients living in lower NTL areas.

Identification of consensus sequence from matrix attachment regions and functional analysis of its activity in stably transfected Chinese hamster ovary cells.

Matrix attachment regions (MARs) can enhance transgene expression levels and maintain stability. However, the consensus sequence from MARs and its functional analysis remains to be examined. Here, we assessed a possible consensus sequence from MARs and assessed its activity in stably transfected Chinese hamster ovary (CHO) cells. First, we analyzed the effects of 10 MARs on transfected CHO cells and then analyzed the consensus motifs from these MARs using a bioinformatics method. The consensus sequence was synthesized and cloned upstream or downstream of the eukaryotic vector. The constructs were transfected into CHO cells and the expression levels and stability of enhanced green fluorescent protein were detected by flow cytometry. The results indicated that eight of the ten MARs increased transgene expression in transfected CHO cells. Three consensus motifs were found after bioinformatics analyses. The consensus sequence tandemly enhanced transgene expression when it was inserted into the eukaryotic expression vector; the effect of the addition upstream was stronger than that downstream. Thus, we found a MAR consensus sequence that may regulate the MAR-mediated increase in transgene expression.

A chimeric HS4 insulator-scaffold attachment region enhances transgene expression in transfected Chinese hamster ovary cells.

Chinese hamster ovary (CHO) cells are one of the most commonly used expression systems for the production of recombinant proteins but low levels of transgene expression and transgene silencing are frequently encountered. Epigenetic regulatory elements such as the chicken ß-globin locus control region hypersensitive site 4 (HS4) and scaffold/matrix attachment regions (S/MARs) have positive effects on transgene expression. In this study, a chimeric HS4-SAR was cloned upstream or downstream of an enhanced green fluorescent protein (eGFP) expression cassette in a eukaryotic vector, and the resulting vectors were transfected into CHO cells. eGFP was detected by flow cytometry. Real-time quantitative PCR (qPCR) was used to determine copy numbers of the stably transfected cells. And fluorescence in situ hybridization (FISH) was used to detect the status of vector in the host cell chromosome. The results showed that HS4-SAR positioned downstream of the expression cassette could enhance eGFP expression by 4.83-fold compared with the control vector. There may not be a relationship between transgene copy number and gene expression level. HS4-SAR did not appear to alter the integration of the transgene into the host cell chromosome or its position in the chromosome. We found a synthetic chimeric HS4-SAR positively increased transgene expression in CHO cells.

Episomal Lentiviral Vector-Mediated miR-145 Overexpression Inhibits Proliferation and Induces Apoptosis of Human Esophageal Carcinomas Cells.

BACKGROUND: Gene therapy is a promising approach for the treatment of various cancers. However, most viral vectors used for this purpose carry risks, including potential integration into the host genome. OBJECTIVE: We addressed this issue in the present study by constructing an episomal lentiviral vector using the .-interferon matrix attachment region to express the microRNA -145(miR-145), and examining the effect of miR-145 overexpression on human esophageal carcinomas (EC) cells. Some recent relevant patents are also discussed. METHOD: Expression levels of miR-145 and the marker protein enhanced green fluorescent protein (EGFP) in infected ECA109 and EC9706 human esophageal carcinoma cells were detected by quantitative PCR and flow cytometry, respectively. Cell proliferation and apoptosis were assessed by Cell Counting Kit-8 and flow cytometry, respectively. Plasmid rescue experiments and fluorescence in situ hybridization were used to determine the episomal status of the transfected vector. RESULTS: We found that EGFP and miR-145 were highly expressed in EC cells, and miR-145 overexpression inhibited cell proliferation and induced apoptosis. Moreover, the lentiviral vector did not integrate into the host genome, but was maintained episomally at lower copy numbers. CONCLUSION: Taken together, our results demonstrate that miR-145-expressing episomal lentiviral vectors are a promising tool for gene therapy in the treatment of EC.

Crosstalk among the proteome, lysine phosphorylation, and acetylation in romidepsin-treated colon cancer cells.

Romidepsin (FK228) is one of the most promising histone-deacetylase inhibitors due to its potent antitumor activity, and has been used as a practical option for cancer therapy. However, FK228-induced changes in protein modifications and the crosstalk between different modifications has not been reported. To better understand the underlying mechanisms of FK228-related cancer therapy, we investigated the acetylome, phosphorylation, and crosstalk between modification datasets in colon cancer cells treated with FK228 by using stable-isotope labeling with amino acids in cell culture and affinity enrichment, followed by high-resolution liquid chromatography tandem mass spectrometry analysis. In total, 2728 protein groups, 1175 lysine-acetylation sites, and 4119 lysine-phosphorylation sites were quantified. When the quantification ratio thresholds were set to > 2.0 and < 0.5, respectively, a total of 115 and 38 lysine-acetylation sites in 85 and 32 proteins were quantified as increased and decreased targets, respectively, and 889 and 370 lysine-phosphorylation sites in 599 and 289 proteins were quantified as increased and decreased targets, respectively. Furthermore, we identified 274 proteins exhibiting both acetylation and phosphorylation modifications. These findings indicated possible involvement of these proteins in FK228-related treatment of colon cancer, and provided insight for further analysis of their biological function.

A study on the inhibitory effect of Radix Semiaquilegiae extract on human hepatoma HEPG-2 and SMMC-7721 cells.

The main objective of this paper was to investigate the extraction process of ethanol extract of Radix Semiaquilegiae, as well as its inhibitory activity on human hepatoma HepG-2 and SMMC-7721 cells, and to compare the inhibitory effects of different concentrations of ethanol extracts against these two hepatoma cells. Ethanol reflux extraction and ultrasound-assisted extraction with ethanol at room temperature were used in the extraction process, and MTT assay was mainly used in the activity experiment to perform in-vitro anti HepG-2 and SMMC-7721 cell activity screening of ethanol extract, and to calculate the cell inhibition rates of the extracts. The results showed that among the two types of extracts, ethanol reflux extract had more superior antitumour activity to that of the ultrasonic extract, but all of the extracts obtained had certain anti-cancer activities, and the anti-proliferative activity increased with the increase of concentration.

Effect of traditional Chinese medicine (Xiaochaihu Tang) on the expression of MMP-2 and MMP-9 in rats with endometriosis.

The aim of this study was to explore the effect of a traditional Chinese medicine (Xiaochaihu Tang, XCHT) on the expression of matrix metalloproteinase-2 (MMP-2) and MMP-9 in rats with endometriosis (EMs). A total of 48 specific-pathogen-free (SPF) female Sprague-Dawley (SD) rats were randomly divided into control (n=8) and EMs (n=40) groups. The EMs model was established using a surgical procedure. At 21 days, the rats with EMs were screened and divided into four subgroups (n=8): the model control, low-dose (7.5 g/kg) XCHT-treated, high-dose (15 g/kg) XCHT-treated and gestrinone-treated (0.5 mg/kg) groups. Following 21 days of treatment, the rats were sacrificed. Reverse transcription-polymerase chain reaction (RT-PCR) and western blotting were used to examine the mRNA and protein levels of MMP-2 and MMP-9 in the endometrium. The expression levels of MMP-2 and MMP-9 were significantly increased in the rats with EMs compared with those in normal rats. Moreover, XCHT was able to significantly inhibit the expression of MMP-2 and MMP-9 compared with that in the model control group. In conclusion, XCHT was able to decrease the expression of MMP-2 and MMP-9 in the ectopic endometrium. The present results may provide a potential theoretical basis for the therapy of EMs.

Molecular epidemiology investigation of beta-thalassemia in Zhongshan City, Guangdong Province, People's Republic of China.

Beta-THAlassemia (beta-thal) is one of the most common genetic diseases in southern China. In order to obtain detailed epidemiology data to be used for primary prevention programs, we have analyzed 2,055 independent subjects living in Zhongshan City, Guangdong Province, People's Republic of China (P.R. China), by using hematological biochemical screening and DNA technology. The results indicate a higher prevalence (3.07%) of beta-thal and coinheritance of alpha- and beta-thal (0.49%) than previously reported for Guandong Province. Ten beta-thal mutations were found in 63 independent chromosomes. The four most common mutations [codons 41/42 (-TCTT), IVS-II-654 (C>T), -28 (A>G), codon 17 (A>T)] accounted for 90.46% of the total. The uncommon mutations profile was different from that of other cities in Guangdong Province and the rare mutation IVS-II-2 (-T), once reported in Hong Kong, was also detected. This study will contribute to the development of prevention strategies in the region, allowing better genetic counseling and prenatal diagnosis of beta-thal.

[Matrine-induced erythroid differentiation of K562 cells is associated with activation of the apoptotic pathway].

OBJECTIVE: To observe matrine-induced erythroid differentiation of K562 cells in relation to activation of the apoptotic pathway in vitro. METHODS: K562 cells were cultured in the presence or absence of matrine at different concentrations for 4 days, and the morphological and ultramicrostructural changes of the cells were observed using inverted microscopy and transmission electron microscopy, respectively. The expression of apoptosis-related protein p27kip1 was detected by immunocytochemistry. RESULTS: Compared to untreated K562 cells, the cells treated with matrine at 0.10 g/L exhibited apoptostic characteristics in the cellular morphology and ultramicrostructure, with the expression of p27kip1 protein upregulated in a concentration- and time-dependent manner. CONCLUSION: Matrine-induced erythroid differentiation of K562 cells is associated with cell apoptosis, and upregulation of p27kip1 protein expression may play a crucial role in the process of apoptosis.