The draft genome assembly of Rhododendron delavayi Franch. var. delavayi

Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family. The genome assembly will have further applications in genome-assisted cultivar breeding. The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb, estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of ×482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving ×352.55 coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83 kb. Gene prediction resulted in the annotation of 32 938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO and reached 95.97% and 92.8%, respectively. The gene annotation completeness was also evaluated by CEGMA and BUSCO and reached 97.01% and 87.4%, respectively. Genome annotation revealed that 51.77% of the R. delavayi genome is composed of transposable elements, and 37.48% of long terminal repeat elements (LTRs). The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.

The safety and efficacy of transarterial chemoembolization combined with sorafenib and sorafenib mono-therapy in patients with BCLC stage B/C hepatocellular carcinoma

BACKGROUND

Sorafenib and transarterial chemoembolization (TACE) are recommended therapies for advanced hepatocellular carcinoma (HCC), but their combined efficacy remains unclear.

METHODS

Between August 2004 and November 2014, 104 patients with BCLC stage B/C HCC were enrolled at the Affiliated Tumor Hospital of Guangxi Medical University, China. Forty-eight patients were treated with sorafenib alone (sorafenib group) and 56 with TACE plus sorafenib (TACE + sorafenib group). Baseline demographic/clinical data were collected. The primary outcomes were median overall survival (OS) and progression-free survival (PFS). Secondary outcomes were overall response rate (ORR) and sorafenib-related adverse events (AEs). Baseline characteristics associated with disease prognosis were identified using multivariate Cox hazards regression.

RESULTS

The mean age of the 104 patients (94 males; 90.38%) was 49.02 ± 12.29 years. Of the baseline data, only albumin level (P = 0.028) and Child-Pugh class (P = 0.017) differed significantly between groups. Median OS did not differ significantly between the sorafenib and TACE + sorafenib groups (18.0 vs. 22.0 months, P = 0.223). Median PFS was significantly shorter in the sorafenib group than that in the TACE + sorafenib group (6.0 vs. 8.0 months, P = 0.004). Six months after treatments, the ORRs were similar between the sorafenib and TACE + sorafenib groups (12.50% vs. 18.75%, P = 0.425). The rates of grade III-IV adverse events in sorafenib and TACE + sorafenib groups were 29.2% vs. 23.2%, respectively. TACE plus sorafenib treatment (HR = 0.498, 95% CI = 0.278-0.892), no vascular invasion (HR = 0.354, 95% CI = 0.183-0.685) and Child-Pugh class A (HR = 0.308, 95% CI = 0.141-0.674) were significantly associated with better OS, while a larger tumor number was predictive of poorer OS (HR = 1.286, 95% CI = 1.031-1.604). TACE plus sorafenib treatment (HR = 0.461, 95% CI = 0.273-0.780) and no vascular invasion (HR = 0.557, 95% CI = 0.314-0.988) were significantly associated with better PFS.

CONCLUSIONS

Compared with sorafenib alone, combining TACE with sorafenib might prolong survival and delay disease progression in patients with advanced HCC.

High-efficient and high-content cytotoxic recording via dynamic and continuous cell-based impedance biosensor technology

Cell-based bioassays were effective method to assess the compound toxicity by cell viability, and the traditional label-based methods missed much information of cell growth due to endpoint detection, while the higher throughputs were demanded to obtain dynamic information. Cell-based biosensor methods can dynamically and continuously monitor with cell viability, however, the dynamic information was often ignored or seldom utilized in the toxin and drug assessment. Here, we reported a high-efficient and high-content cytotoxic recording method via dynamic and continuous cell-based impedance biosensor technology. The dynamic cell viability, inhibition ratio and growth rate were derived from the dynamic response curves from the cell-based impedance biosensor. The results showed that the biosensors has the dose-dependent manners to diarrhetic shellfish toxin, okadiac acid based on the analysis of the dynamic cell viability and cell growth status. Moreover, the throughputs of dynamic cytotoxicity were compared between cell-based biosensor methods and label-based endpoint methods. This cell-based impedance biosensor can provide a flexible, cost and label-efficient platform of cell viability assessment in the shellfish toxin screening fields.

[Correlation between serum uric acid level and acute renal injury after coronary artery bypass grafting]

Objective: To evaluate whether early postoperative serum uric acid level can predict postoperative acute renal injury (AKI) among patients undergoing coronary artery bypass grafting (CABG). Methods: The study retrospectively enrolled 1 306 patients undergoing CABG in Fuwai Hospital between September 2012 and December 2013. The patients were divided into 5 groups by the concentrations of serum uric acid measured on the morning of the first postoperative day, and uric acid categories were as follow: less than 195 μmol/L (Q1 group, 262 cases), 195-236 μmol/L (Q2 group, 263 cases), 237-280 μmol/L (Q3 group, 260 cases), 281-336 μmol/L (Q4 group, 261 cases), more than 336 μmol/L (Q5 group, 260 cases). The primary end points were AKI (RIFLE criteria), severe AKI (AKI≥stage Ⅰ), postoperative continuous renal replacement therapy (CRRT) requirement, in-hospital death, length of stay in hospital and intensive care unit(ICU). The area under the receiver-operating characteristic (ROC) curve (AUC) was used to determine the ability of the early postoperative serum uric acid level as a risk factor for postoperative AKI prediction. Results: Among the 1 306 patients enrolled in the study, AKI was found in 335 patients (25.65%). After adjusting for variables that were different between the 5 groups, the Q5 group had significantly higher risk of AKI, AKI≥ stage Ⅰ and the requirement of CRRT (P<0.01). The ROC for the outcome of postoperative AKI had an AUC of 0.648 (95% CI: 0.612-0.683) when serum creatinine levels alone were used and 0.722 (95% CI: 0.688-0.755) when serum uric acid levels alone were used (both P<0.001). Early postoperative serum uric acid was a better predictor than serum creatinine(P<0.001). Conclusion: The serum uric acid concentration within 12 hours after operation is an independent predictor of postoperative AKI in patients undergoing CABG, which could be used to identify patients at high risk for AKI.

Single-trial EEG-informed fMRI analysis of emotional decision problems in hot executive function

BACKGROUND

Executive function refers to conscious control in psychological process which relates to thinking and action. Emotional decision is a part of hot executive function and contains emotion and logic elements. As a kind of important social adaptation ability, more and more attention has been paid in recent years.

OBJECTIVE

Gambling task can be well performed in the study of emotional decision. As fMRI researches focused on gambling task show not completely consistent brain activation regions, this study adopted EEG-fMRI fusion technology to reveal brain neural activity related with feedback stimuli.

METHODS

In this study, an EEG-informed fMRI analysis was applied to process simultaneous EEG-fMRI data. First, relative power-spectrum analysis and K-means clustering method were performed separately to extract EEG-fMRI features. Then, Generalized linear models were structured using fMRI data and using different EEG features as regressors.

RESULTS

The results showed that in the win versus loss stimuli, the activated regions almost covered the caudate, the ventral striatum (VS), the orbital frontal cortex (OFC), and the cingulate. Wide activation areas associated with reward and punishment were revealed by the EEG-fMRI integration analysis than the conventional fMRI results, such as the posterior cingulate and the OFC. The VS and the medial prefrontal cortex (mPFC) were found when EEG power features were performed as regressors of GLM compared with results entering the amplitudes of feedback-related negativity (FRN) as regressors. Furthermore, the brain region activation intensity was the strongest when theta-band power was used as a regressor compared with the other two fusion results.

CONCLUSIONS

The EEG-based fMRI analysis can more accurately depict the whole-brain activation map and analyze emotional decision problems.

Bone marrow fibrosis at diagnosis predicts survival for primary acute myeloid leukemia

PURPOSE

As a desmoplastic reaction, tissue fibrosis played crucial roles in solid tumor progression, chemo-resistance, and consequently heralded poor clinical outcome. Previous studies implied the effects of marrow fibrosis on prognosis for acute lymphoblastic leukemia were disputable. In this study, we aimed to investigate the potential role of bone marrow fibrosis on clinical survival in acute myeloid leukemia (AML) patients.

METHODS

Bone marrow fibrosis (evaluated as reticulin fiber density, RFD) in bone marrow sections was evaluated at diagnosis via computer technology. Receiver operating characteristic curve (ROC) was used to analyze the predictive value of RFD for relapse and survival status. Kaplan-Meier method was used to estimate survival rates per subgroup between patients with different RFD. Cox proportional hazard regression was used to model the overall survival.

RESULTS

High RFD at diagnosis in bone marrow sections from primary AML might predict early relapse and shorter survival (P = 0.003 and 0.001, respectively). The optimal cutoff value of RFD at diagnosis was determined to be 7.2%. Furthermore, the Kaplan-Meier analysis indicated that patients with high marrow RFD had shorter relapse-free survival (RFS) and overall survival (OS) than patients with low RFD (P = 0.007 and 0.000, respectively). Multivariate analysis suggested that similar with cytogenetics, marrow RFD at diagnosis was an independent prognostic factor for RFS [HR 0.564, 95% confidence interval (CI) 0.338-0.940, P = 0.028] and OS (HR 0.457, 95% CI 0.225-0.929, P = 0.031) in primary AML patients.

CONCLUSIONS

Our data suggest that marrow RFD before treatment should be seemed as prognostic factor in primary AML, it may provide valuable clues for developing new targeted therapy.

Directed connectivity of brain default networks in resting state using GCA and motif

Nowadays, there is a lot of interest in assessing functional interactions between key brain regions. In this paper, Granger causality analysis (GCA) and motif structure are adopted to study directed connectivity of brain default mode networks (DMNs) in resting state. Firstly, the time series of functional magnetic resonance imaging (fMRI) data in resting state were extracted, and the causal relationship values of the nodes representing related brain regions are analyzed in time domain to construct a default network. Then, the network structures were searched from the default networks of controls and patients to determine the fixed connection mode in the networks. The important degree of motif structures in directed connectivity of default networks was judged according to p-value and Z-score. Both node degree and average distance were used to analyze the effect degree an information transfer rate of brain regions in motifs and default networks, and efficiency of the network. Finally, activity and functional connectivity strength of the default brain regions are researched according to the change of energy distributions between the normals and the patients' brain regions. Experimental results demonstrate that, both normal subjects and stroke patients have some corresponding fixed connection mode of three nodes, and the efficiency and power spectrum of the patient's default network is somewhat lower than that of the normal person. In particular, the Right Posterior Cingulate Gyrus (PCG.R) has a larger change in functional connectivity and its activity. The research results verify the feasibility of the application of GCA and motif structure to study the functional connectivity of default networks in resting state.

Abstract MS2-1: MS2-1 Targeting the ATR checkpoint in cancer therapy

Rémi Buisson1, Michael S. Lawrence2, Cyril H. Benes1 & Lee Zou1,3

1. Massachusetts General Hospital Cancer Center & Harvard Medical School, Boston, MA. 2. Broad Institute of Harvard and MIT, Cambridge, MA. 3. Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA.

Recent cancer genomics studies have revealed that the mutation signatures of APOBEC3A/B are commonly detected in several cancer types, such as bladder, breast, head and neck cancers, lung adenocarcinoma, and lung squamous cell carcinoma. APOBEC3A/B are members of the APOBEC family of cytosine deaminases. While APOBEC3 proteins are important for the innate immunity against viral infection, they are not expressed in normal tissues. When APOBEC3A/B are aberrantly expressed in cancer cells, they become potent “mutators”, which may promote genomic instability and contribute to tumor evolution. Interestingly, recent studies have suggested that APOBEC3A/B may act during DNA replication. However, whether the APOBEC3A/B activity in cancer cells induces DNA replication stress, and whether this activity creates a vulnerability in cancer cells that can be exploited therapeutically, remains unknown.

In this study, we show that APOBEC3A imposes a unique type of mutator-driven DNA replication stress, and that the ATR kinase plays a crucial role in antagonizing this stress. APOBEC3A expression activates ATR during DNA replication through UNG2-generated abasic sites. Surprisingly, ATR inhibition in APOBEC3A-expressing cells results in a drastic surge of abasic sites at replication forks, revealing an ATR-mediated feedback loop countering the action of APOBEC3A during replication. Mechanistically, ATR inhibition unleashes APOBEC3A-driven ssDNA accumulation at replication forks, which propagates the substrate of APOBEC3A and ultimately drives cells into replication catastrophe. In a panel of cancer cell lines, ATR inhibitor selectively induces replication catastrophe in those harboring high APOBEC3A/B activity, showing that the APOBEC3A/B activity in cancer cells confers susceptibility to ATR inhibition. Together, these results suggest that the unique APOBEC-driven replication stress in cancer cells may offer a new opportunity for ATR-targeted therapy.

Citation Format: Zou L. MS2-1 Targeting the ATR checkpoint in cancer therapy [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr MS2-1.

Hepatitis B Virus Core Antigen Stimulates IL-6 Expression via p38, ERK and NF-κB Pathways in Hepatocytes

Background: Hepatitis B virus (HBV) causes both acute and chronic liver injury. Viral proteins are involved in the pathological progress. Hepatitis B core antigen (HBcAg), a component of viral nucleocapsid, is not only essential for HBV lifecycle, but also exhibits strong immunogenicity. The cytoplasmic location of HBcAg in liver biopsy is associated with liver injury and inflammation, but the exact mechanisms remain to be elaborated. Methods: Huh7, SMMC-7721 and L-02 cells were transfected with pEGFP-N1-HBcAg to establish an intracellular HBcAg expression model. The mRNA and protein levels of Interleukin (IL)-6 were detected by qPCR and ELISA respectively. The signaling pathway-related proteins were investigated by western blot and immunofluorescence assay. Results: HBcAg increased the expression and secretion of IL-6 through activating extracellular signal-related kinase (ERK), p38 mitogen-activated protein kinase (p38 MAPK) and nuclear factor-kappa B (NF-κB). These activations can be blocked by specific inhibitors of the three pathways. Conclusions: HBcAg actives p38, ERK1/2 and NF-κB to enhance the production of IL-6 in hepatocytes. This provides a molecular mechanism to explain the association of cytoplasmic HBcAg with severe liver injury and inflammation.

Frontal Hypoactivation During a Working Memory Task in Children With 22q11 Deletion Syndrome

Impairments in executive function, such as working memory, are almost universal in children with chromosome 22q11.2 deletion syndrome. Delineating the neural underpinnings of these functions would enhance understanding of these impairments. In this study, children and adolescents with 22q11 deletion syndrome were compared with healthy control participants in a functional magnetic resonance imaging (MRI) study of working memory. When the 2-back condition was contrasted with the 1-back and 0-back conditions, the participants with 22q11 deletion syndrome showed lower activation in several brain areas involved in working memory-notably dorsolateral prefrontal cortex, anterior cingulate, and precuneus. This hypoactivation may be due to reduced gray matter volumes or white matter connectivity in the frontal and parietal regions, differences that have previously been documented in children with 22q11 deletion syndrome. Understanding differences in brain function will provide a foundation for future interventions to address the wide range of neurodevelopmental deficits observed in 22q11 deletion syndrome.

Efficacy of three-dimensional conformal radiotherapy combined with transarterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombus

Objective

The current study aimed to evaluate the efficacy and outcomes of three-dimensional conformal radiotherapy (3DCRT) combined with transarterial chemoembolization (TACE) for treating patients with hepatocellular carcinoma involving portal vein tumor thrombus.

Methods

Between January 2000 and December 2013, a total of 182 hepatocellular carcinoma patients with portal vein tumor thrombus were retrospectively analyzed: 68 patients were treated by 3DCRT alone (group A), 74 by TACE alone (group B), and 40 by a combination of 3DCRT + TACE (group C). The overall survival (OS) of the three groups was compared using the Kaplan–Meier method. The independent predictors of survival were identified using multivariate analysis.

Results

The total effective rate (complete response + partial response) among all patients was 44% (80/182). The objective response rate (complete response + partial response) was higher in group C than in group A or B, but the differences were not significant. OS rates at 1, 2, and 3 years were significantly higher in group C than in group A or B (P<0.05), while OS rates were similar between groups A and B. Multivariate analysis identified serum levels of alpha-fetoprotein <400 ng/mL and the use of 3DCRT + TACE as independent predictors of better OS.

Conclusion

These results suggest that combining 3DCRT with TACE may provide better OS than either technique alone in hepatocellular carcinoma patients with portal vein tumor thrombus.

A Molecular Basis for Innovation in Drug Excipients

Excipients are ubiquitous in drug formulation, ensuring that active ingredient drugs are properly released on dosing, retain their properties over time, and are palatable, among other roles. Despite their crucial roles, surprisingly little is known about their systemic availability and activities on molecular targets. Here we review key excipient properties, introduce a public-accessible database that enumerates and categorizes them, and sketch a strategy for exploring their possible direct actions on molecular targets.

Thyroid-stimulating hormone receptor affects metastasis and prognosis in papillary thyroid carcinoma

OBJECTIVE

Although endocrine therapy of papillary thyroid carcinoma (PTC) by inhibiting thyroid-stimulating hormone (TSH) has been used for many years, its mechanism of action is not clear. This study aimed to explore the expression and role of TSH receptor (TSHR) in PTC, to provide a theoretical basis for optimization of endocrine treatment options in PTC.

PATIENTS AND METHODS

Expression of TSHR was tested by immunohistochemistry of tissues from 150 cases of PTC and 21 normal thyroid tissues. Survival analysis was performed by Kaplan-Meier and log-rank analyses, and multivariate analysis was done using a Cox model. The regulatory effects of the TSH-TSHR signal transduction pathway on differentiated thyroid carcinoma cells were explored in vitro.

RESULTS

The positive expression rate of TSHR in PTC was 68% (102/150). TSHR expression was an independent factor affecting the prognosis of PTC patients aged > 45 years (p = 0.006), and TSHR might have a role in decreasing distant metastasis (p = 0.024). In vitro experiments showed that up-regulation of TSHR promoted apoptosis of thyroid cancer cells and inhibited metastasis significantly. There was no significant regulatory effect of the TSH-TSHR signal transduction pathway on the proliferation of thyroid carcinoma cells.

CONCLUSIONS

TSHR expression is an independent factor that affects the prognosis of PTC patients, and might decrease distant metastasis in patient aged > 45 years. Up-regulation of TSHR could inhibit metastasis and promote apoptosis in PTC cells.

[Detection of Solitary Pulmonary Nodules Based on Geometric Features]

The possibility of solitary pulmonary nodules tending to lung cancer is very high in the middle and late stage.In order to detect the middle and late solitary pulmonary nodules,we present a new computer-aided diagnosis method based on the geometric features.The new algorithm can overcome the disadvantage of the traditional algorithm which can’t eliminate the interference of vascular cross section.The proposed algorithm was implemented by multiple clustering of the extracted geometric features of region of interest(ROI)through K-means algorithm,including degree of slenderness,similar degree of circle,degree of compactness and discrete degree.The 232 lung CT images were selected from Lung Image Database Consortium(LIDC)database to do contrast experiment.Compared with the traditional algorithm,the detection rate of the new algorithm was 92.3%,and the error rate was 14.8%.At the same time,the detection rate of the traditional algorithm was only 83.9%,and the error rate was 78.2%.The results show that the proposed algorithm can mark the solitary pulmonary nodules more accurately and reduce the error rate due to precluding the disturbance of vessel section.