Analytical evaluation of circulating tumor DNA sequencing assays.

In China, circulating tumor DNA analysis is widely used and numerous assays are available. Systematic evaluation to help users make informed selections is needed. Nine circulating tumor DNA assays, including one benchmark assay, were evaluated using 23 contrived reference samples. There were two sample types (cell-free DNA and plasma samples), three circulating tumor DNA inputs (low, < 20 ng; medium, 20-50 ng; high, > 50 ng), two variant allele frequency ranges (low, 0.1-0.5%; intermediate, 0.5-2.5%), and four variant types (single nucleotide, insertion/deletion, structural, and copy number). Sensitivity, specificity, reproducibility, and all processes from cell-free DNA extraction to bioinformatics analysis were assessed. The test assays were generally comparable or superior to the benchmark assay, demonstrating high analytical sensitivity. Variations in circulating tumor DNA extraction and quantification efficiency, sensitivity, and reproducibility were observed, particularly at lower inputs. These findings will guide circulating tumor DNA assay choice for research and clinical studies, allowing consideration of multiple technical parameters.

First-Line Ipatasertib, Atezolizumab, and Taxane Triplet for Metastatic Triple-Negative Breast Cancer: Clinical and Biomarker Results.

PURPOSE: To evaluate a triplet regimen combining immune checkpoint blockade, AKT pathway inhibition, and (nab-) paclitaxel as first-line therapy for locally advanced/metastatic triple-negative breast cancer (mTNBC). PATIENTS AND METHODS: The single-arm CO40151 phase Ib study (NCT03800836), the single-arm signal-seeking cohort of IPATunity130 (NCT03337724), and the randomized phase III IPATunity170 trial (NCT04177108) enrolled patients with previously untreated mTNBC. Triplet therapy comprised intravenous atezolizumab 840 mg (days 1 and 15), oral ipatasertib 400 mg/day (days 1-21), and intravenous paclitaxel 80 mg/m2 (or nab-paclitaxel 100 mg/m2; days 1, 8, and 15) every 28 days. Exploratory translational research aimed to elucidate mechanisms and molecular markers of sensitivity and resistance. RESULTS: Among 317 patients treated with the triplet, efficacy ranged across studies as follows: median progression-free survival (PFS) 5.4 to 7.4 months, objective response rate 44% to 63%, median duration of response 5.6 to 11.1 months, and median overall survival 15.7 to 28.3 months. The safety profile was consistent with the known toxicities of each agent. Grade ≥3 adverse events were more frequent with the triplet than with doublets or single-agent paclitaxel. Patients with PFS >10 months were characterized by NF1, CCND3, and PIK3CA alterations and increased immune pathway activity. PFS <5 months was associated with CDKN2A/CDKN2B/MTAP alterations and lower predicted phosphorylated AKT-S473 levels. CONCLUSIONS: In patients with mTNBC receiving an ipatasertib/atezolizumab/taxane triplet regimen, molecular characteristics may identify those with particularly favorable or unfavorable outcomes, potentially guiding future research efforts.

Validation of a Spatiotemporal Gait Model Using Inertial Measurement Units for Early-Stage Parkinson's Disease Detection During Turns.

OBJECTIVE: Current inertial-based models were mostly limited to gait assessment of straight walking, which may not be efficient for detecting subtle gait disorders at an early stage of Parkinson's disease (PD). As PD patients exhibit more severe gait impairments during turns even before the appearance of gait disorders, gait characteristics during turning can provide promise in the identification of early-stage PD. METHODS: We proposed a novel spatiotemporal gait model using inertial measurement units that can assess gait performance in both straight walking and turning. Ten healthy young, ten healthy elderly subjects and ten early-stage PD patients were enrolled in the validation experiment. All participants performed a 7-meter walk test consisting of a straight walking path and turns at a self-selected speed. Spatiotemporal gait parameters from the proposed model were compared with the Vicon motion capture system. RESULTS: A strong correlation of all spatiotemporal parameters (Pearson's R between 0.82  âˆ¼  0.99) between the inertial-based model and the reference was observed. Most measurement differences were within the mean ±1.96 standard deviation lines. The absolute bias was below 6.21 ms for all temporal gait parameters, 2.19 cm for stride length and 0.02 m/s for walking speed. We show that the proposed model does not only achieve a highly accurate and reliable spatiotemporal gait measurement but also enable the detection of significantly decreased stride length and reduced walking speed in early-stage PD patients at turns compared to the control groups. SIGNIFICANCE: Our model offers a potential approach for early-stage PD detection.

Network Anonymity and Cyberbullying among Chinese Adolescents: A Moderated Mediation Model.

Cyberbullying is an important issue which prevails among children and adolescents. The present study aimed to investigate the association between network anonymity and cyberbullying behavior and examine the mediating role of network morality and the moderating role of self-control in the linkage of network anonymity and cyberbullying behavior. A total of 620 participants were recruited from three high schools in southeast China and were required to complete a questionnaire measuring network anonymity, cyberbullying behavior, network morality, and self-control. A moderated mediation model was conducted by using PROCESS Macro for SPSS 3.5. The results showed that network anonymity was negatively associated with cyberbullying behavior among Chinese adolescents. Network morality mediated the association and self-control moderated the indirect association between network anonymity and cyberbullying behavior via network morality. These findings indicate that improving the network morality and self-control of adolescents with the joint efforts of individuals, families, government, and society as a whole may be an effective intervention strategy for cyberbullying behavior under the framework of digital citizens.

Impact of gender and age on 6-Minute Walking Test performance of patients with coronary heart disease compared to healthy elders.

The performance of 6-minute walking test (6MWT) of patients with coronary heart disease (CHD) was significantly related to patients' cardiopulmonary functions. The 6MWT may provide prognostic information for patients. However, the impact of gender and age on the 6MWT performance and related cardiopulmonary parameters of patients with CHD compared to the healthy group has not be fully investigated and discussed. In this study, a total of 118 subjects, including 70 CHD patients and 48 healthy elders, were enrolled. The subjects performed the 6MWT while fourteen cardiopulmonary parameters were measured during the task and the walking distance was recorded at the end. Factors of gender, age, and disease on the 6MWT performance were analyzed using multivariate analysis of variance and the parameters between the patients and healthy people in age- and gender-specific subgroups were compared by Pearson's correlation coefficient. Results showed that age (60-65 and ≥65 years) and gender significantly influenced the 6MWT performance of subjects. Featured parameters were observed in older subgroups (≥65 years) between the patients and healthy people while patients aged 60-65 had similar 6MWT performance with the healthy control group. It would be potential to distinguish patients with CHD from healthy elders based on the 6MWT where factors of age and gender should be considered.

An inertial sensor-based algorithm for turning detection during gait.

Patients with Parkinson's disease (PD) can be divided into two subtypes based on clinical features, namely tremor-dominant (TD) and postural instability and gait difficulty (PIGD). Detection of PIGD symptoms is crucial for early diagnosis of PD and timely clinical intervention. However, patients at the early stage may not exhibit obvious motor dysfunctions during normal straight walking leading to difficulties in PD identification. Researchers have found that patients would show significant motor deteriorations in turning due to their cognition limitation. Therefore, turning detection is essential for quantitative motion analysis in the gait assessment of PD patients. In this study, we proposed a novel inertial-sensor-based algorithm for turning detection. Ten healthy young participants were enrolled in the experiment where they were required to walk along a 7-meter pathway with two 180 degree turns at their comfortable walking speed. Five inertial sensors were attached to the upper trunk, the shank and the foot of both legs. The algorithm performance was validated using an optical motion capture system for reference and two sensor combination options (upper trunk and shank sensors, upper trunk and foot sensors) were compared. The results showed that the proposed algorithm achieved accuracy over 98% for identifying the turning state of both legs. The integration of the upper trunk and foot sensors had no significant effect on the detection accuracy compared to that with the use of the upper trunk and shank sensors. Our algorithm has the potential to be implemented in the motion analysis model for complicated gait tasks, which has great potential in the early diagnosis of PIGD.

Comprehensive genomic and immunological characterization of Chinese non-small cell lung cancer patients.

Deep understanding of the genomic and immunological differences between Chinese and Western lung cancer patients is of great importance for target therapy selection and development for Chinese patients. Here we report an extensive molecular and immune profiling study of 245 Chinese patients with non-small cell lung cancer. Tumor-infiltrating lymphocyte estimated using immune cell signatures is found to be significantly higher in adenocarcinoma (ADC, 72.5%) compared with squamous cell carcinoma (SQCC, 54.4%). The correlation of genomic alterations with immune signatures reveals that low immune infiltration was associated with EGFR mutations in ADC samples, PI3K and/or WNT pathway activation in SQCC. While KRAS mutations are found to be significantly associated with T cell infiltration in ADC samples. The SQCC patients with high antigen presentation machinery and cytotoxic T cell signature scores are found to have a prolonged overall survival time.

Effect of Tai Chi for the prevention or treatment of osteoporosis in elderly adults: protocol for a systematic review and meta-analysis.

INTRODUCTION: Osteoporosis (OP) has been defined as a degenerative bone disease characterised by low bone mass and microstructural deterioration of bone tissue, leading to fragility and an increased risk of fractures, especially of the hip, spine and wrist. Exercise has been shown to benefit the maintenance of bone health and improvement of muscle strength, balance and coordination, thereby reducing the risk of falls and fractures. However, prior findings regarding the optimal types and regimens of exercise for treating low bone mineral density (BMD) in elderly people are not consistent. As an important component of traditional Chinese Qigong exercises, Tai Chi (TC) is an ancient art and science of healthcare derived from the martial arts. The objective of this study is to attempt to conduct a systematic review and meta-analysis of the existing studies on TC exercise as an intervention for the prevention or treatment of OP in elderly adults and to draw more useful conclusions regarding the safety and the effectiveness of TC in preventing or treating OP. METHODS AND ANALYSIS: Eight electronic databases (Science Citation Index, PubMed Database, Embase (Ovid) Database, the Cochrane Central Register of Controlled Trials, and Chinese databases, including Chinese BioMedical Database, China National Knowledge Infrastructure, Wanfang database and the Chongqing VIP Chinese Science and Technology Periodical Database) will be searched from the beginning of each database to 1 April 2018. Potential outcomes of interest will include rates of fractures or falls, BMD at the total hip and the total spine, bone formation biomarkers, bone resorption biomarkers, bone biomarkers, health-related quality of life and adverse events. Only randomised controlled trials comparing TC exercise against each other or non-intervention will be included. The Cochrane risk of bias assessment tool will be used for quality assessment. ETHICS AND DISSEMINATION: Ethical approval is not required as the study will be a review of existing studies. This review may help to elucidate whether TC exercise is effective for the prevention or treatment of OP in elderly adults. The findings of the study will be published in a peer-reviewed publication and will be disseminated electronically or in print. We will share the findings in the fourth quarter of 2018. TRIAL REGISTRATION NUMBER: CRD42018084950.

NitroSynapsin therapy for a mouse MEF2C haploinsufficiency model of human autism.

Transcription factor MEF2C regulates multiple genes linked to autism spectrum disorder (ASD), and human MEF2C haploinsufficiency results in ASD, intellectual disability, and epilepsy. However, molecular mechanisms underlying MEF2C haploinsufficiency syndrome remain poorly understood. Here we report that Mef2c +/-(Mef2c-het) mice exhibit behavioral deficits resembling those of human patients. Gene expression analyses on brains from these mice show changes in genes associated with neurogenesis, synapse formation, and neuronal cell death. Accordingly, Mef2c-het mice exhibit decreased neurogenesis, enhanced neuronal apoptosis, and an increased ratio of excitatory to inhibitory (E/I) neurotransmission. Importantly, neurobehavioral deficits, E/I imbalance, and histological damage are all ameliorated by treatment with NitroSynapsin, a new dual-action compound related to the FDA-approved drug memantine, representing an uncompetitive/fast off-rate antagonist of NMDA-type glutamate receptors. These results suggest that MEF2C haploinsufficiency leads to abnormal brain development, E/I imbalance, and neurobehavioral dysfunction, which may be mitigated by pharmacological intervention.

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling.

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort.

Broadly neutralizing antibodies (bnAbs) are thought to be a critical component of a protective HIV vaccine. However, designing vaccines immunogens able to elicit bnAbs has proven unsuccessful to date. Understanding the correlates and immunological mechanisms leading to the development of bnAb responses during natural HIV infection is thus critical to the design of a protective vaccine. The IAVI Protocol C program investigates a large longitudinal cohort of primary HIV-1 infection in Eastern and South Africa. Development of neutralization was evaluated in 439 donors using a 6 cross-clade pseudo-virus panel predictive of neutralization breadth on larger panels. About 15% of individuals developed bnAb responses, essentially between year 2 and year 4 of infection. Statistical analyses revealed no influence of gender, age or geographical origin on the development of neutralization breadth. However, cross-clade neutralization strongly correlated with high viral load as well as with low CD4 T cell counts, subtype-C infection and HLA-A*03(-) genotype. A correlation with high overall plasma IgG levels and anti-Env IgG binding titers was also found. The latter appeared not associated with higher affinity, suggesting a greater diversity of the anti-Env responses in broad neutralizers. Broadly neutralizing activity targeting glycan-dependent epitopes, largely the N332-glycan epitope region, was detected in nearly half of the broad neutralizers while CD4bs and gp41-MPER bnAb responses were only detected in very few individuals. Together the findings suggest that both viral and host factors are critical for the development of bnAbs and that the HIV Env N332-glycan supersite may be a favorable target for vaccine design.

The invadopodia scaffold protein Tks5 is required for the growth of human breast cancer cells in vitro and in vivo.

The ability of cancer cells to invade underlies metastatic progression. One mechanism by which cancer cells can become invasive is through the formation of structures called invadopodia, which are dynamic, actin-rich membrane protrusions that are sites of focal extracellular matrix degradation. While there is a growing consensus that invadopodia are instrumental in tumor metastasis, less is known about whether they are involved in tumor growth, particularly in vivo. The adaptor protein Tks5 is an obligate component of invadopodia, and is linked molecularly to both actin-remodeling proteins and pericellular proteases. Tks5 appears to localize exclusively to invadopodia in cancer cells, and in vitro studies have demonstrated its critical requirement for the invasive nature of these cells, making it an ideal surrogate to investigate the role of invadopodia in vivo. In this study, we examined how Tks5 contributes to human breast cancer progression. We used immunohistochemistry and RNA sequencing data to evaluate Tks5 expression in clinical samples, and we characterized the role of Tks5 in breast cancer progression using RNA interference and orthotopic implantation in SCID-Beige mice. We found that Tks5 is expressed to high levels in approximately 50% of primary invasive breast cancers. Furthermore, high expression was correlated with poor outcome, particularly in those patients with late relapse of stage I/II disease. Knockdown of Tks5 expression in breast cancer cells resulted in decreased growth, both in 3D in vitro cultures and in vivo. Moreover, our data also suggest that Tks5 is important for the integrity and permeability of the tumor vasculature. Together, this work establishes an important role for Tks5 in tumor growth in vivo, and suggests that invadopodia may play broad roles in tumor progression.

Overexpression of zinc-finger protein 777 (ZNF777) inhibits proliferation at low cell density through down-regulation of FAM129A.

Krüppel-associated box-containing zinc finger proteins (KRAB-ZFPs) regulate a wide range of cellular processes. KRAB-ZFPs have a KRAB domain, which binds to transcriptional corepressors, and a zinc finger domain, which binds to DNA to activate or repress gene transcription. Here, we characterize ZNF777, a member of KRAB-ZFPs. We show that ZNF777 localizes to the nucleus and inducible overexpression of ZNF777 inhibits cell proliferation in a manner dependent on its zinc finger domain but independent of its KRAB domain. Intriguingly, ZNF777 overexpression drastically inhibits cell proliferation at low cell density but slightly inhibits cell proliferation at high cell density. Furthermore, ZNF777 overexpression decreases the mRNA level of FAM129A irrespective of cell density. Importantly, the protein level of FAM129A strongly decreases at low cell density, but at high cell density the protein level of FAM129A does not decrease to that observed at low cell density. ZNF777-mediated inhibition of cell proliferation is attenuated by overexpression of FAM129A at low cell density. Furthermore, ZNF777-mediated down-regulation of FAM129A induces moderate levels of the cyclin-dependent kinase inhibitor p21. These results suggest that ZNF777 overexpression inhibits cell proliferation at low cell density and that p21 induction by ZNF777-mediated down-regulation of FAM129A plays a role in inhibition of cell proliferation.

Transcriptional profiling of MEF2-regulated genes in human neural progenitor cells derived from embryonic stem cells.

[Briefly describe the contents of the Data in Brief article. Tell the reader the repository and reference number for the data in the abstract to.] The myocyte enhancer factor 2 (MEF2) family of transcription factors is highly expressed in the brain, and constitutes a key determinant of neuronal survival, differentiation, and synaptic plasticity. However, genome-wide transcriptional profiling of MEF2-regulated genes has not yet been fully elucidated, particularly at the neural stem cell stage. Here we report the results of microarray analysis comparing mRNAs isolated from human neural progenitor/stem cells (hNPCs) derived from embryonic stem cells expressing a control vector versus progenitors expressing a constitutively-active form of MEF2 (MEF2CA), which increases MEF2 activity. Microarray experiments were performed using the Illumina Human HT-12 V4.0 expression beadchip (GEO#: GSE57184). By comparing vector-control cells to MEF2CA cells, microarray analysis identified 1880 unique genes that were differentially expressed. Among these genes, 1121 genes were upregulated and 759 genes were down-regulated. Our results provide a valuable resource for identifying transcriptional targets of MEF2 in hNPCs.

S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death.

Redox-mediated posttranslational modifications represent a molecular switch that controls major mechanisms of cell function. Nitric oxide (NO) can mediate redox reactions via S-nitrosylation, representing transfer of an NO group to a critical protein thiol. NO is known to modulate neurogenesis and neuronal survival in various brain regions in disparate neurodegenerative conditions. However, a unifying molecular mechanism linking these phenomena remains unknown. Here, we report that S-nitrosylation of myocyte enhancer factor 2 (MEF2) transcription factors acts as a redox switch to inhibit both neurogenesis and neuronal survival. Structure-based analysis reveals that MEF2 dimerization creates a pocket, facilitating S-nitrosylation at an evolutionally conserved cysteine residue in the DNA binding domain. S-Nitrosylation disrupts MEF2-DNA binding and transcriptional activity, leading to impaired neurogenesis and survival in vitro and in vivo. Our data define a molecular switch whereby redox-mediated posttranslational modification controls both neurogenesis and neurodegeneration via a single transcriptional signaling cascade.

Synaptic protein α1-takusan mitigates amyloid-ß-induced synaptic loss via interaction with tau and postsynaptic density-95 at postsynaptic sites.

The synaptic toxicity of soluble amyloid-ß (Aß) oligomers plays a critical role in the pathophysiology of Alzheimer's disease (AD). Here we report that overexpressed α1-takusan, which we previously identified as a protein that enhances synaptic activity via interaction with PSD-95, mitigates oligomeric Aß-induced synaptic loss. In contrast, takusan knockdown results in enhanced synaptic damage. α1-Takusan interacts with tau either directly or indirectly, and prevents Aß-induced tau hyperphosphorylation and mitochondrial fragmentation. Deletion analysis identified the second domain (D2) within the takusan protein that is required for PSD-95 clustering and synaptic protection from Aß. A 51 aa sequence linking D2 to the PDZ-binding C terminus was found to be as effective as full-length takusan in protecting synapses from Aß-induced damage. Moreover, a sequence containing the D2 from the human protein discs large homolog 5, when linked to a C-terminal PDZ-binding motif, can also increase the clustering of PSD-95 in cortical dendrites. In summary, α1-takusan protects synapses from Aß-induced insult via interaction with PSD-95 and tau. Thus, takusan-based protein sequences from either mouse or human may be of potential therapeutic benefit in AD.

N-aroyloxylthioxo-naphthalimides as DNA photocleavers of aroyloxyl oxygen radicals: synthesis, evaluation, and substituents' effect.

Novel N-Aroyloxylthioxo-naphthalimides as highly efficient 'time-resolved' DNA photocleavers of aroyloxyl radicals type were designed and synthesized. The substituents at the aroyloxyl moiety have an important and unusual influence on the DNA photocleavage, and DNA photodamages of the compounds were unusually not depended on the electronic effects of substituents on the corresponding oxygen-centered radicals. With AM1 semi-empirical quantum calculation, it was found that their photocleaving activities were correlated with the densities of electron clouds on the N-O bonds in the triplet state. N-(m-Dichloro-benzoyloxy)-thioxo-naphthalimide could photodamage DNA effectively at less than the concentration of 2 microM.