Modulation of MicroRNA-194 and cell migration by HER2-targeting trastuzumab in breast cancer

Conceived and designed the experiments: XFL GAC RCB. Performed the experiments: XFL MIA WM RS MSN SZ. Analyzed the data: XFL SR. Contributed reagents/materials/analysis tools: YW GAC. Wrote the paper: XFL RCB.Trastuzumab, a humanized monoclonal antibody directed against the extracellular domain of the HER2 oncoprotein, can effectively target HER2-positive breast cancer through several mechanisms. Although the effects of trastuzumab on cancer cell proliferation, angiogenesis and apoptosis have been investigated in depth, the effect of trastuzumab on microRNA (miRNA) has not been extensively studied. We have performed miRNA microarray profiling before and after trastuzumab treatment in SKBr3 and BT474 human breast cancer cells that overexpress HER2. We found that trastuzumab treatment of SKBr3 cells significantly decreased five miRNAs and increased three others, whereas treatment of BT474 cells significantly decreased two miRNAs and increased nine. The only change in miRNA expression observed in both cell lines following trastuzumab treatment was upregulation of miRNA-194 (miR-194) that was further validated in vitro and in vivo. Forced expression of miR-194 in breast cancer cells that overexpress HER2 produced no effect on apoptosis, modest inhibition of proliferation, significant inhibition of cell migration/invasion in vitro and significant inhibition of xenograft growth in vivo. Conversely, knockdown of miR-194 promoted cell migration. Increased miR-194 expression markedly reduced levels of the cytoskeletal protein talin2 and specifically inhibited luciferase reporter activity of a talin2 wild-type 39-untranslated region, but not that of a mutant reporter, indicating that talin2 is a direct downstream target of miR-194. Trastuzumab treatment inhibited breast cancer cell migration and reduced talin2 expression in vitro and in vivo. Knockdown of talin2 inhibited cell migration/invasion. Knockdown of trastuzumab-induced miR-194 expression with a miR-194 inhibitor compromised trastuzumab-inhibited cell migration in HER2-overexpressing breast cancer cells. Consequently, trastuzumab treatment upregulates miR-194 expression and may exert its cell migration-inhibitory effect through miR-194-mediated downregulation of cytoskeleton protein talin2 in HER2-overexpressing human breast cancer cells.This work was supported by the Anne and Henry Zarrow Foundation, kind gifts from Stuart and Gaye Lynn Zarrow and from Mrs. Delores Wilkenfeld, the Laura and John Arnold Foundation, the RGK Foundation, and the MD Anderson NCI CCSG P30 CA16672. G.A.C. is supported as a Fellow at the University of Texas MD Anderson Research Trust, as a University of Texas System Regents Research Scholar and by the CLL Global Research Foundation

Interface Coupling in Twisted Multilayer Graphene by Resonant Raman Spectroscopy of Layer Breathing Modes.

Raman spectroscopy is the prime nondestructive characterization tool for graphene and related layered materials. The shear (C) and layer breathing modes (LBMs) are due to relative motions of the planes, either perpendicular or parallel to their normal. This allows one to directly probe the interlayer interactions in multilayer samples. Graphene and other two-dimensional (2d) crystals can be combined to form various hybrids and heterostructures, creating materials on demand with properties determined by the interlayer interaction. This is the case even for a single material, where multilayer stacks with different relative orientations have different optical and electronic properties. In twisted multilayer graphene there is a significant enhancement of the C modes due to resonance with new optically allowed electronic transitions, determined by the relative orientation of the layers. Here we show that this applies also to the LBMs, which can be now directly measured at room temperature. We find that twisting has a small effect on LBMs, quite different from the case of the C modes. This implies that the periodicity mismatch between two twisted layers mostly affects shear interactions. Our work shows that ultralow-frequency Raman spectroscopy is an ideal tool to uncover the interface coupling of 2d hybrids and heterostructures

Sedimentology of reefal buildups of the Xiannüdong Formation (Cambrian Series 2), SW China

© 2019, The Author(s). The reefs in the Xiannüdong Formation (Cambrian Series 2) are the oldest archaeocyathan–microbial bioconstructions in China, but the details of their microbial structures have not been previously described. However, a new section at Tangjiahe site, northern Sichuan Province, contains very well-preserved microbial fabrics that provide these details, and is described in this study. The Tangjiahe section contains three levels of reefal buildups that were constructed by a consortium of archaeocyaths and calcimicrobes in varying proportions. The lowest (oldest) reefal buildup is a calcimicrobial biostrome, possibly in the form of a wide mound with a low relief (unconfirmed due to outcrop limitation), which was formed by Epiphyton with rare small archaeocyaths, and is sandwiched by flat-pebble conglomerates. The middle reefal buildup is a high-relief calcimicrobial mound, enclosed by oolites, that was built by intergrown Renalcis and Tarthinia. Archaeocyath fossils are uncommon, and were bound into the framework by microbial carbonates. The uppermost (youngest) reefal buildup is a low-relief archaeocyathan mound lacking calcimicrobes but partly having microbially-clotted textures attached on archaeocyaths. Calcimicrobes built or aided archaeocyaths to form the framework of Tangjiahe reefs. The three buildups formed in low-energy lagoons behind ooid shoals, and the environment was nutrient-rich due to terrigenous influx from adjacent lands. Tangjiahe reefs thus resemble most Early Cambrian reefs, in settings consistent with eutrophic, calm environments, and are characterized by the domination or aid of calcimicrobial components in framework construction.National Natural Science Foundation of China (41602166), National Scientific and Technology Major Project (2016ZX05004 002-001), PetroChina Innovation Fund (2018D-5007-0105), Scientific Research Starting Project of SWPU (2017QHZ005) and Shandong Provincial Key Laboratory of Depositional Mineralization (DMsMzO1TO35)

Copy number variation analysis based on AluScan sequences

BACKGROUND: AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing. RESULTS: In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained. CONCLUSIONS: The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.published_or_final_versio

Testing for Differentially-Expressed MicroRNAs with Errors-in-Variables Nonparametric Regression

MicroRNA is a set of small RNA molecules mediating gene expression at post-transcriptional/translational levels. Most of well-established high throughput discovery platforms, such as microarray, real time quantitative PCR, and sequencing, have been adapted to study microRNA in various human diseases. The total number of microRNAs in humans is approximately 1,800, which challenges some analytical methodologies requiring a large number of entries. Unlike messenger RNA, the majority of microRNA (60%) maintains relatively low abundance in the cells. When analyzed using microarray, the signals of these low-expressed microRNAs are influenced by other non-specific signals including the background noise. It is crucial to distinguish the true microRNA signals from measurement errors in microRNA array data analysis. In this study, we propose a novel measurement error model-based normalization method and differentially-expressed microRNA detection method for microRNA profiling data acquired from locked nucleic acids (LNA) microRNA array. Compared with some existing methods, the proposed method significantly improves the detection among low-expressed microRNAs when assessed by quantitative real-time PCR assay

A web-based appointment system to reduce waiting for outpatients: A retrospective study

<p>Abstract</p> <p>Background</p> <p>Long waiting times for registration to see a doctor is problematic in China, especially in tertiary hospitals. To address this issue, a web-based appointment system was developed for the Xijing hospital. The aim of this study was to investigate the efficacy of the web-based appointment system in the registration service for outpatients.</p> <p>Methods</p> <p>Data from the web-based appointment system in Xijing hospital from January to December 2010 were collected using a stratified random sampling method, from which participants were randomly selected for a telephone interview asking for detailed information on using the system. Patients who registered through registration windows were randomly selected as a comparison group, and completed a questionnaire on-site.</p> <p>Results</p> <p>A total of 5641 patients using the online booking service were available for data analysis. Of them, 500 were randomly selected, and 369 (73.8%) completed a telephone interview. Of the 500 patients using the usual queuing method who were randomly selected for inclusion in the study, responses were obtained from 463, a response rate of 92.6%. Between the two registration methods, there were significant differences in age, degree of satisfaction, and total waiting time (<it>P </it>< 0.001). However, gender, urban residence, and valid waiting time showed no significant differences (<it>P </it>> 0.05). Being ignorant of online registration, not trusting the internet, and a lack of ability to use a computer were three main reasons given for not using the web-based appointment system. The overall proportion of non-attendance was 14.4% for those using the web-based appointment system, and the non-attendance rate was significantly different among different hospital departments, day of the week, and time of the day (<it>P </it>< 0.001).</p> <p>Conclusion</p> <p>Compared to the usual queuing method, the web-based appointment system could significantly increase patient's satisfaction with registration and reduce total waiting time effectively. However, further improvements are needed for broad use of the system.</p

The yeast P5 type ATPase, Spf1, regulates manganese transport into the endoplasmic reticulum

The endoplasmic reticulum (ER) is a large, multifunctional and essential organelle. Despite intense research, the function of more than a third of ER proteins remains unknown even in the well-studied model organism Saccharomyces cerevisiae. One such protein is Spf1, which is a highly conserved, ER localized, putative P-type ATPase. Deletion of SPF1 causes a wide variety of phenotypes including severe ER stress suggesting that this protein is essential for the normal function of the ER. The closest homologue of Spf1 is the vacuolar P-type ATPase Ypk9 that influences Mn2+ homeostasis. However in vitro reconstitution assays with Spf1 have not yielded insight into its transport specificity. Here we took an in vivo approach to detect the direct and indirect effects of deleting SPF1. We found a specific reduction in the luminal concentration of Mn2+ in ∆spf1 cells and an increase following it’s overexpression. In agreement with the observed loss of luminal Mn2+ we could observe concurrent reduction in many Mn2+-related process in the ER lumen. Conversely, cytosolic Mn2+-dependent processes were increased. Together, these data support a role for Spf1p in Mn2+ transport in the cell. We also demonstrate that the human sequence homologue, ATP13A1, is a functionally conserved orthologue. Since ATP13A1 is highly expressed in developing neuronal tissues and in the brain, this should help in the study of Mn2+-dependent neurological disorders