Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye.

Transl Vis Sci Technol. 2017 Jul;6(4):12

Authors: Smith JR, Todd S, Ashander LM, Charitou T, Ma Y, Yeh S, Crozier I, Michael MZ, Appukuttan B, Williams KA, Lynn DJ, Marsh GA

Abstract
PURPOSE: Success of Ebola virus (EBOV) as a human pathogen relates at the molecular level primarily to blockade the host cell type I interferon (IFN) antiviral response. Most individuals who survive Ebola virus disease (EVD) develop a chronic disease syndrome: approximately one-quarter of survivors suffer from uveitis, which has been associated with presence of EBOV within the eye. Clinical observations of post-Ebola uveitis indicate involvement of retinal pigment epithelial cells.
METHODS: We inoculated ARPE-19 human retinal pigment epithelial cells with EBOV, and followed course of infection by immunocytochemistry and measurement of titer in culture supernatant. To interrogate transcriptional responses of infected cells, we combined RNA sequencing with in silico pathway, gene ontology, transcription factor binding site, and network analyses. We measured infection-induced changes of selected transcripts by reverse transcription-quantitative polymerase chain reaction.
RESULTS: Human retinal pigment epithelial cells were permissive to infection with EBOV, and supported viral replication and release of virus in high titer. Unexpectedly, 28% of 560 upregulated transcripts in EBOV-infected cells were type I IFN responsive, indicating a robust type I IFN response. Following EBOV infection, cells continued to express multiple immunomodulatory molecules linked to ocular immune privilege.
CONCLUSIONS: Human retinal pigment epithelial cells may serve as an intraocular reservoir for EBOV, and the molecular response of infected cells may contribute to the persistence of live EBOV within the human eye.
TRANSLATIONAL RELEVANCE: This bedside-to-bench research links ophthalmic findings in survivors of EVD who suffer from uveitis with interactions between retinal pigment epithelial cells and EBOV.

PMID: 28721309 [PubMed]

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology.

F1000Res. 2017;6:1026

Authors: Carlson H, Deutschbauer A, Coates J

Abstract
Multidimensional gradients of inorganic compounds influence microbial activity in diverse pristine and anthropogenically perturbed environments. Here, we suggest that high-throughput cultivation and genetics can be systematically applied to generate quantitative models linking gene function, microbial community activity, and geochemical parameters. Metal resistance determinants represent a uniquely universal set of parameters around which to study and evaluate microbial fitness because they represent a record of the environment in which all microbial life evolved. By cultivating microbial isolates and enrichments in laboratory gradients of inorganic ions, we can generate quantitative predictions of limits on microbial range in the environment, obtain more accurate gene annotations, and identify useful strategies for predicting and engineering the trajectory of natural ecosystems.

PMID: 28721211 [PubMed]

39 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2017/07/19

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Draft genome sequencing of the sugarcane hybrid SP80-3280.

F1000Res. 2017;6:861

Authors: Riaño-Pachón DM, Mattiello L

Abstract
Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.

PMID: 28713559 [PubMed]

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus.

Front Microbiol. 2017;8:1219

Authors: Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B

Abstract
The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the need for a standardized approach to accurately determine what constitutes an active, viable virus infection after detection by molecular based methods.

PMID: 28713347 [PubMed]

Cell cycle perturbation induced by gemcitabine in human tumor cells in cell culture, xenografts and bladder cancer patients: implications for clinical trial designs combining gemcitabine with a Chk1 inhibitor.

Oncotarget. 2017 Jun 28;:

Authors: Montano R, Khan N, Hou H, Seigne J, Ernstoff MS, Lewis LD, Eastman A

Abstract
Gemcitabine irreversibly inhibits ribonucleotide reductase and induces S phase arrest but whether this occurs in tumors in mice or patients has not been established. Tumor cells in culture were incubated with gemcitabine for 6 h to approximate the administration schedule in a patient. Concentrations that induced persistent S phase arrest thereafter correlated with cell killing. Administration of gemcitabine to mice also demonstrated a persistent S phase arrest in their tumor. The minimum dose that induced almost complete S phase arrest after 24 h (40 mg/kg) was well below the maximum tolerated dose in mice. S phase arrest was also observed in tumors of bladder cancer patients receiving gemcitabine. The Chk1 inhibitor MK-8776 sensitized cells to gemcitabine with the greatest cell killing when added 18 h after gemcitabine. In mice, the administration of MK-8776 18 h after gemcitabine elicited positivity for the DNA damage marker γH2AX; this also occurred at relatively low dose (40 mg/kg) gemcitabine. Hence, in both cell culture and xenografts, MK-8776 can markedly enhance cell killing of cells reversibly arrested in S phase by gemcitabine. Some cell lines are hypersensitive to MK-8776 as monotherapy, but this was not observed in xenograft models. Effective monotherapy requires a higher dose of Chk1 inhibitor, and target inhibition over a longer time period as compared to its use in combination. These results have important implications for combining Chk1 inhibitors with gemcitabine and suggest that Chk1 inhibitors with increased bioavailability may have improved efficacy both in combination and as monotherapy.

PMID: 28711946 [PubMed - as supplied by publisher]

Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS).

Exp Mol Pathol. 2017 Jul 12;:

Authors: Chen Y, Marotti JD, Jenson EG, Onega TL, Johnson KC, Christensen BC

Abstract
The utility and reliability of assessing molecular biomarkers for translational applications on pre-operative core biopsy specimens assume consistency of molecular profiles with larger surgical specimens. Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. DNA was extracted from guided 2mm cores of formalin fixed paraffin embedded (FFPE) specimens, bisulfite-modified, and measured on the Illumina HumanMethylation450 BeadChip. DNA methylation profiles of core biopsies exhibited high concordance with matched surgical specimens. Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P<2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P<0.05). Between patient-matched core biopsy and surgical specimens, <0.6% of CpGs measured had changes in median DNA methylation >15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.

PMID: 28711544 [PubMed - as supplied by publisher]

CancerGD: A Resource for Identifying and Interpreting Genetic Dependencies in Cancer.

Cell Syst. 2017 Jul 11;:

Authors: Bridgett S, Campbell J, Lord CJ, Ryan CJ

Abstract
Genes whose function is selectively essential in the presence of cancer-associated genetic aberrations represent promising targets for the development of precision therapeutics. Here, we present CancerGD, a resource that integrates genotypic profiling with large-scale loss-of-function genetic screens in tumor cell lines to identify such genetic dependencies. CancerGD provides tools for searching, visualizing, and interpreting these genetic dependencies through the integration of functional interaction networks. CancerGD includes different screen types (siRNA, shRNA, CRISPR), and we describe a simple format for submitting new datasets.

PMID: 28711281 [PubMed - as supplied by publisher]

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Cell Syst. 2017 Jul 11;:

Authors: Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS

Abstract
Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models. We applied eADAGE to a compendium of Pseudomonas aeruginosa gene expression profiling experiments performed in 78 media. eADAGE revealed a phosphate starvation response controlled by PhoB in media with moderate phosphate and predicted that a second stimulus provided by the sensor kinase, KinB, is required for this PhoB activation. We validated this relationship using both targeted and unbiased genetic approaches. eADAGE, which captures stable biological patterns, enables cross-experiment comparisons that can highlight measured but undiscovered relationships.

PMID: 28711280 [PubMed - as supplied by publisher]

Short communication: Implementation of a breeding value for heat tolerance in Australian dairy cattle.

J Dairy Sci. 2017 Jul 12;:

Authors: Nguyen TTT, Bowman PJ, Haile-Mariam M, Nieuwhof GJ, Hayes BJ, Pryce JE

Abstract
Excessive ambient temperature and humidity can impair milk production and fertility of dairy cows. Selection for heat-tolerant animals is one possible option to mitigate the effects of heat stress. To enable selection for this trait, we describe the development of a heat tolerance breeding value for Australian dairy cattle. We estimated the direct genomic values of decline in milk, fat, and protein yield per unit increase of temperature-humidity index (THI) using 46,726 single nucleotide polymorphisms and a reference population of 2,236 sires and 11,853 cows for Holsteins and 506 sires and 4,268 cows for Jerseys. This new direct genomic value is the Australian genomic breeding value for heat tolerance (HT ABVg). The components of the HT ABVg are the decline in milk, fat, and protein per unit increase in THI when THI increases above the threshold of 60. These components are weighted by their respective economic values, assumed to be equivalent to the weights applied to milk, fat, and protein yield in the Australian selection indices. Within each breed, the HT ABVg is then standardized to have a mean of 100 and standard deviation (SD) of 5, which is consistent with the presentation of breeding values for many other traits in Australia. The HT ABVg ranged from -4 to +3 SD in Holsteins and -3 to +4 SD in Jerseys. The mean reliabilities of HT ABVg among validation sires, calculated from the prediction error variance and additive genetic variance, were 38% in both breeds. The range in ABVg and their reliability suggests that HT can be improved using genomic selection. There has been a deterioration in the genetic trend of HT, and to moderate the decline it is suggested that the HT ABVg should be included in a multitrait economic index with other traits that contribute to farm profit.

PMID: 28711268 [PubMed - as supplied by publisher]

Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.

Rheum Dis Clin North Am. 2017 Aug;43(3):449-466

Authors: Laufer VA, Chen JY, Langefeld CD, Bridges SL

Abstract
The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses. We illustrate how analyses of large datasets provide hope for improved approaches to the diagnosis, treatment, and prevention of rheumatic diseases.

PMID: 28711145 [PubMed - in process]

Chitosan Membranes application on the Prostatic Neurovascular Bundles following Robot-assisted Radical Prostatectomy: a phase II study.

BJU Int. 2017 Jul 15;:

Authors: Porpiglia F, Bertolo R, Fiori C, Manfredi M, De Cillis S, Geuna S

Abstract
OBJECTIVE: To evaluate the feasibility and the safety of the application of chitosan membranes on the neuro-vascular bundles after nerve-sparing Robot-Assisted Radical Prostatectomy (RARP). The secondary aim of the study was to report preliminary data and more particularly potency recovery data.
MATERIALS AND METHODS: Single-center, single-arm prospective study. Enrolment from July 2015 to September 2016 of all patients with localized prostate cancer scheduled for RARP with IIEF-5 score > 17 after San Luigi Gonzaga Hospital Ethics Committee (Orbassano) approval (80/2015) and patient's acceptance. All patients underwent nerve-sparing RARP with application of Chitosan Membranes on the neuro-vascular bundles. Demographics, peri-operative, postoperative data and complications were evaluated. Potency recovery data were particularly evaluated. Specifically for the purpose of the study, any referred sign/symptom of local allergy/intolerance to the chitosan membranes was recorded and evaluated.
RESULTS: Hundred-forty patients underwent nerve-sparing RARP with chitosan membranes application on the neuro-vascular bundles. The application was easy in almost all the cases and did not compromise the safety of the procedure. None of the patients reported signs of intolerance/allergy attributable to the membranes.
CONCLUSION: In our experience chitosan membranes application on the neuro-vascular bundles after nerve-sparing RARP was feasible and safe, without compromising the length, the difficulty and the complications rate of the "standard" procedure. No patients experienced signs of intolerance/allergy attributable to the membranes. Potency recovery data were encouraging. Comparative cohort would have added value to the study. The present paper was performed pre-CE mark achievement. This article is protected by copyright. All rights reserved.

PMID: 28710845 [PubMed - as supplied by publisher]

Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter.

Sci Rep. 2017 Jul 14;7(1):5399

Authors: Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A

Abstract
Dopamine transporter (DAT) has been shown to accumulate in filopodia in neurons and non-neuronal cells. To examine the mechanisms of DAT filopodial targeting, we used quantitative live-cell fluorescence microscopy, and compared the effects of the DAT inhibitor cocaine and its fluorescent analog JHC1-64 on the plasma membrane distribution of wild-type DAT and two non-functional DAT mutants, R60A and W63A, that do not accumulate in filopodia. W63A did not bind JHC1-64, whereas R60A did, although less efficiently compared to the wild-type DAT. Molecular dynamics simulations predicted that R60A preferentially assumes an outward-facing (OF) conformation through compensatory intracellular salt bridge formation, which in turn favors binding of cocaine. Imaging analysis showed that JHC1-64-bound R60A mutant predominantly localized in filopodia, whereas free R60A molecules were evenly distributed within the plasma membrane. Cocaine binding significantly increased the density of R60A, but not that of W63A, in filopodia. Further, zinc binding, known to stabilize the OF state, also increased R60A concentration in filopodia. Finally, amphetamine, that is thought to disrupt DAT OF conformation, reduced the concentration of wild-type DAT in filopodia. Altogether, these data indicate that OF conformation is required for the efficient targeting of DAT to, and accumulation in, filopodia.

PMID: 28710426 [PubMed - in process]

Sarcomatoid renal cell carcinoma has a distinct molecular pathogenesis, driver mutation profile and transcriptional landscape.

Clin Cancer Res. 2017 Jul 14;:

Authors: Wang Z, Kim TB, Peng B, Karam JA, Creighton CJ, Joon AY, Kawakami F, Trevisan P, Jonasch E, Chow CW, Rodriguez-Canales J, Tamboli P, Tannir NM, Wood CG, Monzon FA, Baggerly KA, Varella-Garcia M, Czerniak B, Wistuba II, Mills GB, Shaw K, Chen K, Sircar K

Abstract
PURPOSE: Sarcomatoid renal cell carcinoma (SRCC) ranks among the most aggressive clinicopathologic phenotypes of RCC. However, the paucity of high-quality, genome-wide molecular examinations of SRCC has hindered our understanding of this entity.<br /><br />Experimental Design: We interrogated the mutational, copy number, and transcriptional characteristics of SRCC and compared these data with those of non-sarcomatoid RCC (RCC). We evaluated whole exome sequencing, single nucleotide polymorphism, and RNA sequencing data from patients with SRCC (n=65) and RCC (n=598) across different parent RCC subtypes, including clear cell RCC, papillary RCC, and chromophobe RCC subtypes.  <br /><br />Results: SRCC was molecularly discrete from RCC and clustered according to its parent RCC subtype, though with upregulation of TGFβ signaling across all subtypes.  The epithelioid (E-) and spindled (S-) histologic components of SRCC did not show differences in mutational load among cancer related genes, despite a higher mutational burden in S-.  Notably, sarcomatoid clear cell RCC (SccRCC) showed significantly fewer deletions at 3p21-25, a lower rate of two-hit loss for VHL and PBRM1, and more mutations in PTEN, TP53, and RELN compared to clear cell RCC (ccRCC).  A two-hit loss involving VHL predicted for ccRCC and a better prognosis whereas mutations in PTEN, TP53, or RELN predicted for SccRCC and worse prognosis.  <br /><br />Conclusions: Sarcomatoid RCC segregates by parent subtype and SccRCC has a fundamentally different early molecular pathogenesis, usually lacking the classic 3p21-25 deletion and showing distinctive mutational and transcriptional profiles.  These features prompt a more precise molecular classification of RCC with diagnostic, prognostic, and therapeutic implications.

PMID: 28710314 [PubMed - as supplied by publisher]

Phylogenetic Quantification of Intratumor Heterogeneity.

Cold Spring Harb Perspect Med. 2017 Jul 14;:

Authors: Watkins TBK, Schwarz RF

Abstract
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies. We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles. We show their relevance in detecting clonal expansions and deriving summary statistics quantifying the overall degree of ITH, and discuss how the relationship of metastatic clades might give us insight into the dominant mode of cancer progression. We further outline how multisample studies might help us better understand selective processes acting on cancer genomes and help to detect neutral evolution and mutator phenotypes.

PMID: 28710259 [PubMed - as supplied by publisher]

The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia.

EMBO Rep. 2017 Jul 14;:

Authors: Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B

Abstract
Primary cilia are sensory, antennae-like organelles present on the surface of many cell types. They have been involved in a variety of diseases collectively termed ciliopathies. As cilia are essential regulators of cell signaling, the composition of the ciliary membrane needs to be strictly regulated. To understand regulatory processes at the ciliary membrane, we report the targeting of a genetically engineered enzyme specifically to the ciliary membrane to allow biotinylation and identification of the membrane-associated proteome. Bioinformatic analysis of the comprehensive dataset reveals high-stoichiometric presence of actin-binding proteins inside the cilium. Immunofluorescence stainings and complementary interaction proteomic analyses confirm these findings. Depolymerization of branched F-actin causes further enrichment of the actin-binding and actin-related proteins in cilia, including Myosin 5a (Myo5a). Interestingly, Myo5a knockout decreases ciliation while enhanced levels of Myo5a are observed in cilia upon induction of ciliary disassembly. In summary, we present a novel approach to investigate dynamics of the ciliary membrane proteome in mammalian cells and identify actin-binding proteins as mechanosensitive components of cilia that might have important functions in cilia membrane dynamics.

PMID: 28710093 [PubMed - as supplied by publisher]

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with Workflow4Metabolomics 3.0, the Galaxy online infrastructure for metabolomics.

Int J Biochem Cell Biol. 2017 Jul 11;:

Authors: Guitton Y, Tremblay-Franco M, Le Corguillé G, Martin JF, Pétéra M, Roger-Mele P, Delabrière A, Goulitquer S, Monsoor M, Duperier C, Canlet C, Servien R, Tardivel P, Caron C, Giacomoni F, Thévenot EA

Abstract
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows.

PMID: 28710041 [PubMed - as supplied by publisher]

Local network component analysis for quantifying transcription factor activities.

Methods. 2017 Jul 11;:

Authors: Shi Q, Zhang C, Guo W, Zeng T, Lu L, Jiang Z, Wang Z, Liu J, Chen L

Abstract
Transcription factors (TFs) could regulate physiological transitions or determine stable phenotypic diversity. The accurate estimation on TF regulatory signals or functional activities is of great significance to guide biological experiments or elucidate molecular mechanisms, but still remains challenging. Traditional methods identify TF regulatory signals at the population level, which masks heterogeneous regulation mechanisms in individuals or subgroups, thus resulting in inaccurate analyses. Here, we propose a novel computational framework, namely Local Network Component Analysis (LNCA), to exploit data heterogeneity and automatically quantify accurate transcription factor activity (TFA) in practical terms, through integrating the partitioned expression sets (i.e., local information) and prior TF-gene regulatory knowledge. Specifically, LNCA adopts an adaptive optimization strategy, which evaluates the local similarities of regulation controls and corrects biases during data integration, to construct the TFA landscape. In particular, we first numerically demonstrate the effectiveness of LNCA for the simulated data sets, compared with traditional methods, such as FastNCA, ROBNCA and NINCA. Then, we apply our model to two real data sets with implicit temporal or spatial regulation variations. The results show that LNCA not only recognizes the periodic mode along the S. cerevisiae cell cycle process, but also substantially outperforms over other methods in terms of accuracy and consistency. In addition, the cross-validation study for glioblastomas multiforme (GBM) indicates that the TFAs, identified by LNCA, can better distinguish clinically distinct tumor groups than the expression values of the corresponding TFs, thus opening a new way to classify tumor subtypes and also providing a novel insight into cancer heterogeneity.
AVAILABILITY: LNCA was implemented as a Matlab package, which is available at http://www.sysbio.ac.cn/cb/chenlab/images/LNCApackage_0.1.rar.

PMID: 28710010 [PubMed - as supplied by publisher]

mRNA interactome capture in mammalian cells.

Methods. 2017 Jul 11;:

Authors: Kastelic N, Landthaler M

Abstract
Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates. In addition to determining the RBP catalog in a given biological system, mRNA interactome capture allows the examination of changes in protein-mRNA interactions in response to internal and external stimuli, altered cellular programs and disease.

PMID: 28710009 [PubMed - as supplied by publisher]

Ganoderma triterpenes retard renal cyst development by downregulating Ras/MAPK signaling and promoting cell differentiation.

Kidney Int. 2017 Jul 11;:

Authors: Su L, Liu L, Jia Y, Lei L, Liu J, Zhu S, Zhou H, Chen R, Lu HAJ, Yang B

Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenetic disease characterized by the progressive development of renal cysts with further need for effective therapy. Here our aim was to investigate the effect of Ganoderma triterpenes (GT) on the development of kidney cysts. Importantly, GT attenuated cyst development in two mouse models of ADPKD with phenotypes of severe cystic kidney disease. Assays for tubulogenesis showed that GT promoted epithelial tubule formation in MDCK cells, suggesting a possible effect on epithelial cell differentiation. The role of GT in regulating key signaling pathways involved in the pathogenesis of PKD was further investigated by immune blotting. This showed that GT specifically downregulated the activation of the Ras/MAPK signaling pathway both in vitro and in vivo without detectable effect on the mTOR pathway. This mechanism may be involved in GT downregulating intracellular cAMP levels. Screening of 15 monomers purified from GT for their effects on cyst development indicated that CBLZ-7 (ethyl ganoderate C2) had a potent inhibitory effect on cyst development in vitro. Additionally, like GT, CBLZ-7 was able to downregulate forskolin-induced activation of the Ras/MAPK pathway. Thus, GT and its purified monomer CBLZ-7 may be potential therapeutic regents for treating ADPKD.

PMID: 28709639 [PubMed - as supplied by publisher]