Centrally Acting Perindopril Attenuates the Exercise Induced Increase in Muscle Sympathetic Nerve Activity during Heavy Dynamic Exercise

Central angiotensin II (Ang II) linked free radical (FR) production scavenges nitric oxide (NO) enabling an increased central sympathetic neural outflow (SNA). The pathophysiological increase in Ang II linked FR production is recognized as a major mechanism involved in neurogenic hypertension. During exercise, there is a physiological increase in Ang II and muscle sympathetic nerve activity (MSNA) in direct relation to increasing exercise intensity. We tested the hypothesis that the exercise induced increase in Ang II linked FR production and MSNA activity during exercise is located within the brain. Six healthy subjects performed three randomly ordered trials of 70° upright back-supported dynamic leg cycling after ingestion of two different lipid soluble Angiotensin converting enzyme inhibitors ((ACEi) Perindopril (PER) - highly lipid soluble; Captopril (CAP) non-lipid soluble)) and/or placebo (PL). Repeated measurements of whole venous blood, MSNA, and mean arterial pressures (MAP) were obtained at rest and during steady-state heavy intensity exercise at heart rates (HR) of 120 bpm (e120). Peripheral venous superoxide concentrations as measured by electron paramagnetic resonance (EPR) were not significantly altered at rest (P≥0.4) and during E120 by the ACE inhibitors (P≥0.07). Likewise, baseline MSNA (PL, 25 ± 1.5 bust/min; CAP, 21 ± 0.7 bust/min; PER, 25 ± 0.7 bust/min) and MAP (PL, 86 ± 2.8 mmHg vs. CAP, 84 ± 2.6 mmHg; PER, 84 ± 0.7 mmHg) were unchanged at rest (P≥0.1; P≥0.8 respectively). However, during E120 central acting PER attenuated the increases in MSNA and MAP, increasing only 15±6% for MAP and 24±8% for MSNA when compared to PL (26 ± 6% MAP; 57±16% MSNA; P\u3c0.05) and CAP (26±4%MAP; 69±13%MSNA P\u3c0.05). From these data we conclude that centrally acting PER attenuated the central increase in the exercise induced Ang II linked free radical production resulting in an increased central NO activity induced reduction in MSNA during heavy intensity dynamic exercise

Antioxidants Attenuate the Exercise Induced Resetting of the Arterial Baroreflex in Healthy Human Subjects: Implications for Exercise Induced Hypertension

Patients with Exercise-induced-Hypertension (EiHT) exhibit exaggerated increases in arterial pressure at the onset of exercise which may prevent EiHT patients from participating in exercise training programs. EiHT is thought to occur due to dysregulated resetting of the arterial baroreflex (ABR). Prior studies in animal models demonstrate that reactive oxygen species (ROS) generated in the brainstem scavenge the sympathoinhibitory function of central Nitric Oxide (NO) and, thereby enable ABR resetting of the operating point (OP) pressure and hypertension. We tested the hypothesis that a centrally and peripherally active antioxidant cocktail (CT; composed of Vitamin E and C with Co-Q10) will attenuate the exercise induced resetting of the ABR‘s centering point (CP) and OP pressures compared to the same exercise intensity performed with a vehicle placebo (PL). Seven healthy human subjects were recruited and performed 700 back-supported semi-recumbent dynamic leg exercise at moderate (HR at 120 beats per minute: e120) and heavy (HR at 150 beats per minute: e150) intensities. Mean arterial pressure (MAP) was continuously recorded using photoplethysmography at the finger, while HR was recorded via a three lead electrocardiogram (ECG). On experimental day 1, subjects were either given the CT or PL 1 hr. (time of peak plasma concentrations) prior to the start of exercise. On a separate experiment day 2, the subjects repeated the same exercise intensity protocol with the other test article (CT or PL) in a randomized repeated measures design. During exercise with the PL ingestion, the CP of the ABR was reset to higher MAPs from rest to e120 (100 ± 3 mm Hg to 121 ± 3 mm Hg, P\u3c0.02) but not e150 (113 ± 3 mm Hg, P=0.15). The absence of resetting at the higher work intensity was likely due to cardiovascular drift (decreasing MAP). Ingestion of the CT prior to the exercise protocols prevented the increase of the CP to higher MAPs from rest to e120 and e150 (rest: 97 ± 3 mm Hg, e120: 106 ± 3 mm Hg, e150: 106 ± 3 mm Hg, P \u3e0.21). Furthermore, the OP- pressure of the ABR was attenuated with CT ingestion compared to PL at e120 (placebo e120: 116 ± 0.8 mm Hg, CT e120: 111 ± 0.8 mm Hg, P = 0.04). These data: (a) confirm that centrally derived ROS contribute to exercise induced ABR resetting; and (b) indicate that EiHT could be treated by ingestion of an anti-oxidant cocktail prior to the start of exercise

Nonparametric variable importance assessment using machine learning techniques

In a regression setting, it is often of interest to quantify the importance of various features in predicting the response. Commonly, the variable importance measure used is determined by the regression technique employed. For this reason, practitioners often only resort to one of a few regression techniques for which a variable importance measure is naturally defined. Unfortunately, these regression techniques are often sub-optimal for predicting response. Additionally, because the variable importance measures native to different regression techniques generally have a different interpretation, comparisons across techniques can be difficult. In this work, we study a novel variable importance measure that can be used with any regression technique, and whose interpretation is agnostic to the technique used. Specifically, we propose a generalization of the ANOVA variable importance measure, and discuss how it facilitates the use of possibly-complex machine learning techniques to flexibly estimate the variable importance of a single feature or group of features. Using the tools of targeted learning, we also describe how to construct an efficient estimator of this measure, as well as a valid confidence interval. Through simulations, we show that our proposal has good practical operating characteristics, and we illustrate its use with data from a study of the median house price in the Boston area, and a study of risk factors for cardiovascular disease in South Africa

Preparation of multiplexed small RNA libraries from plants

[EN] High-throughput sequencing is a powerful tool for exploring small RNA populations in plants. The ever-increasing output from an Illumina Sequencing System allows for multiplexing multiple samples while still obtaining sufficient data for small RNA discovery and characterization. Here we describe a protocol for generating multiplexed small RNA libraries for sequencing up to 12 samples in one lane of an Illumina HiSeq System single-end, 50 base pair run. RNA ligases are used to add the 3¿ and 5¿ adaptors to purified small RNAs; ligation products that lack a small RNA molecule (adaptor-adaptor products) are intentionally depleted. After cDNA synthesis, a linear PCR step amplifies the DNA fragments. The 3¿ PCR primers used here include unique 6- nucleotide sequences to allow for multiplexing up to 12 samples.The original version of this protocol was described in Carbonell et al. (2012). The updated version of the protocol was described in Carbonell et al. (2014). This work was supported by grants from the National Science Foundation (MCB-0956526, MCB-1231726) and National Institutes of Health (AI043288)Gilbert, KB.; Fahlgren, N.; Kasschau, KD.; Chapman, EJ.; Carrington, JC.; Carbonell, A. (2014). Preparation of multiplexed small RNA libraries from plants. Bio-protocol. 4(21):1-17. https://doi.org/10.21769/BioProtoc.1275S11742

Enterocyte STAT5 promotes mucosal wound healing via suppression of myosin light chain kinase-mediated loss of barrier function and inflammation

Epithelial myosin light chain kinase (MLCK)-dependent barrier dysfunction contributes to the pathogenesis of inflammatory bowel diseases (IBD). We reported that epithelial GM-CSF–STAT5 signalling is essential for intestinal homeostatic response to gut injury. However, mechanism, redundancy by STAT5 or cell types involved remained foggy. We here generated intestinal epithelial cell (IEC)-specific STAT5 knockout mice, these mice exhibited a delayed mucosal wound healing and dysfunctional intestinal barrier characterized by elevated levels of NF-κB activation and MLCK, and a reduction of zonula occludens expression in IECs. Deletion of MLCK restored intestinal barrier function in STAT5 knockout mice, and facilitated mucosal wound healing. Consistently, knockdown of stat5 in IEC monolayers led to increased NF-κB DNA binding to MLCK promoter, myosin light chain phosphorylation and tight junction (TJ) permeability, which were potentiated by administration of tumour necrosis factor-α (TNF-α), and prevented by concurrent NF-κB knockdown. Collectively, enterocyte STAT5 signalling protects against TJ barrier dysfunction and promotes intestinal mucosal wound healing via an interaction with NF-κB to suppress MLCK. Targeting IEC STAT5 signalling may be a novel therapeutic approach for treating intestinal barrier dysfunction in IBD

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world

Existing climate change will lead to pronounced shifts in the diversity of soil prokaryotes

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 3 (2018): e00167-18, doi:10.1128/mSystems.00167-18.Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.This work was supported by the Strategic Priority Research Program (XDB15010101, XDA05050404) of the Chinese Academy of Sciences, the National Program on Key Basic Research Project (2014CB954002, 2014CB954004), the National Natural Science Foundation of China (41701298, 41371254), the “135” Plan and Frontiers Projects of Institute of Soil Science (ISSASIP1641), and the National Science and Technology Foundation project (2015FY110100). J.A.G. was supported by the U.S. Dept. of Energy under contract DE-AC02-06CH11357. N.F. was supported by a grant from the National Science Foundation (DEB-0953331). K.S.P. and J.L. were supported by the National Science Foundation (DMS-1069303), the Gordon and Betty Moore Foundation (grant no. 3300), the Gladstone Institutes, and a gift from the San Simeon Fund

Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants

[EN] In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were used to examine several AGO functions, including small RNA binding, interaction with target RNA, slicing or destabilization of target RNA, secondary small interfering RNA formation, and antiviral activity. Complementation analyses in ago mutant plants revealed that the catalytic residues of AGO1, AGO2, and AGO7 are required to restore the defects of Arabidopsis ago1-25, ago2-1, and zip-1 (AGO7-defective) mutants, respectively. AGO2 had slicer activity in transient assays but could not trigger secondary small interfering RNA biogenesis, and catalytically active AGO2 was necessary for local and systemic antiviral activity against Turnip mosaic virus. Slicer-defective AGOs associated with miRNAs and stabilized AGO-miRNA-target RNA ternary complexes in individual target coimmunoprecipitation assays. In genome-wide AGO-miRNA-target RNA coimmunoprecipitation experiments, slicer-defective AGO1-miRNA associated with target RNA more effectively than did wild-type AGO1-miRNA. These data not only reveal functional roles for AGO1, AGO2, and AGO7 slicer activity, but also indicate an approach to capture ternary complexes more efficiently for genome-wide analyses.We thank Goretti Nguyen for excellent technical assistance. A. C. was supported by a postdoctoral fellowship from the Ministerio de Ciencia e Innovacion (BMC-2008-0188). H.G.-R. was the recipient of a Helen Hay Whitney Postdoctoral fellowship (F-972). This work was supported by grants from the National Science Foundation (MCB-1231726), the National Institutes of Health (AI043288), and Monsanto Corporation.Carbonell, A.; Fahlgren, N.; García-Ruíz, H.; Gilbert, KB.; Montgomery, TA.; Nguyen, T.; Cuperus, JT.... (2012). Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. The Plant Cell. 24(9):3613-3629. https://doi.org/10.1105/tpc.112.099945S36133629249Allen, E., Xie, Z., Gustafson, A. M., & Carrington, J. C. (2005). microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants. Cell, 121(2), 207-221. doi:10.1016/j.cell.2005.04.004Aukerman, M. J., & Sakai, H. (2003). Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes. The Plant Cell, 15(11), 2730-2741. doi:10.1105/tpc.016238Axtell, M. J., Jan, C., Rajagopalan, R., & Bartel, D. P. (2006). A Two-Hit Trigger for siRNA Biogenesis in Plants. Cell, 127(3), 565-577. doi:10.1016/j.cell.2006.09.032Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P., & Bartel, D. P. (2008). The impact of microRNAs on protein output. Nature, 455(7209), 64-71. doi:10.1038/nature07242Baumberger, N., & Baulcombe, D. C. (2005). Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences, 102(33), 11928-11933. doi:10.1073/pnas.0505461102Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y. Y., Sieburth, L., & Voinnet, O. (2008). Widespread Translational Inhibition by Plant miRNAs and siRNAs. Science, 320(5880), 1185-1190. doi:10.1126/science.1159151Chekanova, J. A., Gregory, B. D., Reverdatto, S. V., Chen, H., Kumar, R., Hooker, T., … Belostotsky, D. A. (2007). Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome. Cell, 131(7), 1340-1353. doi:10.1016/j.cell.2007.10.056Chen, H.-M., Chen, L.-T., Patel, K., Li, Y.-H., Baulcombe, D. C., & Wu, S.-H. (2010). 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proceedings of the National Academy of Sciences, 107(34), 15269-15274. doi:10.1073/pnas.1001738107Chen, X. (2004). A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development. Science, 303(5666), 2022-2025. doi:10.1126/science.1088060Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009). Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature, 460(7254), 479-486. doi:10.1038/nature08170Clough, S. J., & Bent, A. F. (1998). Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana. The Plant Journal, 16(6), 735-743. doi:10.1046/j.1365-313x.1998.00343.xCuperus, J. T., Carbonell, A., Fahlgren, N., Garcia-Ruiz, H., Burke, R. T., Takeda, A., … Carrington, J. C. (2010). Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature Structural & Molecular Biology, 17(8), 997-1003. doi:10.1038/nsmb.1866Curtis, M. D., & Grossniklaus, U. (2003). A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta. Plant Physiology, 133(2), 462-469. doi:10.1104/pp.103.027979Dunoyer, P., Himber, C., & Voinnet, O. (2005). DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nature Genetics, 37(12), 1356-1360. doi:10.1038/ng1675Eulalio, A., Huntzinger, E., & Izaurralde, E. (2008). Getting to the Root of miRNA-Mediated Gene Silencing. Cell, 132(1), 9-14. doi:10.1016/j.cell.2007.12.024Fahlgren, N., Sullivan, C. M., Kasschau, K. D., Chapman, E. J., Cumbie, J. S., Montgomery, T. A., … Carrington, J. C. (2009). Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA, 15(5), 992-1002. doi:10.1261/rna.1473809Filipowicz, W., Bhattacharyya, S. N., & Sonenberg, N. (2008). Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Reviews Genetics, 9(2), 102-114. doi:10.1038/nrg2290Gandikota, M., Birkenbihl, R. P., Höhmann, S., Cardon, G. H., Saedler, H., & Huijser, P. (2007). The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. The Plant Journal, 49(4), 683-693. doi:10.1111/j.1365-313x.2006.02983.xGarcia-Ruiz, H., Takeda, A., Chapman, E. J., Sullivan, C. M., Fahlgren, N., Brempelis, K. J., & Carrington, J. C. (2010). Arabidopsis RNA-Dependent RNA Polymerases and Dicer-Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection  . The Plant Cell, 22(2), 481-496. doi:10.1105/tpc.109.073056Gasciolli, V., Mallory, A. C., Bartel, D. P., & Vaucheret, H. (2005). Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs. Current Biology, 15(16), 1494-1500. doi:10.1016/j.cub.2005.07.024Guo, H., Ingolia, N. T., Weissman, J. S., & Bartel, D. P. (2010). Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466(7308), 835-840. doi:10.1038/nature09267Harvey, J. J. W., Lewsey, M. G., Patel, K., Westwood, J., Heimstädt, S., Carr, J. P., & Baulcombe, D. C. (2011). An Antiviral Defense Role of AGO2 in Plants. PLoS ONE, 6(1), e14639. doi:10.1371/journal.pone.0014639Havecker, E. R., Wallbridge, L. M., Hardcastle, T. J., Bush, M. S., Kelly, K. A., Dunn, R. M., … Baulcombe, D. C. (2010). TheArabidopsisRNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci  . The Plant Cell, 22(2), 321-334. doi:10.1105/tpc.109.072199Hendrickson, D. G., Hogan, D. J., McCullough, H. L., Myers, J. W., Herschlag, D., Ferrell, J. E., & Brown, P. O. (2009). Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA. PLoS Biology, 7(11), e1000238. doi:10.1371/journal.pbio.1000238Hunter, C., Sun, H., & Poethig, R. S. (2003). The Arabidopsis Heterochronic Gene ZIPPY Is an ARGONAUTE Family Member. Current Biology, 13(19), 1734-1739. doi:10.1016/j.cub.2003.09.004Huntzinger, E., & Izaurralde, E. (2011). Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nature Reviews Genetics, 12(2), 99-110. doi:10.1038/nrg2936Iki, T., Yoshikawa, M., Nishikiori, M., Jaudal, M. C., Matsumoto-Yokoyama, E., Mitsuhara, I., … Ishikawa, M. (2010). In Vitro Assembly of Plant RNA-Induced Silencing Complexes Facilitated by Molecular Chaperone HSP90. Molecular Cell, 39(2), 282-291. doi:10.1016/j.molcel.2010.05.014Jaubert, M., Bhattacharjee, S., Mello, A. F. S., Perry, K. L., & Moffett, P. (2011). ARGONAUTE2 Mediates RNA-Silencing Antiviral Defenses against Potato virus X in Arabidopsis    . Plant Physiology, 156(3), 1556-1564. doi:10.1104/pp.111.178012Ji, L., Liu, X., Yan, J., Wang, W., Yumul, R. E., Kim, Y. J., … Chen, X. (2011). ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis. PLoS Genetics, 7(3), e1001358. doi:10.1371/journal.pgen.1001358Kim, V. N., Han, J., & Siomi, M. C. (2009). Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology, 10(2), 126-139. doi:10.1038/nrm2632Lanet, E., Delannoy, E., Sormani, R., Floris, M., Brodersen, P., Crété, P., … Robaglia, C. (2009). Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs. The Plant Cell, 21(6), 1762-1768. doi:10.1105/tpc.108.063412Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. doi:10.1186/gb-2009-10-3-r25Leung, A. K. L., Young, A. G., Bhutkar, A., Zheng, G. X., Bosson, A. D., Nielsen, C. B., & Sharp, P. A. (2011). Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nature Structural & Molecular Biology, 18(2), 237-244. doi:10.1038/nsmb.1991Llave, C., Xie, Z., Kasschau, K. D., & Carrington, J. C. (2002). Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA. Science, 297(5589), 2053-2056. doi:10.1126/science.1076311Lobbes, D., Rallapalli, G., Schmidt, D. D., Martin, C., & Clarke, J. (2006). SERRATE: a new player on the plant microRNA scene. EMBO reports, 7(10), 1052-1058. doi:10.1038/sj.embor.7400806Mallory, A., & Vaucheret, H. (2010). Form, Function, and Regulation of ARGONAUTE Proteins. The Plant Cell, 22(12), 3879-3889. doi:10.1105/tpc.110.080671Manavella, P. A., Koenig, D., & Weigel, D. (2012). Plant secondary siRNA production determined by microRNA-duplex structure. Proceedings of the National Academy of Sciences, 109(7), 2461-2466. doi:10.1073/pnas.1200169109Matranga, C., Tomari, Y., Shin, C., Bartel, D. P., & Zamore, P. D. (2005). Passenger-Strand Cleavage Facilitates Assembly of siRNA into Ago2-Containing RNAi Enzyme Complexes. Cell, 123(4), 607-620. doi:10.1016/j.cell.2005.08.044Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., … Qi, Y. (2008). Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide. Cell, 133(1), 116-127. doi:10.1016/j.cell.2008.02.034Montgomery, T. A., Howell, M. D., Cuperus, J. T., Li, D., Hansen, J. E., Alexander, A. L., … Carrington, J. C. (2008). Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation. Cell, 133(1), 128-141. doi:10.1016/j.cell.2008.02.033Montgomery, T. A., Yoo, S. J., Fahlgren, N., Gilbert, S. D., Howell, M. D., Sullivan, C. M., … Carrington, J. C. (2008). AGO1-miR173 complex initiates phased siRNA formation in plants. Proceedings of the National Academy of Sciences, 105(51), 20055-20062. doi:10.1073/pnas.0810241105Morel, J.-B., Godon, C., Mourrain, P., Béclin, C., Boutet, S., Feuerbach, F., … Vaucheret, H. (2002). Fertile Hypomorphic ARGONAUTE (ago1) Mutants Impaired in Post-Transcriptional Gene Silencing and Virus Resistance. The Plant Cell, 14(3), 629-639. doi:10.1105/tpc.010358Peragine, A. (2004). SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes & Development, 18(19), 2368-2379. doi:10.1101/gad.1231804Qi, Y., He, X., Wang, X.-J., Kohany, O., Jurka, J., & Hannon, G. J. (2006). Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443(7114), 1008-1012. doi:10.1038/nature05198Rajagopalan, R., Vaucheret, H., Trejo, J., & Bartel, D. P. (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Development, 20(24), 3407-3425. doi:10.1101/gad.1476406Scholthof, H. B., Alvarado, V. Y., Vega-Arreguin, J. C., Ciomperlik, J., Odokonyero, D., Brosseau, C., … Moffett, P. (2011). Identification of an ARGONAUTE for Antiviral RNA Silencing in Nicotiana benthamiana        . Plant Physiology, 156(3), 1548-1555. doi:10.1104/pp.111.178764Song, J.-J., Smith, S. K., Hannon, G. J., & Joshua-Tor, L. (2004). Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity. Science, 305(5689), 1434-1437. doi:10.1126/science.1102514Souret, F. F., Kastenmayer, J. P., & Green, P. J. (2004). AtXRN4 Degrades mRNA in Arabidopsis and Its Substrates Include Selected miRNA Targets. Molecular Cell, 15(2), 173-183. doi:10.1016/j.molcel.2004.06.006Wang, L., Si, Y., Dedow, L. K., Shao, Y., Liu, P., & Brutnell, T. P. (2011). A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq. PLoS ONE, 6(10), e26426. doi:10.1371/journal.pone.0026426Wang, X.-B., Jovel, J., Udomporn, P., Wang, Y., Wu, Q., Li, W.-X., … Ding, S.-W. (2011). The 21-Nucleotide, but Not 22-Nucleotide, Viral Secondary Small Interfering RNAs Direct Potent Antiviral Defense by Two Cooperative Argonautes in Arabidopsis thaliana    . The Plant Cell, 23(4), 1625-1638. doi:10.1105/tpc.110.082305Wang, Y., Juranek, S., Li, H., Sheng, G., Wardle, G. S., Tuschl, T., & Patel, D. J. (2009). Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature, 461(7265), 754-761. doi:10.1038/nature08434Wu, L., & Belasco, J. G. (2008). Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs. Molecular Cell, 29(1), 1-7. doi:10.1016/j.molcel.2007.12.010Xie, Z., Allen, E., Wilken, A., & Carrington, J. C. (2005). DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 102(36), 12984-12989. doi:10.1073/pnas.0506426102Yang, L., Wu, G., & Poethig, R. S. (2011). Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proceedings of the National Academy of Sciences, 109(1), 315-320. doi:10.1073/pnas.1114673109Yoshikawa, M. (2005). A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Development, 19(18), 2164-2175. doi:10.1101/gad.1352605Zhang, X., Zhao, H., Gao, S., Wang, W.-C., Katiyar-Agarwal, S., Huang, H.-D., … Jin, H. (2011). Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393∗-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12. Molecular Cell, 42(3), 356-366. doi:10.1016/j.molcel.2011.04.010Zhu, H., Hu, F., Wang, R., Zhou, X., Sze, S.-H., Liou, L. W., … Zhang, X. (2011). Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development. Cell, 145(2), 242-256. doi:10.1016/j.cell.2011.03.024Zisoulis, D. G., Lovci, M. T., Wilbert, M. L., Hutt, K. R., Liang, T. Y., Pasquinelli, A. E., & Yeo, G. W. (2010). Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nature Structural & Molecular Biology, 17(2), 173-179. doi:10.1038/nsmb.174

Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer

The underpinnings of STAT3 hyperphosphorylation resulting in enhanced signaling and cancer progression are incompletely understood. Loss-of-function mutations of enzymes that dephosphorylate STAT3, such as receptor protein tyrosine phosphatases, which are encoded by the PTPR gene family, represent a plausible mechanism of STAT3 hyperactivation. We analyzed whole exome sequencing (n = 374) and reverse-phase protein array data (n = 212) from head and neck squamous cell carcinomas (HNSCCs). PTPR mutations are most common and are associated with significantly increased phospho-STAT3 expression in HNSCC tumors. Expression of receptor-like protein tyrosine phosphatase T (PTPRT) mutant proteins induces STAT3 phosphorylation and cell survival, consistent with a “driver” phenotype. Computational modeling reveals functional consequences of PTPRT mutations on phospho-tyrosine–substrate interactions. A high mutation rate (30%) of PTPRs was found in HNSCC and 14 other solid tumors, suggesting that PTPR alterations, in particular PTPRT mutations, may define a subset of patients where STAT3 pathway inhibitors hold particular promise as effective therapeutic agents.Fil: Lui, Vivian Wai Yan. University of Pittsburgh; Estados UnidosFil: Peyser, Noah D.. University of Pittsburgh; Estados UnidosFil: Ng, Patrick Kwok-Shing. University Of Texas Md Anderson Cancer Center;Fil: Hritz, Jozef. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados Unidos. Masaryk University; República ChecaFil: Zeng, Yan. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Lu, Yiling. University Of Texas Md Anderson Cancer Center;Fil: Li, Hua. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Wang, Lin. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Gilbert, Breean R.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: General, Ignacio. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Bahar, Ivet. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Ju, Zhenlin. University Of Texas Md Anderson Cancer Center;Fil: Wang, Zhenghe. Case Western Reserve University; Estados UnidosFil: Pendleton, Kelsey P.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Xiao, Xiao. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Du, Yu. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Vries, John K.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados UnidosFil: Hammerman, Peter S.. Harvard Medical School; Estados UnidosFil: Garraway, Levi A.. Harvard Medical School; Estados UnidosFil: Mills, Gordon B.. University Of Texas Md Anderson Cancer Center;Fil: Johnson, Daniel E.. University of Pittsburgh at Johnstown; Estados Unidos. University of Pittsburgh; Estados UnidosFil: Grandis, Jennifer R.. University of Pittsburgh; Estados Unidos. University of Pittsburgh at Johnstown; Estados Unido