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https://www.readbyqxmd.com/read/28329682/the-swi-snf-protein-pbrm1-restrains-vhl-loss-driven-clear-cell-renal-cell-carcinoma
#1
Amrita M Nargund, Can G Pham, Yiyu Dong, Patricia I Wang, Hatice U Osmangeyoglu, Yuchen Xie, Omer Aras, Song Han, Toshinao Oyama, Shugaku Takeda, Chelsea E Ray, Zhenghong Dong, Mathieu Berge, A Ari Hakimi, Sebastien Monette, Carl L Lekaye, Jason A Koutcher, Christina S Leslie, Chad J Creighton, Nils Weinhold, William Lee, Satish K Tickoo, Zhong Wang, Emily H Cheng, James J Hsieh
PBRM1 is the second most commonly mutated gene after VHL in clear cell renal cell carcinoma (ccRCC). However, the biological consequences of PBRM1 mutations for kidney tumorigenesis are unknown. Here, we find that kidney-specific deletion of Vhl and Pbrm1, but not either gene alone, results in bilateral, multifocal, transplantable clear cell kidney cancers. PBRM1 loss amplified the transcriptional outputs of HIF1 and STAT3 incurred by Vhl deficiency. Analysis of mouse and human ccRCC revealed convergence on mTOR activation, representing the third driver event after genetic inactivation of VHL and PBRM1...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28322723/nucleosomes-influence-multiple-steps-during-replication-initiation
#2
Ishara F Azmi, Shinya Watanabe, Michael F Maloney, Sukhyun Kang, Jason A Belsky, David M MacAlpine, Craig L Peterson, Stephen P Bell
Eukaryotic replication origin licensing, activation and timing are influenced by chromatin but a mechanistic understanding is lacking. Using reconstituted nucleosomal DNA replication assays, we assessed the impact of nucleosomes on replication initiation. To generate distinct nucleosomal landscapes, different chromatin-remodeling enzymes (CREs) were used to remodel nucleosomes on origin-DNA templates. Nucleosomal organization influenced two steps of replication initiation: origin licensing and helicase activation...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28303890/baf60b-mediated-atm-p53-activation-blocks-cell-identity-conversion-by-sensing-chromatin-opening
#3
Shuyi Ji, Linying Zhu, Yimeng Gao, Xiaoran Zhang, Yupeng Yan, Jin Cen, Rongxia Li, Rong Zeng, Lujian Liao, Chunhui Hou, Yawei Gao, Shaorong Gao, Gang Wei, Lijian Hui
Lineage conversion by expression of lineage-specific transcription factors is a process of epigenetic remodeling that has low efficiency. The mechanism by which a cell resists lineage conversion is largely unknown. Using hepatic-specific transcription factors Foxa3, Hnf1α and Gata4 (3TF) to induce hepatic conversion in mouse fibroblasts, we showed that 3TF induced strong activation of the ATM-p53 pathway, which led to proliferation arrest and cell death, and it further prevented hepatic conversion. Notably, ATM activation, independent of DNA damage, responded to chromatin opening during hepatic conversion...
March 17, 2017: Cell Research
https://www.readbyqxmd.com/read/28300755/vitamin-d-impacts-the-expression-of-runx2-target-genes-and-modulates-inflammation-oxidative-stress-and-membrane-vesicle-biogenesis-gene-networks-in-143b-osteosarcoma-cells
#4
Rama Garimella, Priyanka Tadikonda, Ossama Tawfik, Sumedha Gunewardena, Peter Rowe, Peter Van Veldhuizen
Osteosarcoma (OS) is an aggressive malignancy of bone affecting children, adolescents and young adults. Understanding vitamin D metabolism and vitamin D regulated genes in OS is an important aspect of vitamin D/cancer paradigm, and in evaluating vitamin D as adjuvant therapy for human OS. Vitamin D treatment of 143B OS cells induced significant and novel changes in the expression of genes that regulate: (a) inflammation and immunity; (b) formation of reactive oxygen species, metabolism of cyclic nucleotides, sterols, vitamins and mineral (calcium), quantity of gap junctions and skeletogenesis; (c) bone mineral density; and (d) cell viability of skeletal cells, aggregation of bone cancer cells and exocytosis of secretory vesicles...
March 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28297605/identifying-cell-cycle-modulators-that-selectively-target-arid1a-deficiency-using-high-throughput-image-based-screening
#5
Lihong Zhang, Jianfeng Shen, Yuping Yin, Yang Peng, Lulu Wang, Hui-Ju Hsieh, Qian Shen, Powel H Brown, Kaixiong Tao, Ivan P Uray, Guang Peng
ARID1A, a component of the chromatin remodeling complex SWI/SNF, is an evolutionarily conserved complex that uses the energy of adenosine triphosphate hydrolysis to remodel chromatin structure and functions as a master regulator of gene transcription. Recent genomic studies have revealed that ARID1A is one of the most frequently mutated genes in human cancers. However, therapeutic approaches that selectively target ARID1A-mutant tumors are not yet clinically available. Our previous study showed that ARID1A facilitates chromatin response and cell cycle checkpoint activation after DNA damage...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28292935/selective-killing-of-smarca2-and-smarca4-deficient-small-cell-carcinoma-of-the-ovary-hypercalcemic-type-cells-by-inhibition-of-ezh2-in-vitro-and-in-vivo-preclinical-models
#6
Elayne Chan-Penebre, Kelli Armstrong, Allison Drew, Alexandra R Grassian, Igor Feldman, Sarah K Knutson, Kristy Kuplast-Barr, Maria Roche, John Campbell, Peter Ho, Robert A Copeland, Richard Chesworth, Jesse J Smith, Heike Keilhack, Scott A Ribich
The SWI/SNF complex is a major regulator of gene expression and is increasingly thought to play an important role in human cancer, as evidenced by the high frequency of subunit mutations across virtually all cancer types. We previously reported that in preclinical models, malignant rhabdoid tumors, which are deficient in the SWI/SNF core component INI1 (SMARCB1), are selectively killed by inhibitors of the H3K27 histone methyltransferase EZH2. Given the demonstrated antagonistic activities of the SWI/SNF complex and the EZH2-containing PRC2 complex, we investigated whether additional cancers with SWI/SNF mutations are sensitive to selective EZH2 inhibition...
March 14, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28291122/smarcb1-ini-1-deficient-sinonasal-carcinoma-a-series-of-39-cases-expanding-the-morphologic-and-clinicopathologic-spectrum-of-a-recently-described-entity
#7
Abbas Agaimy, Arndt Hartmann, Cristina R Antonescu, Simion I Chiosea, Samir K El-Mofty, Helene Geddert, Heinrich Iro, James S Lewis, Bruno Märkl, Stacey E Mills, Marc-Oliver Riener, Thomas Robertson, Ann Sandison, Sabine Semrau, Roderick H W Simpson, Edward Stelow, William H Westra, Justin A Bishop
To more fully characterize the clinical and pathologic spectrum of a recently described tumor entity of the sinonasal tract characterized by loss of nuclear expression of SMARCB1 (INI1), we analyzed 39 SMARCB1-deficient sinonasal carcinomas collected from multiple medical centers. The tumors affected 23 males and 16 females with an age range of 19 to 89 years (median, 52). All patients presented with locally advanced disease (T3, n=5; T4, n=27) involving the sinuses (mainly ethmoid) with variable involvement of the nasal cavity...
April 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28289221/gentamicin-b1-is-a-minor-gentamicin-component-with-major-nonsense-mutation-suppression-activity
#8
Alireza Baradaran-Heravi, Jürgen Niesser, Aruna D Balgi, Kunho Choi, Carla Zimmerman, Andrew P South, Hilary J Anderson, Natalie C Strynadka, Marcel B Bally, Michel Roberge
Nonsense mutations underlie about 10% of rare genetic disease cases. They introduce a premature termination codon (PTC) and prevent the formation of full-length protein. Pharmaceutical gentamicin, a mixture of several related aminoglycosides, is a frequently used antibiotic in humans that can induce PTC readthrough and suppress nonsense mutations at high concentrations. However, testing of gentamicin in clinical trials has shown that safe doses of this drug produce weak and variable readthrough activity that is insufficient for use as therapy...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28283928/estimating-the-efficiency-of-phosphopeptide-identification-by-tandem-mass-spectrometry
#9
Chuan-Chih Hsu, Liang Xue, Justine V Arrington, Pengcheng Wang, Juan Sebastian Paez Paez, Yuan Zhou, Jian-Kang Zhu, W Andy Tao
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events...
March 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28279729/access-to-post-hospitalization-acute-care-facilities-is-associated-with-payer-status-for-open-abdominal-aortic-repair-and-open-lower-extremity-revascularization-in-the-vascular-quality-initiative
#10
Jesus G Ulloa, Karen Woo, Chi-Hong Tseng, Melinda Maggard-Gibbons, David Rigberg
OBJECTIVE: Uninsured patients may not have access to post-acute care facilities that play an important role in clinical recovery and functional outcomes after vascular surgery. We sought to determine whether discharge disposition is associated with insurance status. METHODS: We retrospectively reviewed data from the Vascular Quality Initiative(®) for patients who underwent open abdominal aortic repair (OAR), infra-inguinal bypass (IB) or supra-inguinal bypass (SB) between January 2012 and July 2015...
March 6, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28267694/the-association-between-medicare-eligibility-and-gains-in-access-to-rehabilitative-care-a-national-regression-discontinuity-assessment-of-patients-ages-64-versus-65-years
#11
Cheryl K Zogg, John W Scott, David Metcalfe, Anupamaa J Seshadri, Thomas C Tsai, W Austin Davis, John A Rose, Olubode A Olufajo, Syed Nabeel Zafar, Ali Salim, Adil H Haider
OBJECTIVES: The aims of this study were to assess for changes in uninsured rates among trauma patients at age 64 versus 65 years and whether there are associated changes in post-discharge rehabilitation; determine whether changes are driven by rehabilitation provided at home, skilled nursing facilities (SNFs), or acute inpatient facilities; and determine whether changes vary among stratified subgroups of trauma-related "best-practice" factors. SUMMARY BACKGROUND DATA: Rehabilitation is an important component of high-quality trauma systems with access heavily influenced by insurance status...
April 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28262751/the-swi-snf-chromatin-remodelling-complex-is-required-for-maintenance-of-lineage-specific-enhancers
#12
Burak H Alver, Kimberly H Kim, Ping Lu, Xiaofeng Wang, Haley E Manchester, Weishan Wang, Jeffrey R Haswell, Peter J Park, Charles W M Roberts
Genes encoding subunits of SWI/SNF (BAF) chromatin remodelling complexes are collectively altered in over 20% of human malignancies, but the mechanisms by which these complexes alter chromatin to modulate transcription and cell fate are poorly understood. Utilizing mouse embryonic fibroblast and cancer cell line models, here we show via ChIP-seq and biochemical assays that SWI/SNF complexes are preferentially targeted to distal lineage specific enhancers and interact with p300 to modulate histone H3 lysine 27 acetylation...
March 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28259401/replacing-alfalfa-silage-with-tannin-containing-birdsfoot-trefoil-silage-in-total-mixed-rations-for-lactating-dairy-cows
#13
G A Broderick, J H Grabber, R E Muck, U C Hymes-Fecht
Two lactation trials were conducted comparing the feeding value of silages made from birdsfoot trefoil (BFT, Lotus corniculatus L.) that had been selected for low (BFTL), medium (BFTM), and high (BFTH) levels of condensed tannins (CT) to an alfalfa silage (AS) when fed as the principal forage in total mixed rations. Diets also included corn silage, high-moisture shelled corn, soybean meal, soy hulls, and supplemental fat. In trial 1, 32 lactating Holstein cows were blocked by days in milk, assigned to treatment sequences in 8 balanced 4 × 4 Latin squares, and fed 50% dietary dry matter from AS or 1 of 3 BFT silages containing 0...
March 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28256572/clinicopathological-and-molecular-characterization-of-smarca4-deficient-thoracic-sarcomas-with-comparison-to-potentially-related-entities
#14
Akihiko Yoshida, Eisuke Kobayashi, Takashi Kubo, Makoto Kodaira, Toru Motoi, Noriko Motoi, Kan Yonemori, Yuichiro Ohe, Shun-Ichi Watanabe, Akira Kawai, Takashi Kohno, Hiroshi Kishimoto, Hitoshi Ichikawa, Nobuyoshi Hiraoka
A growing number of studies suggest critical tumor suppressor roles of the SWI/SNF chromatin remodeling complex in a variety of human cancers. The recent discovery of SMARCA4-deficient thoracic sarcomas has added to the list of tumor groups with the SMARCA4 inactivating mutation. To better characterize these tumors and establish their nosological status, we undertook a clinicopathological and molecular analysis of 12 SMARCA4-deficient thoracic sarcomas and compared them with three potentially related disease entities...
March 3, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28253716/arid1a-gene-knockdown-promotes-neuroblastoma-migration-and-invasion
#15
C Li, Z Xu, Z Zhao, Q An, L Wang, Y Yu, D Piao
Neuroblastoma is the most common extracranial solid tumor in childhood which often acquires drug resistance and becomes aggressive phenotypes. The high-risk patients suffer from high mortality due to the limitation of the treatment strategies. ARID1A (AT-rich interactive domain-containing protein 1A), a subunit of SWI/SNF complexes, is considered as a tumor suppressor in many cancers. The aim of the present study was to investigate the effect of ARID1A on migration and invasion in neuroblastoma cells. The shRNA targeting ARID1A was designed and delivered into SK-N-SH cells to knock down ARID1A expression...
March 3, 2017: Neoplasma
https://www.readbyqxmd.com/read/28253434/a-general-non-radioactive-atpase-assay-for-chromatin-remodeling-complexes
#16
Benjamin Z Stanton, Courtney Hodges, Gerald R Crabtree, Keji Zhao
Chromatin remodeling complexes couple the energy released from ATP hydrolysis to facilitate transcription, recombination, and repair mechanisms essential for a wide variety of biologic responses. While recombinant expression of the regulatory subunits of these enzymes is possible, measuring catalytic (ATPase) activity of the intact complexes recovered from normal or mutant cells is critical for understanding their mechanisms. SWI/SNF-like remodeling complexes can be megadaltons in size and include many regulatory subunits, making reconstitution of purified subunits challenging for recapitulating in vivo function...
March 2, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28250416/top2-synergizes-with-baf-chromatin-remodeling-for-both-resolution-and-formation-of-facultative-heterochromatin
#17
Erik L Miller, Diana C Hargreaves, Cigall Kadoch, Chiung-Ying Chang, Joseph P Calarco, Courtney Hodges, Jason D Buenrostro, Kairong Cui, William J Greenleaf, Keji Zhao, Gerald R Crabtree
The resolution and formation of facultative heterochromatin are essential for development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood owing to the difficulty of studying heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription...
February 27, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28249160/loss-of-snf5-induces-formation-of-an-aberrant-swi-snf-complex
#18
Payel Sen, Jie Luo, Arjan Hada, Solomon G Hailu, Mekonnen Lemma Dechassa, Jim Persinger, Sandipan Brahma, Somnath Paul, Jeff Ranish, Blaine Bartholomew
The SWI/SNF chromatin remodeling complex is highly conserved from yeast to human, and aberrant SWI/SNF complexes contribute to human disease. The Snf5/SMARCB1/INI1 subunit of SWI/SNF is a tumor suppressor frequently lost in pediatric rhabdoid cancers. We examined the effects of Snf5 loss on the composition, nucleosome binding, recruitment, and remodeling activities of yeast SWI/SNF. The Snf5 subunit is shown by crosslinking-mass spectrometry (CX-MS) and subunit deletion analysis to interact with the ATPase domain of Snf2 and to form a submodule consisting of Snf5, Swp82, and Taf14...
February 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/28249159/composition-and-function-of-mutant-swi-snf-complexes
#19
Arnob Dutta, Mihaela Sardiu, Madelaine Gogol, Joshua Gilmore, Daoyong Zhang, Laurence Florens, Susan M Abmayr, Michael P Washburn, Jerry L Workman
The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex...
February 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/28249153/deciphering-subunit-specific-functions-within-swi-snf-complexes
#20
Amanda L Hughes, Tom Owen-Hughes
In this issue of Cell Reports, Sen et al. and Dutta et al. reveal the modularity of the yeast SWI/SNF chromatin remodeling complex and show that loss of different subunits leads to distinct consequences for gene expression.
February 28, 2017: Cell Reports
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