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bradley bernstein

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https://www.readbyqxmd.com/read/29251726/orthologous-crispr-cas9-enzymes-for-combinatorial-genetic-screens
#1
Fadi J Najm, Christine Strand, Katherine F Donovan, Mudra Hegde, Kendall R Sanson, Emma W Vaimberg, Meagan E Sullender, Ella Hartenian, Zohra Kalani, Nicolo Fusi, Jennifer Listgarten, Scott T Younger, Bradley E Bernstein, David E Root, John G Doench
Combinatorial genetic screening using CRISPR-Cas9 is a useful approach to uncover redundant genes and to explore complex gene networks. However, current methods suffer from interference between the single-guide RNAs (sgRNAs) and from limited gene targeting activity. To increase the efficiency of combinatorial screening, we employ orthogonal Cas9 enzymes from Staphylococcus aureus and Streptococcus pyogenes. We used machine learning to establish S. aureus Cas9 sgRNA design rules and paired S. aureus Cas9 with S...
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29249691/dual-targeting-of-oncogenic-activation-and-inflammatory-signaling-increases-therapeutic-efficacy-in-myeloproliferative-neoplasms
#2
Maria Kleppe, Richard Koche, Lihua Zou, Peter van Galen, Corinne E Hill, Lauren Dong, Sofie De Groote, Efthymia Papalexi, Amritha V Hanasoge Somasundara, Keith Cordner, Matthew Keller, Noushin Farnoud, Juan Medina, Erin McGovern, Jaime Reyes, Justin Roberts, Matthew Witkins, Franck Rapaport, Julie Teruya-Feldstein, Jun Qi, Raajit Rampal, Bradley E Bernstein, James E Bradner, Ross L Levine
Genetic and functional studies underscore the central role of JAK/STAT signaling in myeloproliferative neoplasms (MPNs). However, the mechanisms that mediate transformation in MPNs are not fully delineated, and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify nuclear factor κB (NF-κB) signaling as a key pathway activated in malignant and non-malignant cells in MPN...
December 1, 2017: Cancer Cell
https://www.readbyqxmd.com/read/29247777/determining-risk-of-barrett-s-esophagus-and-esophageal-adenocarcinoma-based-on-epidemiologic-factors-and-genetic-variants
#3
Jing Dong, Matthew F Buas, Puya Gharahkhani, Bradley J Kendall, Lynn Onstad, Shanshan Zhao, Lesley A Anderson, Anna H Wu, Weimin Ye, Nigel C Bird, Leslie Bernstein, Wong-Ho Chow, Marilie D Gammon, Geoffrey Liu, Carlos Caldas, Paul D Pharoah, Harvey A Risch, Prasad G Iyer, Brian J Reid, Laura J Hardie, Jesper Lagergren, Nicholas J Shaheen, Douglas A Corley, Rebecca C Fitzgerald, David C Whiteman, Thomas L Vaughan, Aaron P Thrift
BACKGROUND & AIMS: We developed comprehensive models to determine risk of Barrett's esophagus (BE) or esophageal adenocarcinoma (EAC) based on genetic and non-genetic factors. METHODS: We used pooled data from 3288 patients with BE, 2511 patients with EAC, and 2177 individuals without either (controls) from participants in the international Barrett's and EAC consortium as well as the United Kingdom's BE gene study and stomach and esophageal cancer study. We collected data on 23 genetic variants associated with risk for BE or EAC, and constructed a polygenic risk score (PRS) for cases and controls by summing the risk allele counts for the variants weighted by their natural log-transformed effect estimates (odds ratios) extracted from genome-wide association studies...
December 13, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29198524/single-cell-transcriptomic-analysis-of-primary-and-metastatic-tumor-ecosystems-in-head-and-neck-cancer
#4
Sidharth V Puram, Itay Tirosh, Anuraag S Parikh, Anoop P Patel, Keren Yizhak, Shawn Gillespie, Christopher Rodman, Christina L Luo, Edmund A Mroz, Kevin S Emerick, Daniel G Deschler, Mark A Varvares, Ravi Mylvaganam, Orit Rozenblatt-Rosen, James W Rocco, William C Faquin, Derrick T Lin, Aviv Regev, Bradley E Bernstein
The diverse malignant, stromal, and immune cells in tumors affect growth, metastasis, and response to therapy. We profiled transcriptomes of ∼6,000 single cells from 18 head and neck squamous cell carcinoma (HNSCC) patients, including five matched pairs of primary tumors and lymph node metastases. Stromal and immune cells had consistent expression programs across patients. Conversely, malignant cells varied within and between tumors in their expression of signatures related to cell cycle, stress, hypoxia, epithelial differentiation, and partial epithelial-to-mesenchymal transition (p-EMT)...
November 30, 2017: Cell
https://www.readbyqxmd.com/read/29051323/epithelial-to-mesenchymal-transition-antagonizes-response-to-targeted-therapies-in-lung-cancer-by-suppressing-bim
#5
Kyung-A Song, Matthew J Niederst, Timothy L Lochmann, Aaron N Hata, Hidenori Kitai, Jungoh Ham, Konstantinos V Floros, Mark A Hicks, Haichuan Hu, Hillary E Mulvey, Yotam Drier, Daniel A R Heisey, Mark T Hughes, Neha U Patel, Elizabeth Lockerman, Angel R Garcia, Shawn Gillepsie, Hannah L Archibald, Maria Gomez-Caraballo, Tara J Nulton, Brad Windle, Zofia Piotrowska, Sinem E Sahingur, Shirley M Taylor, Mikhail G Dozmorov, Lecia V Sequist, Bradley E Bernstein, Hiromichi Ebi, Jeffrey A Engelman, Anthony C Faber
PURPOSE: Epithelial-to-mesenchymal transition (EMT) confers resistance to a number of targeted therapies and chemotherapies. However, it has been unclear why EMT promotes resistance, thereby impairing progress to overcome it. EXPERIMENTAL DESIGN: We have developed several models of EMT-mediated resistance to EGFR inhibitors (EGFRi) in EGFR mutant lung cancers to evaluate a novel mechanism of EMT-mediated resistance. Results: We observed that mesenchymal EGFR mutant lung cancers are resistant to EGFRi-induced apoptosis via insufficient expression of BIM, preventing cell death despite potent suppression of oncogenic signaling following EGFRi treatment...
October 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29045844/a-b-cell-regulome-links-notch-to-downstream-oncogenic-pathways-in-small-b-cell-lymphomas
#6
Russell J H Ryan, Jelena Petrovic, Dylan M Rausch, Yeqiao Zhou, Caleb A Lareau, Michael J Kluk, Amanda L Christie, Winston Y Lee, Daniel R Tarjan, Bingqian Guo, Laura K H Donohue, Shawn M Gillespie, Valentina Nardi, Ephraim P Hochberg, Stephen C Blacklow, David M Weinstock, Robert B Faryabi, Bradley E Bernstein, Jon C Aster, Warren S Pear
Gain-of-function Notch mutations are recurrent in mature small B cell lymphomas such as mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL), but the Notch target genes that contribute to B cell oncogenesis are largely unknown. We performed integrative analysis of Notch-regulated transcripts, genomic binding of Notch transcription complexes, and genome conformation data to identify direct Notch target genes in MCL cell lines. This B cell Notch regulome is largely controlled through Notch-bound distal enhancers and includes genes involved in B cell receptor and cytokine signaling and the oncogene MYC, which sustains proliferation of Notch-dependent MCL cell lines via a Notch-regulated lineage-restricted enhancer complex...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/28985562/cohesin-loss-eliminates-all-loop-domains
#7
Suhas S P Rao, Su-Chen Huang, Brian Glenn St Hilaire, Jesse M Engreitz, Elizabeth M Perez, Kyong-Rim Kieffer-Kwon, Adrian L Sanborn, Sarah E Johnstone, Gavin D Bascom, Ivan D Bochkov, Xingfan Huang, Muhammad S Shamim, Jaeweon Shin, Douglass Turner, Ziyi Ye, Arina D Omer, James T Robinson, Tamar Schlick, Bradley E Bernstein, Rafael Casellas, Eric S Lander, Erez Lieberman Aiden
The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes...
October 5, 2017: Cell
https://www.readbyqxmd.com/read/28894388/bone-anchored-annular-closure-following-lumbar-discectomy-reduces-risk-of-complications-and-reoperations-within-90-days-of-discharge
#8
Peter Douglas Klassen, Derek Thomas Bernstein, Hans-Peter Köhler, Mark P Arts, Bradley Weiner, Larry E Miller, Claudius Thomé
PURPOSE: The purpose of this study was to evaluate perioperative complications of lumbar discectomy with or without bone-anchored annular closure device (ACD) implant in patients at high risk of recurrent disc herniation. METHODS: This was a post hoc analysis of a randomized controlled trial that compared outcomes of lumbar discectomy with or without additional placement of an ACD. Patients presented with imaging evidence of lumbar disc herniation and radicular pain that was unresponsive to conservative care...
2017: Journal of Pain Research
https://www.readbyqxmd.com/read/28891793/regulation-of-the-glucocorticoid-receptor-via-a-bet-dependent-enhancer-drives-antiandrogen-resistance-in-prostate-cancer
#9
Neel Shah, Ping Wang, John Wongvipat, Wouter R Karthaus, Wassim Abida, Joshua Armenia, Shira Rockowitz, Yotam Drier, Bradley E Bernstein, Henry W Long, Matthew L Freedman, Vivek K Arora, Deyou Zheng, Charles L Sawyers
In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of androgen receptor (AR) blockade by the glucocorticoid receptor (GR). In contrast to fixed genomic alterations, here we show that GR-mediated antiandrogen resistance is adaptive and reversible due to regulation of GR expression by a tissue-specific enhancer. GR expression is silenced in prostate cancer by a combination of AR binding and EZH2-mediated repression at the GR locus, but is restored in advanced prostate cancers upon reversion of both repressive signals...
September 11, 2017: ELife
https://www.readbyqxmd.com/read/28818518/seladelpar-mbx-8025-a-selective-ppar-%C3%AE-agonist-in-patients-with-primary-biliary-cholangitis-with-an-inadequate-response-to-ursodeoxycholic-acid-a-double-blind-randomised-placebo-controlled-phase-2-proof-of-concept-study
#10
David Jones, Pol F Boudes, Mark G Swain, Christopher L Bowlus, Michael R Galambos, Bruce R Bacon, Yvonne Doerffel, Norman Gitlin, Stuart C Gordon, Joseph A Odin, David Sheridan, Markus-Alexander Wörns, Virginia Clark, Linsey Corless, Heinz Hartmann, Mark E Jonas, Andreas E Kremer, George F Mells, Peter Buggisch, Bradley L Freilich, Cynthia Levy, John M Vierling, David E Bernstein, Marek Hartleb, Ewa Janczewska, Fedja Rochling, Hemant Shah, Mitchell L Shiffman, John H Smith, Yun-Jung Choi, Alexandra Steinberg, Monika Varga, Harinder Chera, Robert Martin, Charles A McWherter, Gideon M Hirschfield
BACKGROUND: Many patients with primary biliary cholangitis have an inadequate response to first-line therapy with ursodeoxycholic acid. Seladelpar is a potent, selective agonist for the peroxisome proliferator-activated receptor-delta (PPAR-δ), which is implicated in bile acid homoeostasis. This first-in-class study evaluated the anti-cholestatic effects and safety of seladelpar in patients with an inadequate response to ursodeoxycholic acid. METHODS: The study was a 12-week, double-blind, placebo-controlled, phase 2 trial of patients with alkaline phosphatase of at least 1·67 times the upper limit of normal (ULN) despite treatment with ursodeoxycholic acid...
October 2017: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28753427/a-genetic-variant-associated-with-five-vascular-diseases-is-a-distal-regulator-of-endothelin-1-gene-expression
#11
Rajat M Gupta, Joseph Hadaya, Aditi Trehan, Seyedeh M Zekavat, Carolina Roselli, Derek Klarin, Connor A Emdin, Catharina R E Hilvering, Valerio Bianchi, Christian Mueller, Amit V Khera, Russell J H Ryan, Jesse M Engreitz, Robbyn Issner, Noam Shoresh, Charles B Epstein, Wouter de Laat, Jonathan D Brown, Renate B Schnabel, Bradley E Bernstein, Sekar Kathiresan
Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension. Through genetic fine mapping, we prioritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal variant. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature...
July 27, 2017: Cell
https://www.readbyqxmd.com/read/28729483/epigenetic-plasticity-and-the-hallmarks-of-cancer
#12
REVIEW
William A Flavahan, Elizabeth Gaskell, Bradley E Bernstein
Chromatin and associated epigenetic mechanisms stabilize gene expression and cellular states while also facilitating appropriate responses to developmental or environmental cues. Genetic, environmental, or metabolic insults can induce overly restrictive or overly permissive epigenetic landscapes that contribute to pathogenesis of cancer and other diseases. Restrictive chromatin states may prevent appropriate induction of tumor suppressor programs or block differentiation. By contrast, permissive or "plastic" states may allow stochastic oncogene activation or nonphysiologic cell fate transitions...
July 21, 2017: Science
https://www.readbyqxmd.com/read/28678782/transcription-elongation-factors-represent-in-vivo-cancer-dependencies-in-glioblastoma
#13
Tyler E Miller, Brian B Liau, Lisa C Wallace, Andrew R Morton, Qi Xie, Deobrat Dixit, Daniel C Factor, Leo J Y Kim, James J Morrow, Qiulian Wu, Stephen C Mack, Christopher G Hubert, Shawn M Gillespie, William A Flavahan, Thomas Hoffmann, Rohit Thummalapalli, Michael T Hemann, Patrick J Paddison, Craig M Horbinski, Johannes Zuber, Peter C Scacheri, Bradley E Bernstein, Paul J Tesar, Jeremy N Rich
Glioblastoma is a universally lethal cancer with a median survival time of approximately 15 months. Despite substantial efforts to define druggable targets, there are no therapeutic options that notably extend the lifespan of patients with glioblastoma. While previous work has largely focused on in vitro cellular models, here we demonstrate a more physiologically relevant approach to target discovery in glioblastoma. We adapted pooled RNA interference (RNAi) screening technology for use in orthotopic patient-derived xenograft models, creating a high-throughput negative-selection screening platform in a functional in vivo tumour microenvironment...
July 20, 2017: Nature
https://www.readbyqxmd.com/read/28360267/decoupling-genetics-lineages-and-microenvironment-in-idh-mutant-gliomas-by-single-cell-rna-seq
#14
Andrew S Venteicher, Itay Tirosh, Christine Hebert, Keren Yizhak, Cyril Neftel, Mariella G Filbin, Volker Hovestadt, Leah E Escalante, McKenzie L Shaw, Christopher Rodman, Shawn M Gillespie, Danielle Dionne, Christina C Luo, Hiranmayi Ravichandran, Ravindra Mylvaganam, Christopher Mount, Maristela L Onozato, Brian V Nahed, Hiroaki Wakimoto, William T Curry, A John Iafrate, Miguel N Rivera, Matthew P Frosch, Todd R Golub, Priscilla K Brastianos, Gad Getz, Anoop P Patel, Michelle Monje, Daniel P Cahill, Orit Rozenblatt-Rosen, David N Louis, Bradley E Bernstein, Aviv Regev, Mario L Suvà
Tumor subclasses differ according to the genotypes and phenotypes of malignant cells as well as the composition of the tumor microenvironment (TME). We dissected these influences in isocitrate dehydrogenase (IDH)-mutant gliomas by combining 14,226 single-cell RNA sequencing (RNA-seq) profiles from 16 patient samples with bulk RNA-seq profiles from 165 patient samples. Differences in bulk profiles between IDH-mutant astrocytoma and oligodendroglioma can be primarily explained by distinct TME and signature genetic events, whereas both tumor types share similar developmental hierarchies and lineages of glial differentiation...
March 31, 2017: Science
https://www.readbyqxmd.com/read/28175463/142%C3%A2-genetic-and-nongenetic-determinants-of-cellular-architecture-in-idh1-mutant-oligodendrogliomas-and-astrocytomas-using-single-cell-transcriptome-analysis
#15
Andrew Sean Venteicher, Itay Tirosh, Christine Hebert, Leah Escalante, Robert L Martuza, Brian V Nahed, William T Curry, Daniel P Cahill, Bradley Bernstein, David N Louis, Aviv Regev, Mario Suva
No abstract text is available yet for this article.
August 1, 2016: Neurosurgery
https://www.readbyqxmd.com/read/28137873/systematic-dissection-of-genomic-features-determining-transcription-factor-binding-and-enhancer-function
#16
Sharon R Grossman, Xiaolan Zhang, Li Wang, Jesse Engreitz, Alexandre Melnikov, Peter Rogov, Ryan Tewhey, Alina Isakova, Bart Deplancke, Bradley E Bernstein, Tarjei S Mikkelsen, Eric S Lander
Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095557/the-photodynamic-therapy-experience-of-a-high-volume-laser-and-dermatologic-surgery-center
#17
David E Orbuch, Lauren Penn, Bradley S Bloom, Jeremy A Brauer, Daniel B Shin, Joshua Greenbaum, Leonard J Bernstein, Elliot T Weiss, Robert T Anolik, Roy G Geronemus
BACKGROUND: Photodynamic therapy (PDT) is an FDA approved treatment for actinic keratoses (AK's) although multiple off-label indi- cations are reported. Despite frequent use for AK's, no clear consensus exists regarding protocols for overall treatment parameters. METHODS: Retrospective chart review of 1,491 subjects who underwent PDT between 2007 and 2011 at a high volume laser surgery center. Demographic information, clinical history, treatment data, and subsequent diagnosis of skin cancers were recorded...
November 1, 2016: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/27989769/adaptive-chromatin-remodeling-drives-glioblastoma-stem-cell-plasticity-and-drug-tolerance
#18
Brian B Liau, Cem Sievers, Laura K Donohue, Shawn M Gillespie, William A Flavahan, Tyler E Miller, Andrew S Venteicher, Christine H Hebert, Christopher D Carey, Scott J Rodig, Sarah J Shareef, Fadi J Najm, Peter van Galen, Hiroaki Wakimoto, Daniel P Cahill, Jeremy N Rich, Jon C Aster, Mario L Suvà, Anoop P Patel, Bradley E Bernstein
Glioblastoma, the most common and aggressive malignant brain tumor, is propagated by stem-like cancer cells refractory to existing therapies. Understanding the molecular mechanisms that control glioblastoma stem cell (GSC) proliferation and drug resistance may reveal opportunities for therapeutic interventions. Here we show that GSCs can reversibly transition to a slow-cycling, persistent state in response to targeted kinase inhibitors. In this state, GSCs upregulate primitive developmental programs and are dependent upon Notch signaling...
February 2, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/27941797/smarcb1-mediated-swi-snf-complex-function-is-essential-for-enhancer-regulation
#19
Xiaofeng Wang, Ryan S Lee, Burak H Alver, Jeffrey R Haswell, Su Wang, Jakub Mieczkowski, Yotam Drier, Shawn M Gillespie, Tenley C Archer, Jennifer N Wu, Evgeni P Tzvetkov, Emma C Troisi, Scott L Pomeroy, Jaclyn A Biegel, Michael Y Tolstorukov, Bradley E Bernstein, Peter J Park, Charles W M Roberts
SMARCB1 (also known as SNF5, INI1, and BAF47), a core subunit of the SWI/SNF (BAF) chromatin-remodeling complex, is inactivated in nearly all pediatric rhabdoid tumors. These aggressive cancers are among the most genomically stable, suggesting an epigenetic mechanism by which SMARCB1 loss drives transformation. Here we show that, despite having indistinguishable mutational landscapes, human rhabdoid tumors exhibit distinct enhancer H3K27ac signatures, which identify remnants of differentiation programs. We show that SMARCB1 is required for the integrity of SWI/SNF complexes and that its loss alters enhancer targeting-markedly impairing SWI/SNF binding to typical enhancers, particularly those required for differentiation, while maintaining SWI/SNF binding at super-enhancers...
February 2017: Nature Genetics
https://www.readbyqxmd.com/read/27835623/gonorrhea-control-united-states-1972-2015-a-narrative-review
#20
Thomas A Peterman, Kevin O'Connor, Heather M Bradley, Elizabeth A Torrone, Kyle T Bernstein
Gonorrhea is the second most commonly reported infection. It can lead to pelvic inflammatory disease, ectopic pregnancy, and infertility. Rates of gonorrhea decreased after the National Gonorrhea Control Program began in 1972, but stabilized in the mid 1990s. The emergence of antimicrobial resistant strains increases the urgency for enhanced gonorrhea control efforts. To identify possible approaches for improving gonorrhea control, we reviewed historic protocols, reports, and other documents related to the activities of the National Gonorrhea Control Program using Centers for Disease Control and Prevention records and the published literature...
December 2016: Sexually Transmitted Diseases
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