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The Bromodomains Of The Mammalian Swi/Snf (Mswi/Snf) Atpases Brahma (Brm) And Brahma Related Gene 1 (Brg1) Promote Chromatin Interaction And Are Critical For Skeletal Muscle Differentiation, Anthony N. Imbalzano, Hanna Witwicka, Tapan Sharma 2020 University of Massachusetts Medical School

The Bromodomains Of The Mammalian Swi/Snf (Mswi/Snf) Atpases Brahma (Brm) And Brahma Related Gene 1 (Brg1) Promote Chromatin Interaction And Are Critical For Skeletal Muscle Differentiation, Anthony N. Imbalzano, Hanna Witwicka, Tapan Sharma

University of Massachusetts Medical School Faculty Publications

Skeletal muscle differentiation induces changes in the epigenome of myoblasts as they proceed towards a myogenic phenotype. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors and are key regulators of differentiation. Three mSWI/SNF proteins, the mutually exclusive ATPases, BRG1 and BRM, and the BAF180 protein (Polybromo1, PBRM1) contain bromodomains belonging to the same structural subfamily. Bromodomains bind to acetylated lysines on histone N-terminal tails and on other proteins. Pharmacological inhibition of mSWI/SNF bromodomain function using the selective inhibitor PFI-3 reduced differentiation, decreased expression of myogenic genes, and increased the expression of cell cycle-related genes and the ...


Host Immunity Increases Mycobacterium Tuberculosis Reliance On Cytochrome Bd Oxidase, Yi Cai, Eleni Jaecklein, Jared Mackenzie, Kadamba Papavinasasundaram, Michigan State University, Xinchun Chen, Africa Health Research Institute, Christopher M. Sassetti 2020 Shenzhen University

Host Immunity Increases Mycobacterium Tuberculosis Reliance On Cytochrome Bd Oxidase, Yi Cai, Eleni Jaecklein, Jared Mackenzie, Kadamba Papavinasasundaram, Michigan State University, Xinchun Chen, Africa Health Research Institute, Christopher M. Sassetti

University of Massachusetts Medical School Faculty Publications

In order to sustain a persistent infection, Mycobacterium tuberculosis (Mtb) must adapt to a changing environment that is shaped by the developing immune response. This necessity to adapt is evident in the flexibility of many aspects of Mtb metabolism, including a respiratory chain that consists of two distinct terminal cytochrome oxidase complexes. Under the conditions tested thus far, the bc1/aa3 complex appears to play a dominant role, while the alternative bd oxidase is largely redundant. However, presence of two terminal oxidases in this obligate pathogen implies that respiratory requirements might change during infection. We report that the ...


The Rna Phosphatase Pir-1 Regulates Endogenous Small Rna Pathways In C. Elegans, Daniel A. Chaves, Hui Dai, Lichao Li, James J. Moresco, Myung Eun Oh, Darryl Conte Jr., John R. Yates III, Craig C. Mello, Weifeng Gu 2020 University of Massachusetts Medical School

The Rna Phosphatase Pir-1 Regulates Endogenous Small Rna Pathways In C. Elegans, Daniel A. Chaves, Hui Dai, Lichao Li, James J. Moresco, Myung Eun Oh, Darryl Conte Jr., John R. Yates Iii, Craig C. Mello, Weifeng Gu

University of Massachusetts Medical School Faculty Publications

Eukaryotic cells regulate 5' triphosphorylated (ppp-) RNAs to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR1 family of RNA polyphosphatases remove both the β and γ phosphates from ppp-RNAs. Here we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RdRPs and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in ...


The Dhodh Inhibitor Ptc299 Arrests Sars-Cov-2 Replication And Suppresses Induction Of Inflammatory Cytokines, Jeremy Luban, Caterina Strambio De Castilla, Yetao Wang, Allan Jacobson, Stuart Peltz 2020 University of Massachusetts Medical School

The Dhodh Inhibitor Ptc299 Arrests Sars-Cov-2 Replication And Suppresses Induction Of Inflammatory Cytokines, Jeremy Luban, Caterina Strambio De Castilla, Yetao Wang, Allan Jacobson, Stuart Peltz

University of Massachusetts Medical School Faculty Publications

The coronavirus disease 2019 (COVID-19) pandemic has created an urgent need for therapeutics that inhibit the SARS-CoV-2 virus and suppress the fulminant inflammation characteristic of advanced illness. Here, we describe the anti-COVID-19 potential of PTC299, an orally available compound that is a potent inhibitor of dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme of the de novo pyrimidine biosynthesis pathway. In tissue culture, PTC299 manifests robust, dose-dependent, and DHODH-dependent inhibition of SARS CoV-2 replication (EC50 range, 2.0 to 31.6 nM) with a selectivity index >3,800. PTC299 also blocked replication of other RNA viruses, including Ebola virus. Consistent with known ...


Atomistic Mechanism Of Force Generation, Translocation, And Coordination In A Viral Genome Packaging Motor, Joshua Pajak, Erik Dill, Mark A. White, Brian A. Kelch, Paul Jardine, Gaurav Arya, Marc C. Morais 2020 Duke University

Atomistic Mechanism Of Force Generation, Translocation, And Coordination In A Viral Genome Packaging Motor, Joshua Pajak, Erik Dill, Mark A. White, Brian A. Kelch, Paul Jardine, Gaurav Arya, Marc C. Morais

University of Massachusetts Medical School Faculty Publications

Double-stranded DNA viruses package their genomes into pre-assembled protein capsids using virally-encoded ATPase ring motors. While several structures of isolated monomers (subunits) from these motors have been determined, they provide little insight into how subunits within a functional ring coordinate their activities to efficiently generate force and translocate DNA. Here we describe the first atomic-resolution structure of a functional ring form of a viral DNA packaging motor and characterize its atomic-level dynamics via long timescale molecular dynamics simulations. Crystal structures of the pentameric ATPase ring from bacteriophage asccφ28 show that each subunit consists of a canonical N-terminal ASCE ATPase domain ...


Performance Of Abbott Architect, Ortho Vitros, And Euroimmun Assays In Detecting Prior Sars-Cov-2 Infection, Shiwani Mahajan, Carrie A. Redlich, Adam V. Wisnewski, Louis E. Fazen, Lokinendi V. Rao, Karthik Kuppusamy, Albert I. Ko, Harlan M. Krumholz 2020 Yale University

Performance Of Abbott Architect, Ortho Vitros, And Euroimmun Assays In Detecting Prior Sars-Cov-2 Infection, Shiwani Mahajan, Carrie A. Redlich, Adam V. Wisnewski, Louis E. Fazen, Lokinendi V. Rao, Karthik Kuppusamy, Albert I. Ko, Harlan M. Krumholz

University of Massachusetts Medical School Faculty Publications

Background: Several serological assays have been developed to detect anti-SARS-CoV-2 IgG antibodies, but evidence about their comparative performance is limited. We sought to assess the sensitivity of four anti-SARS-CoV-2 IgG enzyme-linked immunosorbent assays (ELISA) in individuals with evidence of prior SARS-CoV-2 infection.

Methods: We obtained sera from 36 individuals with PCR-confirmed SARS-CoV-2 infection between March and May 2020. We evaluated samples collected at around 21 days (±14 days) after their initial PCR test using 3 commercially available ELISA assays, two anti-spike (Ortho-Clinical Diagnostics Vitros, and Euroimmun) and one anti-nucleocapsid (Abbott Architect), and a Yale-developed anti-spike ELISA test. We determined the ...


Basement Membrane Damage By Ros- And Jnk-Mediated Mmp2 Activation Drives Macrophage Recruitment To Overgrown Tissue, Neha Diwanji, Andreas Bergmann 2020 University of Massachusetts Medical School

Basement Membrane Damage By Ros- And Jnk-Mediated Mmp2 Activation Drives Macrophage Recruitment To Overgrown Tissue, Neha Diwanji, Andreas Bergmann

Open Access Articles

Macrophages are a major immune cell type infiltrating tumors and promoting tumor growth and metastasis. To elucidate the mechanism of macrophage recruitment, we utilize an overgrowth tumor model ("undead" model) in larval Drosophila imaginal discs that are attached by numerous macrophages. Here we report that changes to the microenvironment of the overgrown tissue are important for recruiting macrophages. First, we describe a correlation between generation of reactive oxygen species (ROS) and damage of the basement membrane (BM) in all neoplastic, but not hyperplastic, models examined. ROS and the stress kinase JNK mediate the accumulation of matrix metalloproteinase 2 (Mmp2), damaging ...


Structural Analysis Of Potent Hybrid Hiv-1 Protease Inhibitors Containing Bis-Tetrahydrofuran In A Pseudo-Symmetric Dipeptide Isostere, Linah Rusere, Gordon J. Lockbaum, Mina Henes, Sook-Kyung Lee, Ean Spielvogel, Desaboini Nageswara Rao, Klajdi Kosovrasti, Ellen A. Nalivaika, Ronald Swanstrom, Nese Kurt Yilmaz, Celia A. Schiffer, Akbar Ali 2020 University of Massachusetts Medical School

Structural Analysis Of Potent Hybrid Hiv-1 Protease Inhibitors Containing Bis-Tetrahydrofuran In A Pseudo-Symmetric Dipeptide Isostere, Linah Rusere, Gordon J. Lockbaum, Mina Henes, Sook-Kyung Lee, Ean Spielvogel, Desaboini Nageswara Rao, Klajdi Kosovrasti, Ellen A. Nalivaika, Ronald Swanstrom, Nese Kurt Yilmaz, Celia A. Schiffer, Akbar Ali

University of Massachusetts Medical School Faculty Publications

The design, synthesis, and X-ray structural analysis of hybrid HIV-1 protease inhibitors (PIs) containing bis-tetrahydrofuran (bis-THF) in a pseudo-C2-symmetric dipeptide isostere are described. A series of PIs were synthesized by incorporating bis-THF of darunavir on either side of the Phe-Phe isostere of lopinavir in combination with hydrophobic amino acids on the opposite P2/P2' position. Structure-activity relationship studies indicated that the bis-THF moiety can be attached at either the P2 or P2' position without significantly affecting potency. However, the group on the opposite P2/P2' position had a dramatic effect on potency depending on the size and shape of the ...


Jnk-Mediated Disruption Of Bile Acid Homeostasis Promotes Intrahepatic Cholangiocarcinoma, Elisa Manieri, Tamera Barrett, Julie Cavanagh-Kyros, Roger J. Davis, Alfonso Mora, Guadalupe Sabio 2020 National Centre for Cardiovascular Research, Spain

Jnk-Mediated Disruption Of Bile Acid Homeostasis Promotes Intrahepatic Cholangiocarcinoma, Elisa Manieri, Tamera Barrett, Julie Cavanagh-Kyros, Roger J. Davis, Alfonso Mora, Guadalupe Sabio

University of Massachusetts Medical School Faculty Publications

Metabolic stress causes activation of the cJun NH2-terminal kinase (JNK) signal transduction pathway. It is established that one consequence of JNK activation is the development of insulin resistance and hepatic steatosis through inhibition of the transcription factor PPARalpha. Indeed, JNK1/2 deficiency in hepatocytes protects against the development of steatosis, suggesting that JNK inhibition represents a possible treatment for this disease. However, the long-term consequences of JNK inhibition have not been evaluated. Here we demonstrate that hepatic JNK controls bile acid production. We found that hepatic JNK deficiency alters cholesterol metabolism and bile acid synthesis, conjugation, and transport, resulting in ...


Regulation Of The Mammalian Swi/Snf Family Of Chromatin Remodeling Enzymes By Phosphorylation During Myogenesis, Teresita Padilla-Benavides, Pablo Reyes-Gutierrez, Anthony N. Imbalzano 2020 University of Massachusetts Medical School

Regulation Of The Mammalian Swi/Snf Family Of Chromatin Remodeling Enzymes By Phosphorylation During Myogenesis, Teresita Padilla-Benavides, Pablo Reyes-Gutierrez, Anthony N. Imbalzano

University of Massachusetts Medical School Faculty Publications

Myogenesis is the biological process by which skeletal muscle tissue forms. Regulation of myogenesis involves a variety of conventional, epigenetic, and epigenomic mechanisms that control chromatin remodeling, DNA methylation, histone modification, and activation of transcription factors. Chromatin remodeling enzymes utilize ATP hydrolysis to alter nucleosome structure and/or positioning. The mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) family of chromatin remodeling enzymes is essential for myogenesis. Here we review diverse and novel mechanisms of regulation of mSWI/SNF enzymes by kinases and phosphatases. The integration of classic signaling pathways with chromatin remodeling enzyme function impacts myoblast viability and proliferation as well ...


Dgat1 Is A Lipid Metabolism Oncoprotein That Enables Cancer Cells To Accumulate Fatty Acid While Avoiding Lipotoxicity, Daniel J. Wilcock, Melissa Kasheta, Craig J. Ceol 2020 University of Manchester

Dgat1 Is A Lipid Metabolism Oncoprotein That Enables Cancer Cells To Accumulate Fatty Acid While Avoiding Lipotoxicity, Daniel J. Wilcock, Melissa Kasheta, Craig J. Ceol

University of Massachusetts Medical School Faculty Publications

Dysregulated cellular metabolism is a hallmark of cancer. As yet, few druggable oncoproteins directly responsible for this hallmark have been identified. Increased fatty acid acquisition allows cancer cells to meet their membrane biogenesis, ATP, and signaling needs. Excess fatty acids suppress growth factor signaling and cause oxidative stress in non-transformed cells, but surprisingly not in cancer cells. Molecules underlying this cancer adaptation may provide new drug targets. Here, we identify Diacylglycerol O-acyltransferase 1 (DGAT1), an enzyme integral to triacylglyceride synthesis and lipid droplet formation, as a frequently up-regulated oncoprotein allowing cancer cells to tolerate excess fatty acids. DGAT1 over-expression alone ...


Hydrazines As Versatile Chemical Biology Probes And Drug-Discovery Tools For Cofactor-Dependent Enzymes, Zongtao Lin, Xie Wang, Katelyn A. Bustin, Lin He, Radu M. Suciu, Nancy Schek, Mina Ahmadi, Kai Hu, Erika J. Olson, William H. Parsons, Eric S. Witze, Paul D. Morton, Ann M. Gregus, Matthew W. Buczynski, Megan L. Matthews 2020 University of Pennsylvania

Hydrazines As Versatile Chemical Biology Probes And Drug-Discovery Tools For Cofactor-Dependent Enzymes, Zongtao Lin, Xie Wang, Katelyn A. Bustin, Lin He, Radu M. Suciu, Nancy Schek, Mina Ahmadi, Kai Hu, Erika J. Olson, William H. Parsons, Eric S. Witze, Paul D. Morton, Ann M. Gregus, Matthew W. Buczynski, Megan L. Matthews

University of Massachusetts Medical School Faculty Publications

Known chemoproteomic probes generally use warheads that tag a single type of amino acid or modified form thereof to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electron-poor enzyme cofactors, transient intermediates and chemically-labile regulatory modifications, but probes for such species are underdeveloped. Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. Its electron-rich nature allows it to react by both polar and radicaloid mechanisms and to target multiple, pharmacologically important functional classes of enzymes bearing diverse organic ...


Deciphering Complex Mechanisms Of Resistance And Loss Of Potency Through Coupled Molecular Dynamics And Machine Learning, Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer 2020 University of Massachusetts Medical School

Deciphering Complex Mechanisms Of Resistance And Loss Of Potency Through Coupled Molecular Dynamics And Machine Learning, Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer

University of Massachusetts Medical School Faculty Publications

Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially involving those distal from the active site, alter drug binding to confer resistance are poorly understood and thus difficult to counteract. A strategy coupling parallel molecular dynamics simulations and machine learning to identify conserved mechanisms underlying resistance was developed. A series of 28 HIV-1 protease variants with up to 24 varied substitutions were used as a rigorous model of this strategy. Many of the mutations were distal from the active site and the potency to darunavir varied from low ...


Plcg2 Protective Variant P.P522r Modulates Tau Pathology And Disease Progression In Patients With Mild Cognitive Impairment, Luca Kleineidam, Michael T. Heneka, Alfredo Ramirez 2020 University of Cologne

Plcg2 Protective Variant P.P522r Modulates Tau Pathology And Disease Progression In Patients With Mild Cognitive Impairment, Luca Kleineidam, Michael T. Heneka, Alfredo Ramirez

Open Access Articles

A rare coding variant (rs72824905, p.P522R) conferring protection against Alzheimer's disease (AD) was identified in the gene encoding the enzyme phospholipase-C-gamma2 (PLCG2) that is highly expressed in microglia. To explore the protective nature of this variant, we employed latent process linear mixed models to examine the association of p.P522R with longitudinal cognitive decline in 3595 MCI patients, and in 10,097 individuals from population-based studies. Furthermore, association with CSF levels of pTau181, total tau, and Abeta1-42 was assessed in 1261 MCI patients. We found that MCI patients who carried the p.P522R variant showed a slower rate ...


Mrna Stem-Loops Can Pause The Ribosome By Hindering A-Site Trna Binding, Chen Bao, Sarah Loerch, Clarence Ling, Andrei A. Korostelev, Nikolaus Grigorieff, Dmitri N. Ermolenko 2020 University of Rochester

Mrna Stem-Loops Can Pause The Ribosome By Hindering A-Site Trna Binding, Chen Bao, Sarah Loerch, Clarence Ling, Andrei A. Korostelev, Nikolaus Grigorieff, Dmitri N. Ermolenko

Open Access Articles

Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Forster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of ...


A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo 2020 Massachusetts Institute of Technology

A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo

Open Access Articles

CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5[Formula: see text]-NAAN-3[Formula: see text] PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all ...


Variability In Naltrexone Biotransformation, Stephani L. Stancil 2020 Children's Mercy Kansas City

Variability In Naltrexone Biotransformation, Stephani L. Stancil

Research Days

No abstract provided.


Yap1/Taz Drives Ependymoma-Like Tumour Formation In Mice, Noreen Eder, Federico Roncaroli, Marie-Charlotte Dolmart, Stuart Horswell, Felipe Andreiuolo, Helen R. Flynn, Andre T. Lopes, Suzanne Claxton, John-Paul Kilday, Lucy Collinson, Junhao Mao, Torsten Pietsch, Barry Thompson, Ambrosius P. Snijders, Sila K. Ultanir 2020 The Francis Crick Institute

Yap1/Taz Drives Ependymoma-Like Tumour Formation In Mice, Noreen Eder, Federico Roncaroli, Marie-Charlotte Dolmart, Stuart Horswell, Felipe Andreiuolo, Helen R. Flynn, Andre T. Lopes, Suzanne Claxton, John-Paul Kilday, Lucy Collinson, Junhao Mao, Torsten Pietsch, Barry Thompson, Ambrosius P. Snijders, Sila K. Ultanir

Open Access Articles

YAP1 gene fusions have been observed in a subset of paediatric ependymomas. Here we show that, ectopic expression of active nuclear YAP1 (nlsYAP5SA) in ventricular zone neural progenitor cells using conditionally-induced NEX/NeuroD6-Cre is sufficient to drive brain tumour formation in mice. Neuronal differentiation is inhibited in the hippocampus. Deletion of YAP1's negative regulators LATS1 and LATS2 kinases in NEX-Cre lineage in double conditional knockout mice also generates similar tumours, which are rescued by deletion of YAP1 and its paralog TAZ. YAP1/TAZ-induced mouse tumours display molecular and ultrastructural characteristics of human ependymoma. RNA sequencing and quantitative proteomics of ...


A Runx2 Stabilization Pathway Mediates Physiologic And Pathologic Bone Formation, Jung-Min Kim, Yeon-Suk Yang, Xianpeng Ge, Matthew B. Greenblatt, Jae-Hyuck Shim 2020 University of Massachusetts Medical School

A Runx2 Stabilization Pathway Mediates Physiologic And Pathologic Bone Formation, Jung-Min Kim, Yeon-Suk Yang, Xianpeng Ge, Matthew B. Greenblatt, Jae-Hyuck Shim

Open Access Articles

The osteoblast differentiation capacity of skeletal stem cells (SSCs) must be tightly regulated, as inadequate bone formation results in low bone mass and skeletal fragility, and over-exuberant osteogenesis results in heterotopic ossification (HO) of soft tissues. RUNX2 is essential for tuning this balance, but the mechanisms of posttranslational control of RUNX2 remain to be fully elucidated. Here, we identify that a CK2/HAUSP pathway is a key regulator of RUNX2 stability, as Casein kinase 2 (CK2) phosphorylates RUNX2, recruiting the deubiquitinase herpesvirus-associated ubiquitin-specific protease (HAUSP), which stabilizes RUNX2 by diverting it away from ubiquitin-dependent proteasomal degradation. This pathway is important ...


How Can We Stop Cancer?, Joseph R. Current 2020 St. John Fisher College

How Can We Stop Cancer?, Joseph R. Current

The Review: A Journal of Undergraduate Student Research

Cancer is a disease that humans have been struggling to combat for centuries. It originates from the accumulation of several mutations over the life of a cell that causes it to evade cell death and multiply rapidly. It can affect any tissue in the body and can spread to other parts of the body through metastasis. Cancer comes in numerous shapes and sizes with different levels of aggression, growth speeds, and health risks. Many treatments for cancer exist today, three of the most popular being surgery, chemotherapy, and radiation therapy, which can be used in combinations with other treatments to ...


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