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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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Hosono Y, Niknafs YS, Prensner JR, Iyer MK, Dhanasekaran SM, Mehra R, Pitchiaya S, Tien J, Escara-Wilke J, Poliakov A, Chu SC, Saleh S, Sankar K, Su F, Guo S, Qiao Y, Freier SM, Bui HH, Cao X, Malik R, Johnson TM, Beer DG, Feng FY, Zhou W, Chinnaiyan AM. Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. Cell 2023; 186:4254-4255. [PMID: 37714137 DOI: 10.1016/j.cell.2023.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. Wiley Interdiscip Rev RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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Patel P, Nallandhighal S, Scoville D, Tran L, Cotta B, Udager A, Rao A, Palapattu G, Dadhania V, Pitchiaya S, Salami S. Spatial transcriptomic profiling of prostate cancer reveals zone specific androgen receptor signaling and immune infiltration. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Larouche JA, Mohiuddin M, Choi JJ, Ulintz PJ, Fraczek P, Sabin K, Pitchiaya S, Kurpiers SJ, Castor-Macias J, Liu W, Hastings RL, Brown LA, Markworth JF, De Silva K, Levi B, Merajver SD, Valdez G, Chakkalakal JV, Jang YC, Brooks SV, Aguilar CA. Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging. eLife 2021; 10:e66749. [PMID: 34323217 PMCID: PMC8360658 DOI: 10.7554/elife.66749] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/28/2021] [Indexed: 01/29/2023] Open
Abstract
During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function impacting mobility and quality of life. Muscle loss is often associated with denervation and a loss of resident muscle stem cells (satellite cells or MuSCs); however, the relationship between MuSCs and innervation has not been established. Herein, we administered severe neuromuscular trauma to a transgenic murine model that permits MuSC lineage tracing. We show that a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ), the synapse between myofibers and motor neurons, in healthy young adult muscles. In aging and in a mouse model of neuromuscular degeneration (Cu/Zn superoxide dismutase knockout - Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ in a manner akin to young muscle and partially restored MuSC ability to engraft into positions proximal to the NMJ. Using single cell RNA-sequencing of MuSCs isolated from aged muscle, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury and share similarity to synaptic myonuclei. Collectively, these data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors.
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Affiliation(s)
- Jacqueline A Larouche
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Mahir Mohiuddin
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Jeongmoon J Choi
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter J Ulintz
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Internal Medicine-Hematology/Oncology, University of MichiganAnn ArborUnited States
| | - Paula Fraczek
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Kaitlyn Sabin
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | | | - Sarah J Kurpiers
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Jesus Castor-Macias
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Wenxuan Liu
- Department of Pharmacology and Physiology, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of Rochester Medical CenterRochesterUnited States
- Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical CenterRochesterUnited States
| | - Robert Louis Hastings
- Departmentof Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown UniversityProvidenceUnited States
| | - Lemuel A Brown
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - James F Markworth
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Kanishka De Silva
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Benjamin Levi
- Department of Surgery, University of Texas SouthwesternDallasUnited States
- Childrens Research Institute and Center for Mineral MetabolismDallasUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
| | - Sofia D Merajver
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Internal Medicine-Hematology/Oncology, University of MichiganAnn ArborUnited States
| | - Gregorio Valdez
- Departmentof Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown UniversityProvidenceUnited States
| | - Joe V Chakkalakal
- Department of Pharmacology and Physiology, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of Rochester Medical CenterRochesterUnited States
- Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical CenterRochesterUnited States
| | - Young C Jang
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Susan V Brooks
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Childrens Research Institute and Center for Mineral MetabolismDallasUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
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Peltier D, Radosevich M, Ravikumar V, Pitchiaya S, Decoville T, Wood SC, Hou G, Zajac C, Oravecz-Wilson K, Sokol D, Henig I, Wu J, Kim S, Taylor A, Fujiwara H, Sun Y, Rao A, Chinnaiyan AM, Goldstein DR, Reddy P. RNA-seq of human T cells after hematopoietic stem cell transplantation identifies Linc00402 as a regulator of T cell alloimmunity. Sci Transl Med 2021; 13:13/585/eaaz0316. [PMID: 33731431 PMCID: PMC8589011 DOI: 10.1126/scitranslmed.aaz0316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/11/2020] [Accepted: 01/27/2021] [Indexed: 01/26/2023]
Abstract
Mechanisms governing allogeneic T cell responses after solid organ and allogeneic hematopoietic stem cell transplantation (HSCT) are incompletely understood. To identify lncRNAs that regulate human donor T cells after clinical HSCT, we performed RNA sequencing on T cells from healthy individuals and donor T cells from three different groups of HSCT recipients that differed in their degree of major histocompatibility complex (MHC) mismatch. We found that lncRNA differential expression was greatest in T cells after MHC-mismatched HSCT relative to T cells after either MHC-matched or autologous HSCT. Differential expression was validated in an independent patient cohort and in mixed lymphocyte reactions using ex vivo healthy human T cells. We identified Linc00402, an uncharacterized lncRNA, among the lncRNAs differentially expressed between the mismatched unrelated and matched unrelated donor T cells. We found that Linc00402 was conserved and exhibited an 88-fold increase in human T cells relative to all other samples in the FANTOM5 database. Linc00402 was also increased in donor T cells from patients who underwent allogeneic cardiac transplantation and in murine T cells. Linc00402 was reduced in patients who subsequently developed acute graft-versus-host disease. Linc00402 enhanced the activity of ERK1 and ERK2, increased FOS nuclear accumulation, and augmented expression of interleukin-2 and Egr-1 after T cell receptor engagement. Functionally, Linc00402 augmented the T cell proliferative response to an allogeneic stimulus but not to a nominal ovalbumin peptide antigen or polyclonal anti-CD3/CD28 stimulus. Thus, our studies identified Linc00402 as a regulator of allogeneic T cell function.
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Affiliation(s)
- Daniel Peltier
- Division of Hematology and Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Molly Radosevich
- Division of Hematology and Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Visweswaran Ravikumar
- Department of Computational Medicine & Bioinformatics, Biostatistics, Radiation Oncology, and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA, 48109
| | | | - Thomas Decoville
- Division of Hematology and Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Sherri C. Wood
- Department of Internal Medicine, Ann Arbor, MI, USA, 48109
| | - Guoqing Hou
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Cynthia Zajac
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Katherine Oravecz-Wilson
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - David Sokol
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Israel Henig
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Julia Wu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Stephanie Kim
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Austin Taylor
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Hideaki Fujiwara
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Yaping Sun
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109
| | - Arvind Rao
- Department of Computational Medicine & Bioinformatics, Biostatistics, Radiation Oncology, and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Daniel R. Goldstein
- Department of Internal Medicine, Institute of Gerontology, Department of Microbiology and Immunology, Program of Michigan Biology of Cardiovascular Aging, Ann Arbor, MI, USA, 48109
| | - Pavan Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA, 48109.,Corresponding Author: Pavan Reddy,
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Zaslavsky A, Adams M, Cao X, Yamaguchi A, Henderson J, Busch-Østergren P, Udager A, Pitchiaya S, Tourdot B, Kasputis T, Church SJ, Lee SK, Ohl S, Patel S, Morgan TM, Alva A, Wakefield TW, Reichert Z, Holinstat M, Palapattu GS. Antisense oligonucleotides and nucleic acids generate hypersensitive platelets. Thromb Res 2021; 200:64-71. [PMID: 33540294 DOI: 10.1016/j.thromres.2021.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 12/07/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Despite the great promise for therapies using antisense oligonucleotides (ASOs), their adverse effects, which include pro-inflammatory effects and thrombocytopenia, have limited their use. Previously, these effects have been linked to the phosphorothioate (PS) backbone necessary to prevent rapid ASO degradation in plasma. The main aim of this study was to assess the impact of the nucleic acid portion of an ASO-type drug on platelets and determine if it may contribute to thrombosis or thrombocytopenia. METHODS Platelets were isolated from healthy donors and men with advanced prostate cancer. Effects of antisense oligonucleotides (ASO), oligonucleotides, gDNA, and microRNA on platelet activation and aggregation were evaluated. A mouse model of lung thrombosis was used to confirm the effects of PS-modified oligonucleotides in vivo. RESULTS Platelet exposure to gDNA, miRNA, and oligonucleotides longer than 16-mer at a concentration above 8 mM resulted in the formation of hypersensitive platelets, characterized by an increased sensitivity to low-dose thrombin (0.1 nM) and increase in p-Selectin expression (6-8 fold greater than control; p < 0.001). The observed nucleic acid (NA) effects on platelets were toll-like receptor (TLR) -7 subfamily dependent. Injection of a p-Selectin inhibitor significantly (p = 0.02) reduced the formation of oligonucleotide-associated pulmonary microthrombosis in vivo. CONCLUSION Our results suggest that platelet exposure to nucleic acids independent of the presence of a PS modification leads to a generation of hypersensitive platelets and requires TLR-7 subfamily receptors. ASO studies conducted in cancer patients may benefit from testing the ASO effects on platelets ex vivo before initiation of patient treatment.
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Affiliation(s)
- Alexander Zaslavsky
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Mackenzie Adams
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Xiu Cao
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Adriana Yamaguchi
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James Henderson
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Aaron Udager
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sethuramasundaram Pitchiaya
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Benjamin Tourdot
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tadas Kasputis
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Samuel J Church
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Samantha K Lee
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sydney Ohl
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shivam Patel
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ajjai Alva
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine-Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Thomas W Wakefield
- Section of Vascular Surgery, Department of Surgery, Conrad Jobst Vascular Research Laboratories, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zachery Reichert
- Department of Internal Medicine-Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Holinstat
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ganesh S Palapattu
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, Medical University of Vienna, Vienna, Austria.
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Jalihal AP, Schmidt A, Gao G, Little SR, Pitchiaya S, Walter NG. Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles. J Biol Chem 2021; 296:100044. [PMID: 33168632 PMCID: PMC7948973 DOI: 10.1074/jbc.rev120.010899] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/09/2023] Open
Abstract
Biological liquid-liquid phase separation has gained considerable attention in recent years as a driving force for the assembly of subcellular compartments termed membraneless organelles. The field has made great strides in elucidating the molecular basis of biomolecular phase separation in various disease, stress response, and developmental contexts. Many important biological consequences of such "condensation" are now emerging from in vivo studies. Here we review recent work from our group and others showing that many proteins undergo rapid, reversible condensation in the cellular response to ubiquitous environmental fluctuations such as osmotic changes. We discuss molecular crowding as an important driver of condensation in these responses and suggest that a significant fraction of the proteome is poised to undergo phase separation under physiological conditions. In addition, we review methods currently emerging to visualize, quantify, and modulate the dynamics of intracellular condensates in live cells. Finally, we propose a metaphor for rapid phase separation based on cloud formation, reasoning that our familiar experiences with the readily reversible condensation of water droplets help understand the principle of phase separation. Overall, we provide an account of how biological phase separation supports the highly intertwined relationship between the composition and dynamic internal organization of cells, thus facilitating extremely rapid reorganization in response to internal and external fluctuations.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Guoming Gao
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Biophysics Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Saffron R Little
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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9
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Jalihal AP, Pitchiaya S, Xiao L, Bawa P, Jiang X, Bedi K, Parolia A, Cieslik M, Ljungman M, Chinnaiyan AM, Walter NG. Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change. Mol Cell 2020; 79:978-990.e5. [PMID: 32857953 PMCID: PMC7502480 DOI: 10.1016/j.molcel.2020.08.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/11/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular, membraneless compartments that are observed under physiological and stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly (within ∼10 s) phase-separates in mammalian cells during hyperosmotic stress and dissolves upon isosmotic rescue (over ∼100 s) with minimal effect on cell viability even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular hyperosmotic phase separation (HOPS) correlates with the degree of cell volume compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA cleavage factor components from actively transcribing genomic loci, providing a mechanism for hyperosmolarity-induced global impairment of transcription termination. Our data suggest that the multimeric proteome rapidly responds to changes in hydration and molecular crowding, revealing an unexpected mode of globally programmed phase separation and sequestration.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
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10
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Shankar S, Tien JCY, Siebenaler RF, Chugh S, Dommeti VL, Zelenka-Wang S, Wang XM, Apel IJ, Waninger J, Eyunni S, Xu A, Mody M, Goodrum A, Zhang Y, Tesmer JJ, Mannan R, Cao X, Vats P, Pitchiaya S, Ellison SJ, Shi J, Kumar-Sinha C, Crawford HC, Chinnaiyan AM. An essential role for Argonaute 2 in EGFR-KRAS signaling in pancreatic cancer development. Nat Commun 2020; 11:2817. [PMID: 32499547 PMCID: PMC7272436 DOI: 10.1038/s41467-020-16309-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/20/2020] [Indexed: 01/14/2023] Open
Abstract
Both KRAS and EGFR are essential mediators of pancreatic cancer development and interact with Argonaute 2 (AGO2) to perturb its function. Here, in a mouse model of mutant KRAS-driven pancreatic cancer, loss of AGO2 allows precursor lesion (PanIN) formation yet prevents progression to pancreatic ductal adenocarcinoma (PDAC). Precursor lesions with AGO2 ablation undergo oncogene-induced senescence with altered microRNA expression and EGFR/RAS signaling, bypassed by loss of p53. In mouse and human pancreatic tissues, PDAC progression is associated with increased plasma membrane localization of RAS/AGO2. Furthermore, phosphorylation of AGO2Y393 disrupts both the wild-type and oncogenic KRAS-AGO2 interaction, albeit under different conditions. ARS-1620 (G12C-specific inhibitor) disrupts the KRASG12C-AGO2 interaction, suggesting that the interaction is targetable. Altogether, our study supports a biphasic model of pancreatic cancer development: an AGO2-independent early phase of PanIN formation reliant on EGFR-RAS signaling, and an AGO2-dependent phase wherein the mutant KRAS-AGO2 interaction is critical for PDAC progression.
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Affiliation(s)
- Sunita Shankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ronald F Siebenaler
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Seema Chugh
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vijaya L Dommeti
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sylvia Zelenka-Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ingrid J Apel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jessica Waninger
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alice Xu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Malay Mody
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrew Goodrum
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - John J Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stephanie J Ellison
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jiaqi Shi
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
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11
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Parolia A, Cieslik M, Chu SC, Xiao L, Ouchi T, Zhang Y, Wang X, Vats P, Cao X, Pitchiaya S, Su F, Wang R, Feng FY, Wu YM, Lonigro RJ, Robinson DR, Chinnaiyan AM. Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer. Nature 2019; 571:413-418. [PMID: 31243372 PMCID: PMC6661908 DOI: 10.1038/s41586-019-1347-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/03/2019] [Indexed: 12/12/2022]
Abstract
Forkhead box A1 (FOXA1) is a pioneer transcription factor that is essential for the normal development of several endoderm-derived organs, including the prostate gland1,2. FOXA1 is frequently mutated in the hormone-receptor driven prostate, breast, bladder, and salivary gland tumors3–8. However, how FOXA1 alterations affect cancer development is unclear, with FOXA1 previously ascribed both tumor suppressive9–11 and oncogenic12–14 roles. Here we assemble an aggregate cohort of 1546 prostate cancers (PCa) and show that FOXA1 alterations fall into three distinct structural classes that diverge in clinical incidence and genetic co-alteration profiles, with a collective prevalence of 35%. Class1 activating mutations originate in early PCa without ETS/SPOP alterations, selectively recur within the Wing2-region of the DNA-binding Forkhead domain (FKHD), enable enhanced chromatin mobility and binding frequency, and strongly transactivate a luminal androgen receptor (AR) program of prostate oncogenesis. By contrast, class2 activating mutations are acquired in metastatic PCa, truncate the C-terminal domain of FOXA1, enable dominant chromatin binding by increasing DNA affinity, and through TLE3 inactivation promote WNT-pathway driven metastasis. Finally, class3 genomic rearrangements are enriched in metastatic PCa, comprise of duplications and translocations within the FOXA1 locus, and structurally reposition a conserved regulatory element, herein denoted FOXA1 Mastermind (FOXMIND), to drive overexpression of FOXA1 or other oncogenes. Our study reaffirms the central role of FOXA1 in mediating AR-driven oncogenesis, and provides mechanistic insights into how different classes of FOXA1 alterations uniquely promote PCa initiation and/or metastatic progression. Furthermore, these results have direct implications in understanding the pathobiology of other hormone-receptor driven cancers and rationalize therapeutic co-targeting of FOXA1 activity.
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Affiliation(s)
- Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Shih-Chun Chu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Takahiro Ouchi
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.,Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA.,Department of Urology, University of California at San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA. .,Department of Pathology, University of Michigan, Ann Arbor, MI, USA. .,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA. .,Department of Urology, University of Michigan, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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12
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Pitchiaya S, Mourao MDA, Jalihal AP, Xiao L, Jiang X, Chinnaiyan AM, Schnell S, Walter NG. Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality. Mol Cell 2019; 74:521-533.e6. [PMID: 30952514 DOI: 10.1016/j.molcel.2019.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/21/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022]
Abstract
Cellular RNAs often colocalize with cytoplasmic, membrane-less ribonucleoprotein (RNP) granules enriched for RNA-processing enzymes, termed processing bodies (PBs). Here we track the dynamic localization of individual miRNAs, mRNAs, and long non-coding RNAs (lncRNAs) to PBs using intracellular single-molecule fluorescence microscopy. We find that unused miRNAs stably bind to PBs, whereas functional miRNAs, repressed mRNAs, and lncRNAs both transiently and stably localize within either the core or periphery of PBs, albeit to different extents. Consequently, translation potential and 3' versus 5' placement of miRNA target sites significantly affect the PB localization dynamics of mRNAs. Using computational modeling and supporting experimental approaches, we show that partitioning in the PB phase attenuates mRNA silencing, suggesting that physiological mRNA turnover occurs predominantly outside of PBs. Instead, our data support a PB role in sequestering unused miRNAs for surveillance and provide a framework for investigating the dynamic assembly of RNP granules by phase separation at single-molecule resolution.
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Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Marcio D A Mourao
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Consulting for Statistics, Computing and Analytics Research, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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13
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Niknafs Y, Hosono Y, K M, Prensner J, Mehra R, Pitchiaya S, Tien J, Malik R, Zhao W, Chinnaiyan A. Abstract 4982: Oncogenic role of THOR, a conserved cancer/testis long noncoding RNA. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Large scale transcriptome sequencing efforts have vastly expanded the catalog of long non-coding RNAs (lncRNAs) with varying evolutionary conservation, lineage expression, and cancer specificity. Through a recent large-scale transcriptomic analysis over 6,500 tumor RNA-seq samples, we discovered over 50,000 lncRNAs in the human genome, many of which exhibited highly evolutionarily conserved sequence patterns. Building upon the discovery of these highly conserved lncRNAs, we functionally characterized a novel ultraconserved lncRNA, THOR, which exhibits expression exclusively in testis and a broad range of human cancers. We establish THOR as the first discovered cancer/testis lncRNA, and further investigated its functional significance. THOR knockdown and overexpression in multiple cell lines and animal models alters cell or tumor growth supporting an oncogenic role. Namely, we generated CRISPR knockout cell line models, showing a definitive role for THOR in cancer progression. Additionally, given the sequence conservation of THOR through the mouse and zebrafish, we generated a zebrafish knockout model, and also a zebrafish overexpression model for THOR. Through RNA-pulldown followed by mass spectrometry, we discovered a conserved interaction of THOR with the RNA binding protein, IGF2BP1, in both human and zebrafish cells. We further show that THOR contributes to the mRNA stabilization activities of IGF2BP1. These findings are corroborated by iCLIP data for IGF2BP1. Notably, transgenic THOR knockout produced fertilization defects in zebrafish and also conferred a resistance to melanoma onset in an NRAS K61-induced zebrafish melanoma model. Likewise, ectopic expression of human THOR in zebrafish accelerated the onset of melanoma. THOR represents a novel class of functionally important cancer/testis lncRNAs whose structure and function have undergone positive evolutionary selection.
Citation Format: Yashar Niknafs, Yasuyuki Hosono, Matthew K, John Prensner, Rohit Mehra, Sethuramasundaram Pitchiaya, Jean Tien, Rohit Malik, Weibin Zhao, Arul Chinnaiyan. Oncogenic role of THOR, a conserved cancer/testis long noncoding RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4982.
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14
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Zhang Y, Pitchiaya S, Cieślik M, Niknafs YS, Tien JC, Hosono Y, Wang L, Qiao Y, Cao X, Ljungman M, Jiang H, Mehra R, Guo S, Malik R, Chinnaiyan AM. Abstract 2458: The androgen receptor-regulated lncRNA landscape reveals a role for ARlnc1 in prostate cancer progression. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The androgen receptor (AR) signaling plays a key role in the development of the normal prostate as well as prostate cancer. While substantial efforts have been undertaken to study AR-regulated protein-coding genes in primary prostate cancer and castration-resistant prostate cancer, few studies have investigated the role of long noncoding RNAs. In this study, we employed transcriptome sequencing to delineate long noncoding RNAs (lncRNAs) associated with AR signaling in prostate cancer progression. ARlnc1 (AR-regulated lncRNA 1) was identified as being the top AR-induced, cancer-associated lncRNA in an integrative analysis of prostate cancer cell lines and tissues. Not only was ARlnc1 induced by AR, but ARlnc1 also was shown to sustain AR signaling by stabilizing the AR transcript via interaction with the AR 3' UTR. Knockdown of ARlnc1 suppressed AR expression, global AR signaling, and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARlnc1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression, and identifies ARlnc1 as a novel therapeutic target.
Citation Format: Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieślik, Yashar S. Niknafs, Jean C. Tien, Yasuyuki Hosono, Lisha Wang, Yuanyuan Qiao, Xuhong Cao, Mats Ljungman, Hui Jiang, Rohit Mehra, Shuling Guo, Rohit Malik, Arul M. Chinnaiyan. The androgen receptor-regulated lncRNA landscape reveals a role for ARlnc1 in prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2458.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Hui Jiang
- 1University of Michigan, Ann Arbor, MI
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15
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Pitchiaya S, D'silva J, Lee N, Narayanan S, Jiang X, Dhanasekaran SM, Chinnaiyan AM. Abstract 2836: Spatially resolved single-cell analysis of cellular plasticity and mechanisms of drug resistance. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cellular heterogeneity adversely affects clinical stratification, treatment decisions, and development of therapeutic resistance in cancer. Heterogeneity manifests as variability in gene expression and scales with the number of unique cell types and/or the extent of phenotypic plasticity. Therefore, an incisive tool that effectively quantifies heterogeneity, robustly identifies rare cell populations, efficiently predicts cell state transitions, and preserves the associated phenotypic manifestations will provide key insights into the mechanisms of plasticity and development of drug resistance. To this end, we developed High-Throughput Single-cell analysis using single-molecule Fluorescence In Situ Hybridization (HITS-FISH) - a completely automated imaging-based tool that provides absolute quantification of gene expression (mature and immature transcripts that are coding or non-coding), while still preserving spatial and morphological information. Using a combination of HITS-FISH and single cell RNAseq, which provides a high-throughput readout of gene expression signatures, we find that multiple, potentially plastic cell states (genetic, epigenetic, and cell cycle) coexist within a seemingly homogeneous population of cancer cells from various tissues. HITS-FISH suggests that one of the major contributors of such heterogeneity is pervasive aneuploidy, which is accentuated during treatment of cancer cells with chemotherapeutic agents and subsequent development of resistance against such drugs. Currently, we are further characterizing these plastic cells via lineage tracing and single-cell analysis to identify pre-resistant cell states and drug-induced gene-expression reprogramming.
Citation Format: Sethuramasundaram Pitchiaya, Jeremy D'silva, Nicole Lee, Sathiyapandi Narayanan, Xia Jiang, Saravana M. Dhanasekaran, Arul M. Chinnaiyan. Spatially resolved single-cell analysis of cellular plasticity and mechanisms of drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2836.
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Affiliation(s)
| | | | - Nicole Lee
- Univ. of Michigan Comp. Cancer Ctr., Ann Arbor, MI
| | | | - Xia Jiang
- Univ. of Michigan Comp. Cancer Ctr., Ann Arbor, MI
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16
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Zhang Y, Pitchiaya S, Cieślik M, Niknafs YS, Tien JCY, Hosono Y, Iyer MK, Yazdani S, Subramaniam S, Shukla SK, Jiang X, Wang L, Liu TY, Uhl M, Gawronski AR, Qiao Y, Xiao L, Dhanasekaran SM, Juckette KM, Kunju LP, Cao X, Patel U, Batish M, Shukla GC, Paulsen MT, Ljungman M, Jiang H, Mehra R, Backofen R, Sahinalp CS, Freier SM, Watt AT, Guo S, Wei JT, Feng FY, Malik R, Chinnaiyan AM. Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Nat Genet 2018; 50:814-824. [PMID: 29808028 PMCID: PMC5980762 DOI: 10.1038/s41588-018-0120-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/23/2018] [Indexed: 12/23/2022]
Abstract
The androgen receptor (AR) plays a critical role in the development of the normal prostate as well as prostate cancer. Using an integrative transcriptomic analysis of prostate cancer cell lines and tissues, we identified ARLNC1 (AR-regulated long non-coding RNA 1) as an important long non-coding RNA that is strongly associated with AR signaling in prostate cancer progression. Not only was ARLNC1 induced by AR protein, ARLNC1 stabilized the AR transcript via RNA-RNA interaction. ARLNC1 knockdown suppressed AR expression, global AR signaling, and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARLNC1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression, and identifies ARLNC1 as a novel therapeutic target.
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Affiliation(s)
- Yajia Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jean C-Y Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yasuyuki Hosono
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shruthi Subramaniam
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sudhanshu K Shukla
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tzu-Ying Liu
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Michael Uhl
- Department of Computer Science and Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Alexander R Gawronski
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kristin M Juckette
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Utsav Patel
- New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Mona Batish
- New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Medical Laboratory Sciences, University of Delaware, Newark, DE, USA
| | - Girish C Shukla
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State Univesity, Cleveland, OH, USA
| | - Michelle T Paulsen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Mats Ljungman
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rolf Backofen
- Department of Computer Science and Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Cenk S Sahinalp
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA.,Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | | | | | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Breast Oncology Program, University of Michigan, Ann Arbor, MI, USA.,Departments of Radiation Oncology, Urology, and Medicine, Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Rohit Malik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Bristol-Myers Squibb, Princeton, NJ, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA. .,Department of Pathology, University of Michigan, Ann Arbor, MI, USA. .,Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA. .,Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA. .,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA. .,Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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17
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Hosono Y, Niknafs YS, Prensner JR, Iyer MK, Dhanasekaran SM, Mehra R, Pitchiaya S, Tien J, Escara-Wilke J, Poliakov A, Chu SC, Saleh S, Sankar K, Su F, Guo S, Qiao Y, Freier SM, Bui HH, Cao X, Malik R, Johnson TM, Beer DG, Feng FY, Zhou W, Chinnaiyan AM. Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. Cell 2017; 171:1559-1572.e20. [PMID: 29245011 PMCID: PMC5734106 DOI: 10.1016/j.cell.2017.11.040] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/29/2017] [Accepted: 11/20/2017] [Indexed: 01/16/2023]
Abstract
Large-scale transcriptome sequencing efforts have vastly expanded the catalog of long non-coding RNAs (lncRNAs) with varying evolutionary conservation, lineage expression, and cancer specificity. Here, we functionally characterize a novel ultraconserved lncRNA, THOR (ENSG00000226856), which exhibits expression exclusively in testis and a broad range of human cancers. THOR knockdown and overexpression in multiple cell lines and animal models alters cell or tumor growth supporting an oncogenic role. We discovered a conserved interaction of THOR with IGF2BP1 and show that THOR contributes to the mRNA stabilization activities of IGF2BP1. Notably, transgenic THOR knockout produced fertilization defects in zebrafish and also conferred a resistance to melanoma onset. Likewise, ectopic expression of human THOR in zebrafish accelerated the onset of melanoma. THOR represents a novel class of functionally important cancer/testis lncRNAs whose structure and function have undergone positive evolutionary selection.
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Affiliation(s)
- Yasuyuki Hosono
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - John R Prensner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Matthew K Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jean Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Anton Poliakov
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shih-Chun Chu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sahal Saleh
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Keerthana Sankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Malik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Timothy M Johnson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - David G Beer
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Weibin Zhou
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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18
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Pitchiaya S, Malik R, Cieslik M, Zhang Y, Jiang X, Chinnaiyan AM. Abstract 2549: A long non-coding RNA regulates the androgen receptor and mediates prostate cancer progression. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The pervasive expression of long non-coding RNAs (lncRNAs) and their roles in a plethora of cellular processes has revolutionized our understanding of functional genetic elements. Emerging evidence suggest that lncRNAs are promising cancer biomarkers and dysregulation of lncRNAs results in attenuated or accelerated oncogenic phenotypes. In support of these findings, recent reports from the Chinnaiyan lab suggest that lncRNAs can potentially drive and act as independent predictors of aggressive prostate cancer (PCa). Central to PCa progression is the androgen receptor (AR), a nuclear hormone receptor, and the dysregulated transcription program it mediates. Consequently, androgen deprivation therapy (ADT) supplemented with anti-androgens is the initial standard-of-care in treating advanced PCa. Yet, the disease often manifests as a lethal, hormone-refractory castration-resistant prostate cancer (CRPC) after initial ADT and this phenomenon is linked to the resumption of AR activity. Therefore, we sought to identify novel and therapeutically actionable targets of AR that can detect the onset of PCa or stratify PCa variants. To this end, our lab recently characterized the transcriptional landscape of cancer and discovered > 50,000 novel transcripts, a significant fraction of which were tissue- and cancer-specific lncRNAs. Using this updated transcriptome as a reference and performing RNA-seq on PCa cells stimulated with dihydrotestosterone (an androgen), we identified Androgen Receptor regulated lncRNA-1 (ARlnc1) as an important PCa-specific, AR-regulated lncRNA that reciprocally regulates AR. By employing single-molecule fluorescence in situ hybridization (smFISH), we find that ARlnc1 and AR transcripts colocalize within the nucleus of PCa cells and that ARlnc1 promotes transcription of AR. Moreover, we found that ARlnc1 interacts with anti-apoptotic, stress-granule related proteins and regulates PCa cell proliferation in vitro and in mouse xenografts. We have additionally found that anti-sense oligonucleotides (ASOs) that target this lncRNA can reduce tumor growth in xenograft models. Taken together, our data suggests that ARlnc1 and AR reciprocally and positively modulate each other to promote PCa progression and that ARlnc1 may serve as an enhancer RNA that regulates AR transcription. Our data suggests that ARlnc1 can be therapeutically targeted to orthogonally modulate the AR signaling axis for PCa treatment.
Citation Format: Sethuramasundaram Pitchiaya, Rohit Malik, Marcin Cieslik, Yajia Zhang, Xia Jiang, Arul M. Chinnaiyan. A long non-coding RNA regulates the androgen receptor and mediates prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2549. doi:10.1158/1538-7445.AM2017-2549
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Affiliation(s)
| | - Rohit Malik
- Univ. of Michigan Comp. Cancer Ctr., Ann Arbor, MI
| | | | - Yajia Zhang
- Univ. of Michigan Comp. Cancer Ctr., Ann Arbor, MI
| | - Xia Jiang
- Univ. of Michigan Comp. Cancer Ctr., Ann Arbor, MI
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19
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Wang X, Qiao Y, Asangani IA, Ateeq B, Poliakov A, Cieślik M, Pitchiaya S, Chakravarthi BVSK, Cao X, Jing X, Wang CX, Apel IJ, Wang R, Tien JCY, Juckette KM, Yan W, Jiang H, Wang S, Varambally S, Chinnaiyan AM. Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer. Cancer Cell 2017; 31:844-847. [PMID: 28609659 DOI: 10.1016/j.ccell.2017.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Pitchiaya S, Heinicke LA, Park JI, Cameron EL, Walter NG. Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution. Cell Rep 2017; 19:630-642. [PMID: 28423324 PMCID: PMC5482240 DOI: 10.1016/j.celrep.2017.03.075] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/17/2017] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
Regulation of microRNA (miRNA) localization and stability is critical for their extensive cytoplasmic RNA silencing activity and emerging nuclear functions. Here, we have developed single-molecule fluorescence-based tools to assess the subcellular trafficking, integrity, and activity of miRNAs. We find that seed-matched RNA targets protect miRNAs against degradation and enhance their nuclear retention. While target-stabilized, functional, cytoplasmic miRNAs reside in high-molecular-weight complexes, nuclear miRNAs, as well as cytoplasmic miRNAs targeted by complementary anti-miRNAs, are sequestered stably within significantly lower-molecular-weight complexes and rendered repression incompetent. miRNA stability and activity depend on Argonaute protein abundance, whereas miRNA strand selection, unwinding, and nuclear retention depend on Argonaute identity. Taken together, our results show that miRNA degradation competes with Argonaute loading and target binding to control subcellular miRNA abundance for gene silencing surveillance. Probing single cells for miRNA activity, trafficking, and metabolism promises to facilitate screening for effective miRNA mimics and anti-miRNA drugs.
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Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A Heinicke
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Jun I Park
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Elizabeth L Cameron
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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21
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Wang X, Qiao Y, Asangani IA, Ateeq B, Poliakov A, Cieślik M, Pitchiaya S, Chakravarthi BVSK, Cao X, Jing X, Wang CX, Apel IJ, Wang R, Tien JCY, Juckette KM, Yan W, Jiang H, Wang S, Varambally S, Chinnaiyan AM. Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer. Cancer Cell 2017; 31:532-548.e7. [PMID: 28344039 PMCID: PMC5443258 DOI: 10.1016/j.ccell.2017.02.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/19/2017] [Accepted: 02/24/2017] [Indexed: 12/12/2022]
Abstract
Transcription factors play a key role in the development of diverse cancers, and therapeutically targeting them has remained a challenge. In prostate cancer, the gene encoding the transcription factor ERG is recurrently rearranged and plays a critical role in prostate oncogenesis. Here, we identified a series of peptides that interact specifically with the DNA binding domain of ERG. ERG inhibitory peptides (EIPs) and derived peptidomimetics bound ERG with high affinity and specificity, leading to proteolytic degradation of the ERG protein. The EIPs attenuated ERG-mediated transcription, chromatin recruitment, protein-protein interactions, cell invasion and proliferation, and tumor growth. Thus, peptidomimetic targeting of transcription factor fusion products may provide a promising therapeutic strategy for prostate cancer as well as other malignancies.
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Affiliation(s)
- Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Irfan A Asangani
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Bushra Ateeq
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, UP, India
| | - Anton Poliakov
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Balabhadrapatruni V S K Chakravarthi
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Cynthia X Wang
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Ingrid J Apel
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Kristin M Juckette
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Wei Yan
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sooryanarayana Varambally
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, 1400 East Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA.
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22
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Rossiello F, Aguado J, Sepe S, Iannelli F, Nguyen Q, Pitchiaya S, Carninci P, d'Adda di Fagagna F. DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nat Commun 2017; 8:13980. [PMID: 28239143 PMCID: PMC5473644 DOI: 10.1038/ncomms13980] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/17/2016] [Indexed: 12/23/2022] Open
Abstract
The DNA damage response (DDR) is a set of cellular events that follows the generation of DNA damage. Recently, site-specific small non-coding RNAs, also termed DNA damage response RNAs (DDRNAs), have been shown to play a role in DDR signalling and DNA repair. Dysfunctional telomeres activate DDR in ageing, cancer and an increasing number of identified pathological conditions. Here we show that, in mammals, telomere dysfunction induces the transcription of telomeric DDRNAs (tDDRNAs) and their longer precursors from both DNA strands. DDR activation and maintenance at telomeres depend on the biogenesis and functions of tDDRNAs. Their functional inhibition by sequence-specific antisense oligonucleotides allows the unprecedented telomere-specific DDR inactivation in cultured cells and in vivo in mouse tissues. In summary, these results demonstrate that tDDRNAs are induced at dysfunctional telomeres and are necessary for DDR activation and they validate the viability of locus-specific DDR inhibition by targeting DDRNAs.
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Affiliation(s)
- Francesca Rossiello
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Julio Aguado
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sara Sepe
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Fabio Iannelli
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Quan Nguyen
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fabrizio d'Adda di Fagagna
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
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23
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Shankar S, Pitchiaya S, Malik R, Kothari V, Hosono Y, Yocum AK, Gundlapalli H, White Y, Firestone A, Cao X, Dhanasekaran SM, Stuckey J, Bollag G, Shannon K, Walter N, Kumar-Sinha C, Chinnaiyan AM. Abstract LB-008: KRAS engages AGO2 to enhance cellular transformation. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oncogenic mutations in RAS provide a compelling yet intractable therapeutic target. Approximately 30% of all cancers harbor activating mutations in the RAS family of small GTPase proteins, making it one of the most common oncogenic aberrations in humans. Normal RAS proteins (H, K or N-RAS) localize to the inner cell membrane and transduce extracellular growth signals by cycling between an “active” GTP-bound state and “inactive” GDP-bound state. Our understanding of RAS biology is primarily from RAS protein-effector interactions that activate a variety of effectors at the plasma membrane like RAF/PI3K/RalGDS. Yet, targeting mutant RAS proteins or its effectors / pathways remains a challenging endeavor for treating RAS driven cancers.
For a comprehensive identification of RAS interactors, we recently performed co-immunoprecipitation (Co-IP) Mass Spectrometric analysis of RAS immunoprecipitates from multiple cancer cell lines with differing KRAS mutation status. In all the cell lines studies, we uncovered an interaction between RAS and the core component of the RNA silencing machinery, Argonaute 2 (AGO2). Endogenously expressed RAS and AGO2 co-sediment and co-localize in intracellular membrane bound endoplasmic reticulum. AGO2 binds the Switch II region in KRAS, irrespective of GDP/GTP bound to RAS. Both endogenous and overexpressed mutant forms of KRAS, attenuate AGO2 related gene silencing function. Using NIH3T3 AGO2-/- cells, we demonstrate that the RAS-AGO2 interaction is required for maximal mutant KRAS expression and cellular transformation. Overall, our studies suggest that through its interaction with AGO2, RAS function extends well beyond its canonical role in intracellular signaling. We will present detailed characterization of the RAS-AGO2 interaction and its functional aspects that we have discovered so far.
Citation Format: Sunita Shankar, Sethuramasundaram Pitchiaya, Rohit Malik, Vishal Kothari, Yasuyuki Hosono, Anastasia K. Yocum, Harika Gundlapalli, Yasmine White, Ari Firestone, Xuhong Cao, Saravana M. Dhanasekaran, Jeanne Stuckey, Gideon Bollag, Kevin Shannon, Nils Walter, Chandan Kumar-Sinha, Arul M. Chinnaiyan. KRAS engages AGO2 to enhance cellular transformation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-008.
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Affiliation(s)
| | | | | | | | | | | | | | - Yasmine White
- 2University of California, San Francisco, San Francisco, CA
| | - Ari Firestone
- 2University of California, San Francisco, San Francisco, CA
| | | | | | | | | | - Kevin Shannon
- 2University of California, San Francisco, San Francisco, CA
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Malik R, Zhang Y, Cieslik M, Niknafs YS, Pitchiaya S, Hosono Y, Subramaniam S, Yazdani S, Cao X, Robinson D, Chinnaiyan A. Abstract 983: Integrative analysis of androgen receptor regulated long non-coding RNA in prostate cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Androgen receptor (AR) plays a critical role in the development and progression of prostate cancer. AR regulates a large repertoire of genes; however, the effect of androgen signaling on the regulation of long non-coding RNAs (lncRNA) remains incompletely understood. Using transcriptome sequencing (RNA-seq) of AR-positive cell lines VCaP and LNCaP treated with dihydroxytestosterone (DHT), we identified genes, including lncRNAs, which were strongly regulated by AR. To confirm direct regulation by AR, we interrogated AR-ChIP-seq data from VCaP and LNCaP cells, identifying the lncRNAs with direct AR binding. Existence of these lncRNAs in prostate cancer tissue samples was confirmed by analysis of RNA-seq data from prostate tumors, and the degree of differential expression in prostate tumors (localized and castration resistant metastases) versus benign was determined. The most highly overexpressed lncRNA in this analysis was a 2.7kb multi-exonic transcript present on chromosome 16 called ARlnc1. RACE was utilized to determine the exact exon structure of this gene, and its expression levels in various prostate cancer cell lines as well as independent prostate cancer tissue cohorts was assessed. Further, knockdown of ARlnc1 in AR dependent cell lines inhibited cell proliferation and induced apoptosis. Knockdown of ARlnc1 affected molecular signatures related to cell cycle, mitosis and DNA damage. Interestingly, ARlnc1 knockdown also suppressed global androgen signaling as determined by Gene set enrichment analysis using AR gene signature. Upon investigation of the mechanism through which PRCAT47 regulate AR signaling, we discovered that ARlnc1 regulates AR at the level of translation. Taken together, our data suggests that many lncRNAs are regulated by androgen signaling, and we identify one such lncRNA that is involved in a protein-lncRNA positive feedback loop.
Citation Format: Rohit Malik, Yajia Zhang, Marcin Cieslik, Yashar S. Niknafs, Sethuramasundaram Pitchiaya, Yasuyuki Hosono, Shruthi Subramaniam, Sahr Yazdani, Xuhong Cao, Dan Robinson, Arul Chinnaiyan. Integrative analysis of androgen receptor regulated long non-coding RNA in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 983.
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Shankar S, Malik R, Kothari V, Hosono Y, Pitchiaya S, Kalyana-Sundaram S, Yocum A, Escara-Wilke J, Gundlapalli H, Chinnaswamy K, Shuler M, Poliakov A, Wang X, Krishnan V, White Y, Firestone A, Cao X, Dhanasekaran SM, Stuckey J, Bollag G, Shannon K, Walter NG, Kumar-Sinha C, Chinnaiyan A. Abstract LB-058: Novel interactions of the RAS oncoprotein. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Approximately 30% of all cancers harbor activating mutations in the RAS family of small GTPase proteins, making it one of the most common oncogenic aberrations in humans. Normal RAS proteins (H, K or N-RAS) localize to the inner cell membrane and transduce extracellular growth signals by cycling between an “active” GTP-bound state and “inactive” GDP-bound state, through interactions with various “GTPase activating proteins” (GAPs) that promote RAS mediated GTP hydrolysis. Oncogenic mutants of RAS lose their catalytic activity or association with the GAP proteins, resulting in constitutively active GTP-bound state that signals through direct interactions with effector kinases like RAF and PI3K and activate the MEK/ERK and/or Akt, leading to activation of hallmark cancer pathways including growth factor independence, uncontrolled cell proliferation, evasion of apoptosis and immune responses, increased metabolism as well as metastases. Although RAS is the most frequently mutated gene driving multifarious pathways of oncogenesis, our knowledge of protein interactions involving RAS proteins have been largely limited to RAS binding domains in RAF/PI3K/RalGDS. Targeting mutant RAS proteins or its direct effectors, or pathways activated by RAS effectors remains a challenging endeavor for treating RAS driven cancers.
Towards the goal of a thorough understanding of RAS biology through a comprehensive identification of its interactors, we performed IP-Mass Spectrometric analysis of pan-RAS immunoprecipitates from multiple cell lines. Interestingly in our experiments, apart from the well-known interactor RAF, we found evidence of several novel RAS interacting proteins, including many with DNA and RNA binding motifs. Our study validates these findings through cell-free protein interaction analyses and explores the possible biological effects of these novel RAS interactions in mutant KRAS driven cellular transformation.
Note: This abstract was not presented at the meeting.
Citation Format: Sunita Shankar, Rohit Malik, Vishal Kothari, Yasuyuki Hosono, Sethuramasundaram Pitchiaya, Shanker Kalyana-Sundaram, Anastasia Yocum, June Escara-Wilke, Harika Gundlapalli, Krishnapriya Chinnaswamy, Matthew Shuler, Anton Poliakov, Xiaoju Wang, Vishalakshi Krishnan, Yasmine White, Ari Firestone, Xuhong Cao, Saravana M. Dhanasekaran, Jeanne Stuckey, Gideon Bollag, Kevin Shannon, Nils G. Walter, Chandan Kumar-Sinha, Arul Chinnaiyan. Novel interactions of the RAS oncoprotein. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-058. doi:10.1158/1538-7445.AM2015-LB-058
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Bartke RM, Cameron EL, Cristie-David AS, Custer TC, Denies MS, Daher M, Dhakal S, Ghosh S, Heinicke LA, Hoff JD, Hou Q, Kahlscheuer ML, Karslake J, Krieger AG, Li J, Li X, Lund PE, Vo NN, Park J, Pitchiaya S, Rai V, Smith DJ, Suddala KC, Wang J, Widom JR, Walter NG. Meeting report: SMART timing--principles of single molecule techniques course at the University of Michigan 2014. Biopolymers 2015; 103:296-302. [PMID: 25546606 PMCID: PMC4613745 DOI: 10.1002/bip.22603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 12/17/2014] [Indexed: 11/07/2022]
Abstract
Four days after the announcement of the 2014 Nobel Prize in Chemistry for "the development of super-resolved fluorescence microscopy" based on single molecule detection, the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan hosted a "Principles of Single Molecule Techniques 2014" course. Through a combination of plenary lectures and an Open House at the SMART Center, the course took a snapshot of a technology with an especially broad and rapidly expanding range of applications in the biomedical and materials sciences. Highlighting the continued rapid emergence of technical and scientific advances, the course underscored just how brightly the future of the single molecule field shines.
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Affiliation(s)
- Rebecca M Bartke
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055
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Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N, Dosch J, Van Dort ME, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, Rehemtulla A. The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling. Sci Signal 2015; 8:ra1. [PMID: 25564677 DOI: 10.1126/scisignal.2005379] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transforming growth factor-β (TGF-β) signaling regulates cell proliferation and differentiation, which contributes to development and disease. Upon binding TGF-β, the type I receptor (TGFBRI) binds TGFBRII, leading to the activation of the transcription factors SMAD2 and SMAD3. Using an RNA interference screen of the human kinome and a live-cell reporter for TGFBR activity, we identified the kinase BUB1 (budding uninhibited by benzimidazoles-1) as a key mediator of TGF-β signaling. BUB1 interacted with TGFBRI in the presence of TGF-β and promoted the heterodimerization of TGFBRI and TGFBRII. Additionally, BUB1 interacted with TGFBRII, suggesting the formation of a ternary complex. Knocking down BUB1 prevented the recruitment of SMAD3 to the receptor complex, the phosphorylation of SMAD2 and SMAD3 and their interaction with SMAD4, SMAD-dependent transcription, and TGF-β-mediated changes in cellular phenotype including epithelial-mesenchymal transition (EMT), migration, and invasion. Knockdown of BUB1 also impaired noncanonical TGF-β signaling mediated by the kinases AKT and p38 MAPK (mitogen-activated protein kinase). The ability of BUB1 to promote TGF-β signaling depended on the kinase activity of BUB1. A small-molecule inhibitor of the kinase activity of BUB1 (2OH-BNPP1) and a kinase-deficient mutant of BUB1 suppressed TGF-β signaling and formation of the ternary complex in various normal and cancer cell lines. 2OH-BNPP1 administration to mice bearing lung carcinoma xenografts reduced the amount of phosphorylated SMAD2 in tumor tissue. These findings indicated that BUB1 functions as a kinase in the TGF-β pathway in a role beyond its established function in cell cycle regulation and chromosome cohesion.
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Affiliation(s)
- Shyam Nyati
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katerina Chekhovskiy
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Areeb Chator
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nauman Chaudhry
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph Dosch
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcian E Van Dort
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mukesh Kumar Nyati
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brian Dale Ross
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
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Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N, Dosch J, Dort MEV, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, Rehemtulla A. Abstract 1137: Bub1 is a key regulator of TGF-β signaling. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The transforming growth factor-beta (TGF-β) family of cytokines regulates many processes such as immune suppression, angiogenesis, wound healing and epithelial to mesenchymal transition (EMT. Early in tumorigenesis, when epithelial cells retain exquisite growth sensitivity to this ligand, TGF-β signaling elicits a tumor suppressing activity. However, transformed cells become refractory to TGF-β-mediated growth inhibition and acquire a phenotype wherein the intracellular signaling circuitry of the cells is altered, leading to tumorigenic and metastatic effects in response to TGF-β exposure. Although TGF-β activating pathways have been studied, the molecular participants are poorly defined. Here we identify budding uninhibited by benzimidazoles-1 (Bub1) as an integral component of canonical and non-canonical TGF-β signaling pathways, where Bub1 is required for TGFBRI-TGFBRII complex formation and activation. Bub1-depleted cells exhibited reductions in TGF-β dependent Smad2/3 phosphorylation, recruitment of Smad2/3 to the TGFBRI-II complex, PI3K/Akt and p38MAPK activation, Smad binding element driven promoter activity (SBE4-Luc), and invasion and migration. Furthermore, a targeted small molecule inhibitor of Bub1 kinase activity (2OH-BNPP1), as well as an inactive kinase mutant of Bub1, abrogated ligand mediated TGF-β signaling and phenotypic response. These studies demonstrate a role for the Bub1 kinase in mediating TGF-β dependent signaling beyond its established function in cell-cycle regulation and chromosome cohesion and uncover the underlying basis for the pleiotropic cellular response commonly observed upon activation of the pathway.
Citation Format: Shyam Nyati, Katrina Schinske-Sebolt, Sethuramasundaram Pitchiaya, Katerina Chekhovskiy, Areeb Chator, Nauman Chaudhry, Joseph Dosch, Marcian E. Van Dort, Varambally, Kumar-Sinha, Nyati, Ray, Walter, Sooryanarayana Varambally, Chandan Kumar-Sinha, Mukesh K. Nyati, Dipankar Ray, Nils G. Walter, Hongtao Yu, Brian D. Ross, Alnawaz Rehemtulla. Bub1 is a key regulator of TGF-β signaling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1137. doi:10.1158/1538-7445.AM2014-1137
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Affiliation(s)
- Shyam Nyati
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | - Areeb Chator
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | - Joseph Dosch
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | | | - Dipankar Ray
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | - Hongtao Yu
- 3University of Texas Southwestern Medical Center, Dallas, TX
| | - Brian D. Ross
- 1University of Michigan Medical School, Ann Arbor, MI
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Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Pitchiaya S, Krishnan V, Custer TC, Walter NG. Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting. Methods 2013; 63:188-99. [PMID: 23820309 PMCID: PMC3797162 DOI: 10.1016/j.ymeth.2013.05.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/17/2013] [Accepted: 05/18/2013] [Indexed: 12/28/2022] Open
Abstract
Non-coding RNAs (ncRNAs) recently were discovered to outnumber their protein-coding counterparts, yet their diverse functions are still poorly understood. Here we report on a method for the intracellular Single-molecule High-Resolution Localization and Counting (iSHiRLoC) of microRNAs (miRNAs), a conserved, ubiquitous class of regulatory ncRNAs that controls the expression of over 60% of all mammalian protein coding genes post-transcriptionally, by a mechanism shrouded by seemingly contradictory observations. We present protocols to execute single particle tracking (SPT) and single-molecule counting of functional microinjected, fluorophore-labeled miRNAs and thereby extract diffusion coefficients and molecular stoichiometries of micro-ribonucleoprotein (miRNP) complexes from living and fixed cells, respectively. This probing of miRNAs at the single molecule level sheds new light on the intracellular assembly/disassembly of miRNPs, thus beginning to unravel the dynamic nature of this important gene regulatory pathway and facilitating the development of a parsimonious model for their obscured mechanism of action.
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Affiliation(s)
| | - Vishalakshi Krishnan
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Ma J, Liu Z, Michelotti N, Pitchiaya S, Veerapaneni R, Androsavich JR, Walter NG, Yang W. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun 2013; 4:2414. [PMID: 24008311 PMCID: PMC3800679 DOI: 10.1038/ncomms3414] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022] Open
Abstract
The flow of genetic information is regulated by selective nucleocytoplasmic transport of messenger RNA:protein complexes (mRNPs) through the nuclear pore complexes (NPCs) of eukaryotic cells. However, the three-dimensional (3D) pathway taken by mRNPs as they transit through the NPC, and the kinetics and selectivity of transport, remain obscure. Here we employ single-molecule fluorescence microscopy with an unprecedented spatiotemporal accuracy of 8 nm and 2 ms to provide new insights into the mechanism of nuclear mRNP export in live human cells. We find that mRNPs exiting the nucleus are decelerated and selected at the centre of the NPC, and adopt a fast-slow-fast diffusion pattern during their brief, ~12 ms, interaction with the NPC. A 3D reconstruction of the export route indicates that mRNPs primarily interact with the periphery on the nucleoplasmic side and in the centre of the NPC, without entering the central axial conduit utilized for passive diffusion of small molecules, and eventually dissociate on the cytoplasmic side.
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Affiliation(s)
- Jiong Ma
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Zhen Liu
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Nicole Michelotti
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ram Veerapaneni
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - John R. Androsavich
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Pitchiaya S, Androsavich JR, Walter NG. Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO Rep 2012; 13:709-15. [PMID: 22688967 PMCID: PMC3410386 DOI: 10.1038/embor.2012.85] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 05/13/2012] [Accepted: 05/16/2012] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) associate with components of the RNA-induced silencing complex (RISC) to assemble on mRNA targets and regulate protein expression in higher eukaryotes. Here we describe a method for the intracellular single-molecule, high-resolution localization and counting (iSHiRLoC) of miRNAs. Microinjected, singly fluorophore-labelled, functional miRNAs were tracked within diffusing particles, a majority of which contained single such miRNA molecules. Mobility and mRNA-dependent assembly changes suggest the existence of two kinetically distinct pathways for miRNA assembly, revealing the dynamic nature of this important gene regulatory pathway. iSHiRLOC achieves an unprecedented resolution in the visualization of functional miRNAs, paving the way to understanding RNA silencing through single-molecule systems biology.
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Affiliation(s)
| | - John R Androsavich
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, Michigan 48109-1055, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, Michigan 48109-1055, USA
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Kuszak AJ, Pitchiaya S, Anand JP, Mosberg HI, Walter NG, Sunahara RK. Purification and functional reconstitution of monomeric mu-opioid receptors: allosteric modulation of agonist binding by Gi2. J Biol Chem 2009; 284:26732-41. [PMID: 19542234 DOI: 10.1074/jbc.m109.026922] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite extensive characterization of the mu-opioid receptor (MOR), the biochemical properties of the isolated receptor remain unclear. In light of recent reports, we proposed that the monomeric form of MOR can activate G proteins and be subject to allosteric regulation. A mu-opioid receptor fused to yellow fluorescent protein (YMOR) was constructed and expressed in insect cells. YMOR binds ligands with high affinity, displays agonist-stimulated [(35)S]guanosine 5'-(gamma-thio)triphosphate binding to Galpha(i), and is allosterically regulated by coupled G(i) protein heterotrimer both in insect cell membranes and as purified protein reconstituted into a phospholipid bilayer in the form of high density lipoprotein particles. Single-particle imaging of fluorescently labeled receptor indicates that the reconstituted YMOR is monomeric. Moreover, single-molecule imaging of a Cy3-labeled agonist, [Lys(7), Cys(8)]dermorphin, illustrates a novel method for studying G protein-coupled receptor-ligand binding and suggests that one molecule of agonist binds per monomeric YMOR. Together these data support the notion that oligomerization of the mu-opioid receptor is not required for agonist and antagonist binding and that the monomeric receptor is the minimal functional unit in regard to G protein activation and strong allosteric regulation of agonist binding by G proteins.
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Affiliation(s)
- Adam J Kuszak
- Departments of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Pitchiaya S, Androsavich JR, Sobhy MA, Walter NG. Small RNA, Big Impact: Probing miRNA pathways in living cells using single particle tracking. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.665.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Nils G Walter
- Department of ChemistryUniversity of MichiganAnn ArborMI
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Abstract
For the most part DNA was considered Nature's instruction manual for life leading to the popular description 'blueprint of life'. However, DNA is now taking on a new aspect where it is finding use as a construction element for architecture on the nanoscale. This tutorial review addresses the importance of building ordered structures with DNA on the nanoscale, the underlying principles and approaches to build such scaffolds, the current limitations and the anticipated trajectory of the area. This is would be of interest to the chemical biology, supramolecular and bioengineering communities in particular.
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