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Gallegos KM, Patel JR, Llopis SD, Walker RR, Davidson AM, Zhang W, Zhang K, Tilghman SL. Quantitative Proteomic Profiling Identifies a Potential Novel Chaperone Marker in Resistant Breast Cancer. Front Oncol 2021; 11:540134. [PMID: 33718123 PMCID: PMC7951058 DOI: 10.3389/fonc.2021.540134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Development of aromatase inhibitor resistant breast cancer among postmenopausal women continues to be a major clinical obstacle. Previously, our group demonstrated that as breast cancer cells transition from hormone-dependent to hormone-independent, they are associated with increased growth factor signaling, enhanced cellular motility, and the epithelial to mesenchymal transition (EMT). Given the complexity of cancer stem cells (CSC) and their implications on endocrine resistance and EMT, we sought to understand their contribution towards the development of aromatase inhibitor resistant breast cancer. Cells cultured three dimensionally as mammospheres are enriched for CSCs and more accurately recapitulates tumors in vivo. Therefore, a global proteomic analysis was conducted using letrozole resistant breast cancer cells (LTLT-Ca) mammospheres and compared to their adherent counterparts. Results demonstrated over 1000 proteins with quantitative abundance ratios were identified. Among the quantified proteins, 359 were significantly altered (p < 0.05), where 173 were upregulated and 186 downregulated (p < 0.05, fold change >1.20). Notably, midasin, a chaperone protein required for maturation and nuclear export of the pre-60S ribosome was increased 35-fold. Protein expression analyses confirmed midasin is ubiquitously expressed in normal tissue but is overexpressed in lobular and ductal breast carcinoma tissue as well as ER+ and ER- breast cancer cell lines. Functional enrichment analyses indicated that 19 gene ontology terms and one KEGG pathway were over-represented by the down-regulated proteins and both were associated with protein synthesis. Increased midasin was strongly correlated with decreased relapse free survival in hormone independent breast cancer. For the first time, we characterized the global proteomic signature of CSC-enriched letrozole-resistant cells associated with protein synthesis, which may implicate a role for midasin in endocrine resistance.
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Affiliation(s)
- Karen M Gallegos
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Jankiben R Patel
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Shawn D Llopis
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Rashidra R Walker
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - A Michael Davidson
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Wensheng Zhang
- Division of Mathematical and Physical Sciences, Department of Computer Science, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA, United States
| | - Kun Zhang
- Division of Mathematical and Physical Sciences, Department of Computer Science, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA, United States
| | - Syreeta L Tilghman
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
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Orlacchio A, Stark AE, Foray C, Amari F, Sheetz T, Reese E, Tessari A, La Perle K, Palmieri D, Tsichlis PN, Coppola V. Genetic ablation of interacting with Spt6 (Iws1) causes early embryonic lethality. PLoS One 2018; 13:e0201030. [PMID: 30208029 PMCID: PMC6135376 DOI: 10.1371/journal.pone.0201030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/06/2018] [Indexed: 01/12/2023] Open
Abstract
IWS1 is an RNA-polymerase II (RNAPII)-associated transcription elongation factor whose biological functions are poorly characterized. To shed some light on the function of this protein at the organismal level, we performed a systematic tissue analysis of its expression and generated Iws1-deficient mice. A thorough immunohistochemical characterization shows that IWS1 protein is present in the nucleus of all cells in most of the examined tissues, with few notable exceptions. We also report that ablation of Iws1 consistently causes lethality at the pre-implantation stage with high expression of the gene in fertilized oocytes. In summary, we are providing evidence that Iws1 is expressed in all adult organs and it is an essential gene for mouse embryonic development.
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Affiliation(s)
- Arturo Orlacchio
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Aaron E. Stark
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Genetically Engineered Mouse Modeling Core, The Ohio State University, Columbus, Ohio, United States of America
| | - Claudia Foray
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Foued Amari
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Genetically Engineered Mouse Modeling Core, The Ohio State University, Columbus, Ohio, United States of America
| | - Tyler Sheetz
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Erika Reese
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Krista La Perle
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Comparative Pathology & Mouse Phenotyping Shared Resource, Columbus, Ohio, United States of America
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Philip N. Tsichlis
- Molecular Oncology Research Institute, Tufts Medical School, Boston, MA, United States of America
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast. Biochem J 2017; 474:195-214. [PMID: 28062837 DOI: 10.1042/bcj20160516] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022]
Abstract
Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes. Here, we describe principles of ribosome assembly that have emerged from recent studies of biogenesis of the large ribosomal subunit in the yeast Saccharomyces cerevisiae We describe tools that have empowered investigations of ribosome biogenesis, and then summarize recent discoveries about each of the consecutive steps of subunit assembly.
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Molecular basis for protection of ribosomal protein L4 from cellular degradation. Nat Commun 2017; 8:14354. [PMID: 28148929 PMCID: PMC5296656 DOI: 10.1038/ncomms14354] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/19/2016] [Indexed: 12/26/2022] Open
Abstract
Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function to facilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery. Acl4 is a dedicated assembly chaperone for ribosomal protein RpL4 that recognizes RpL4 in the cytoplasm to facilitate its nuclear import. Here the authors reveal the mechanism whereby Acl4 recognizes RpL4 and functions to protect it from Tom1-mediated degradation until RpL4 incorporation into the maturing 60S pre-ribosomal subunit.
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Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat Struct Mol Biol 2017; 24:214-220. [PMID: 28112732 DOI: 10.1038/nsmb.3364] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/01/2023]
Abstract
A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. Here we used cryo-electron microscopy (cryo-EM) to characterize Saccharomyces cerevisiae pre-60S particles purified with epitope-tagged Nmd3. Our structural analysis indicates that these particles belong to a specific late stage of cytoplasmic pre-60S maturation in which ribosomal proteins uL16, uL10, uL11, eL40 and eL41 are deficient, but ribosome assembly factors Nmd3, Lsg1, Tif6 and Reh1 are present. Nmd3 and Lsg1 are located near the peptidyl-transferase center (PTC). In particular, Nmd3 recognizes the PTC in its near-mature conformation. In contrast, Reh1 is anchored to the exit of the polypeptide tunnel, with its C terminus inserted into the tunnel. These findings pinpoint a structural checkpoint role for Nmd3 in PTC assembly, and provide information about functional and mechanistic roles of these assembly factors in the maturation of the 60S ribosomal subunit.
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Pausch P, Singh U, Ahmed YL, Pillet B, Murat G, Altegoer F, Stier G, Thoms M, Hurt E, Sinning I, Bange G, Kressler D. Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Nat Commun 2015; 6:7494. [PMID: 26112308 PMCID: PMC4491177 DOI: 10.1038/ncomms8494] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/14/2015] [Indexed: 12/11/2022] Open
Abstract
Exponentially growing yeast cells produce every minute >160,000 ribosomal proteins. Owing to their difficult physicochemical properties, the synthesis of assembly-competent ribosomal proteins represents a major challenge. Recent evidence highlights that dedicated chaperone proteins recognize the N-terminal regions of ribosomal proteins and promote their soluble expression and delivery to the assembly site. Here we explore the intuitive possibility that ribosomal proteins are captured by dedicated chaperones in a co-translational manner. Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients (Rpl3, Rpl5, Rpl10 and Rps3). X-ray crystallography reveals how the N-terminal, rRNA-binding residues of Rpl10 are shielded by Sqt1's WD-repeat β-propeller, providing mechanistic insight into the incorporation of Rpl10 into pre-60S subunits. Co-translational capturing of nascent ribosomal proteins by dedicated chaperones constitutes an elegant mechanism to prevent unspecific interactions and aggregation of ribosomal proteins on their road to incorporation. The synthesis of ribosomes requires the orderly assembly of many proteins and large RNA molecules, a process that involves several assembly factors. Here the authors show that dedicated chaperones capture the N termini of specific nascent ribosomal proteins to promote folding and assembly into maturing ribosomes.
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Affiliation(s)
- Patrick Pausch
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Ujjwala Singh
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Yasar Luqman Ahmed
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Matthias Thoms
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
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