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Lv Y, Sun S, Zhang J, Wang C, Chen C, Zhang Q, Zhao J, Qi Y, Zhang W, Wang Y, Li M. Loss of RBM45 inhibits breast cancer progression by reducing the SUMOylation of IRF7 to promote IFNB1 transcription. Cancer Lett 2024; 596:216988. [PMID: 38797234 DOI: 10.1016/j.canlet.2024.216988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Type I interferons exhibit anti-proliferative and anti-cancer activities, but their detailed regulatory mechanisms in cancer have not been fully elucidated yet. RNA binding proteins are master orchestrators of gene regulation, which are closely related to tumor progression. Here we show that the upregulated RNA binding protein RBM45 correlates with poor prognosis in breast cancer. Depletion of RBM45 suppresses breast cancer progression both in cultured cells and xenograft mouse models. Mechanistically, RBM45 ablation inhibits breast cancer progression through regulating type I interferon signaling, particularly by elevating IFN-β production. Importantly, RBM45 recruits TRIM28 to IRF7 and stimulates its SUMOylation, thereby repressing IFNB1 transcription. Loss of RBM45 reduced the SUMOylation of IRF7 by reducing the interaction between TRIM28 and IRF7 to promote IFNB1 transcription, leading to the inhibition of breast cancer progression. Taken together, our finding uncovers a vital role of RBM45 in modulating type I interferon signaling and cancer aggressive progression, implicating RBM45 as a potential therapeutic target in breast cancer.
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Affiliation(s)
- Yuesheng Lv
- Department of Oncology of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China
| | - Siwen Sun
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chong Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chaoqun Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Qianyi Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China.
| | - Man Li
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
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2
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Qu S, Yang C, Sun X, Huang H, Li J, Zhu Y, Zhang Y, Li L, Liang H, Zen K. Blockade of pan-viral propagation by inhibition of host cell PNPT1. Int J Antimicrob Agents 2024; 63:107124. [PMID: 38412930 DOI: 10.1016/j.ijantimicag.2024.107124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/29/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
For successful viral propagation within infected cells, the virus needs to overcome the cellular integrated stress response (ISR), triggered during viral infection, which, in turn, inhibits general protein translation. This paper reports a tactic employed by viruses to suppress the ISR by upregulating host cell polyribonucleotide nucleotidyltransferase 1 (PNPT1). The propagation of adenovirus, murine cytomegalovirus and hepatovirus within their respective host cells induces PNPT1 expression. Notably, when PNPT1 is knocked down, the propagation of all three viruses is prevented. Mechanistically, the inhibition of PNPT1 facilitates the relocation of mitochondrial double-stranded RNAs (mt-dsRNAs) to the cytoplasm, where they activate RNA-activated protein kinase (PKR). This activation leads to eukaryotic initiation factor 2α (eIF2α) phosphorylation, resulting in the suppression of translation. Furthermore, by scrutinizing the PNPT1 recognition element and screening 17,728 drugs and bioactive compounds approved by the US Food and Drug Administration, lanatoside C was identified as a potent PNPT1 inhibitor. This compound impedes the propagation of adenovirus, murine cytomegalovirus and hepatovirus, and suppresses production of the severe acute respiratory syndrome coronavirus-2 spike protein. These discoveries shed light on a novel strategy to impede pan-viral propagation by activating the host cell mt-dsRNA-PKR-eIF2α signalling axis.
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Affiliation(s)
- Shuang Qu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Chen Yang
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xinlei Sun
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hai Huang
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiacheng Li
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yujie Zhu
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yaliang Zhang
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Limin Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hongwei Liang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China.
| | - Ke Zen
- Department of Gastroenterology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing, Jiangsu, China.
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Bragazzi Cunha J, Leix K, Sherman EJ, Mirabelli C, Frum T, Zhang CJ, Kennedy AA, Lauring AS, Tai AW, Sexton JZ, Spence JR, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in respiratory epithelial cells during SARS-CoV-2 infection. J Virol 2023; 97:e0127623. [PMID: 37975674 PMCID: PMC10734423 DOI: 10.1128/jvi.01276-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain unclear. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top four genes identified in our screen encode components of the same type I interferon (IFN-I) signaling complex—IFNAR1, IFNAR2, JAK1, and TYK2. The fifth gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response in both Calu-3 cells and iPSC-derived type 2 alveolar epithelial cells. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
- Juliana Bragazzi Cunha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Polynucleotide phosphorylase protects against renal tubular injury via blocking mt-dsRNA-PKR-eIF2α axis. Nat Commun 2023; 14:1223. [PMID: 36869030 PMCID: PMC9984537 DOI: 10.1038/s41467-023-36664-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Renal tubular atrophy is a hallmark of chronic kidney disease. The cause of tubular atrophy, however, remains elusive. Here we report that reduction of renal tubular cell polynucleotide phosphorylase (PNPT1) causes renal tubular translation arrest and atrophy. Analysis of tubular atrophic tissues from renal dysfunction patients and male mice with ischemia-reperfusion injuries (IRI) or unilateral ureteral obstruction (UUO) treatment shows that renal tubular PNPT1 is markedly downregulated under atrophic conditions. PNPT1 reduction leads to leakage of mitochondrial double-stranded RNA (mt-dsRNA) into the cytoplasm where it activates protein kinase R (PKR), followed by phosphorylation of eukaryotic initiation factor 2α (eIF2α) and protein translational termination. Increasing renal PNPT1 expression or inhibiting PKR activity largely rescues IRI- or UUO-induced mouse renal tubular injury. Moreover, tubular-specific PNPT1-knockout mice display Fanconi syndrome-like phenotypes with impaired reabsorption and significant renal tubular injury. Our results reveal that PNPT1 protects renal tubules by blocking the mt-dsRNA-PKR-eIF2α axis.
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Qin A. An anti-cancer surveillance by the interplay between interferon-beta and retinoblastoma protein RB1. Front Oncol 2023; 13:1173467. [PMID: 37182173 PMCID: PMC10174298 DOI: 10.3389/fonc.2023.1173467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Interferon-beta (IFN-β), an extracellular cytokine that initiates signaling pathways for gene regulation, has been demonstrated to function as a tumor suppressor protein through lentiviral gene transduction. In this article, I review the relevant previous works and propose a cell cycle-based, tumor suppressor protein-mediated mechanism of anti-cancer surveillance. IFN-β induces a tumor cell cycle alteration that leads to S phase accumulation, senescence entry, and a loss of tumorigenicity in solid tumor cells. IFN-β does not show a significant cell cycle effect in their normal counterparts. Retinoblastoma protein RB1, another tumor suppressor protein, tightly controls the cell cycle and differentiation of normal cells, preventing them from being significantly impacted by the IFN-β effect. The interplay between IFN-β and RB1 acts as a mechanism of cell cycle-based, tumor suppressor protein-mediated anti-cancer surveillance that can selectively suppress solid tumor or proliferating transformed cells from the loss of control leading to cancer. This mechanism has important implications for the treatment of solid tumors.
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6
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de Rooij LA, Mastebroek DJ, ten Voorde N, van der Wall E, van Diest PJ, Moelans CB. The microRNA Lifecycle in Health and Cancer. Cancers (Basel) 2022; 14:cancers14235748. [PMID: 36497229 PMCID: PMC9736740 DOI: 10.3390/cancers14235748] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ~22 nucleotides that regulate gene expression at the post-transcriptional level. They can bind to around 60% of all protein-coding genes with an average of 200 targets per miRNA, indicating their important function within physiological and pathological cellular processes. miRNAs can be quickly produced in high amounts through canonical and non-canonical pathways that involve a multitude of steps and proteins. In cancer, miRNA biogenesis, availability and regulation of target expression can be altered to promote tumour progression. This can be due to genetic causes, such as single nucleotide polymorphisms, epigenetic changes, differences in host gene expression, or chromosomal remodelling. Alternatively, post-transcriptional changes in miRNA stability, and defective or absent components and mediators of the miRNA-induced silencing complex can lead to altered miRNA function. This review provides an overview of the current knowledge on the lifecycle of miRNAs in health and cancer. Understanding miRNA function and regulation is fundamental prior to potential future application of miRNAs as cancer biomarkers.
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Affiliation(s)
- Laura Adriana de Rooij
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-887-556-557
| | - Dirk Jan Mastebroek
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nicky ten Voorde
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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7
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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8
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Astrocyte Control of Zika Infection Is Independent of Interferon Type I and Type III Expression. BIOLOGY 2022; 11:biology11010143. [PMID: 35053142 PMCID: PMC8772967 DOI: 10.3390/biology11010143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary Zika virus (ZIKV) is a mosquito-borne virus first isolated from the Zika forest, Uganda, in 1947, which has been spreading across continents since then. We now know ZIKV causes both microencephaly in newborns and neurological complications in adults; however, no effective treatment options have yet been found. A more complete understanding of Zika-infection-mediated pathogenesis and host responses is required to enable the development of novel treatment strategies. In this study, efforts were made to elucidate the host responses following Zika virus infection using several astrocyte cell models, as astrocytes are a major cell type within the central nervous system (CNS) with significant antiviral ability. Our data suggest that astrocytes can resist ZIKV both in an interferon type I- and III-independent manner and suggest that an early and more diverse antiviral response may be more effective in controlling Zika infection. This study also identifies astrocyte cellular models that appear to display differential abilities in the control of viral infection, which may assist in the study of alternate neurotropic virus infections. Overall, this work adds to the growing body of knowledge surrounding ZIKV-mediated cellular host interactions and will contribute to a better understanding of ZIKV-mediated pathogenesis. Abstract Zika virus (ZIKV) is a pathogenic neurotropic virus that infects the central nervous system (CNS) and results in various neurological complications. Astrocytes are the dominant CNS cell producer of the antiviral cytokine IFN-β, however little is known about the factors involved in their ability to mediate viral infection control. Recent studies have displayed differential responses in astrocytes to ZIKV infection, and this study sought to elucidate astrocyte cell-specific responses to ZIKV using a variety of cell models infected with either the African (MR766) or Asian (PRVABC59) ZIKV strains. Expression levels of pro-inflammatory (TNF-α and IL-1β) and inflammatory (IL-8) cytokines following viral infection were low and mostly comparable within the ZIKV-resistant and ZIKV-susceptible astrocyte models, with better control of proinflammatory cytokines displayed in resistant astrocyte cells, synchronising with the viral infection level at specific timepoints. Astrocyte cell lines displaying ZIKV-resistance also demonstrated early upregulation of multiple antiviral genes compared with susceptible astrocytes. Interestingly, pre-stimulation of ZIKV-susceptible astrocytes with either poly(I:C) or poly(dA:dT) showed efficient protection against ZIKV compared with pre-stimulation with either recombinant IFN-β or IFN-λ, perhaps indicating that a more diverse antiviral gene expression is necessary for astrocyte control of ZIKV, and this is driven in part through interferon-independent mechanisms.
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9
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Healy FM, Dahal LN, Jones JRE, Floisand Y, Woolley JF. Recent Progress in Interferon Therapy for Myeloid Malignancies. Front Oncol 2021; 11:769628. [PMID: 34778087 PMCID: PMC8586418 DOI: 10.3389/fonc.2021.769628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 12/29/2022] Open
Abstract
Myeloid malignancies are a heterogeneous group of clonal haematopoietic disorders, caused by abnormalities in haematopoietic stem cells (HSCs) and myeloid progenitor cells that originate in the bone marrow niche. Each of these disorders are unique and present their own challenges with regards to treatment. Acute myeloid leukaemia (AML) is considered the most aggressive myeloid malignancy, only potentially curable with intensive cytotoxic chemotherapy with or without allogeneic haematopoietic stem cell transplantation. In comparison, patients diagnosed with chronic myeloid leukaemia (CML) and treated with tyrosine kinase inhibitors (TKIs) have a high rate of long-term survival. However, drug resistance and relapse are major issues in both these diseases. A growing body of evidence suggests that Interferons (IFNs) may be a useful therapy for myeloid malignancies, particularly in circumstances where patients are resistant to existing front-line therapies and have risk of relapse following haematopoietic stem cell transplant. IFNs are a major class of cytokines which are known to play an integral role in the non-specific immune response. IFN therapy has potential as a combination therapy in AML patients to reduce the impact of minimal residual disease on relapse. Alongside this, IFNs can potentially sensitize leukaemic cells to TKIs in resistant CML patients. There is evidence also that IFNs have a therapeutic role in myeloproliferative neoplasms (MPNs) such as polycythaemia vera (PV) and primary myelofibrosis (PMF), where they can restore polyclonality in patients. Novel formulations have improved the clinical effectiveness of IFNs. Low dose pegylated IFN formulations improve pharmacokinetics and improve patient tolerance to therapies, thereby minimizing the risk of haematological toxicities. Herein, we will discuss recent developments and the current understanding of the molecular and clinical implications of Type I IFNs for the treatment of myeloid malignancies.
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Affiliation(s)
- Fiona M Healy
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Lekh N Dahal
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Jack R E Jones
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Yngvar Floisand
- Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - John F Woolley
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
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10
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Grochowska J, Czerwinska J, Borowski LS, Szczesny RJ. Mitochondrial RNA, a new trigger of the innate immune system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1690. [PMID: 34498404 DOI: 10.1002/wrna.1690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria play a pivotal role in numerous cellular processes. One of them is regulation of the innate immune pathway. In this instance, mitochondria function in two different aspects of regulatory mechanisms. First, mitochondria are part of the antiviral signaling cascade that is triggered in the cytoplasm and transmitted to effector proteins through mitochondria-localized proteins. Second, mitochondria can become an endogenous source of innate immune stimuli. Under some pathophysiological conditions, mitochondria release to the cytoplasm immunogenic factors, such as mitochondrial nucleic acids. Here, we focus on immunogenic mitochondrial double-stranded RNA (mt-dsRNA) and its origin and metabolism. We discuss factors that are responsible for regulating mt-dsRNA and its escape from mitochondria, emphasizing the contribution of polynucleotide phosphorylase (PNPase, PNPT1). Finally, we review current knowledge of the role of PNPase in human health and disease. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S Borowski
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
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11
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Akhade AS, Atif SM, Lakshmi BS, Dikshit N, Hughes KT, Qadri A, Subramanian N. Type 1 interferon-dependent repression of NLRC4 and iPLA2 licenses down-regulation of Salmonella flagellin inside macrophages. Proc Natl Acad Sci U S A 2020; 117:29811-29822. [PMID: 33177235 PMCID: PMC7703570 DOI: 10.1073/pnas.2002747117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inflammasomes have been implicated in the detection and clearance of a variety of bacterial pathogens, but little is known about whether this innate sensing mechanism has any regulatory effect on the expression of stimulatory ligands by the pathogen. During infection with Salmonella and many other pathogens, flagellin is a major activator of NLRC4 inflammasome-mediated macrophage pyroptosis and pathogen eradication. Salmonella switches to a flagellin-low phenotype as infection progresses to avoid this mechanism of clearance by the host. However, the host cues that Salmonella perceives to undergo this switch remain unclear. Here, we report an unexpected role of the NLRC4 inflammasome in promoting expression of its microbial ligand, flagellin, and identify a role for type 1 IFN signaling in switching of Salmonella to a flagellin-low phenotype. Early in infection, activation of NLRC4 by flagellin initiates pyroptosis and concomitant release of lysophospholipids which in turn enhance expression of flagellin by Salmonella thereby amplifying its ability to elicit cell death. TRIF-dependent production of type 1 IFN, however, later represses NLRC4 and the lysophospholipid biosynthetic enzyme iPLA2, causing a decline in intracellular lysophospholipids that results in down-regulation of flagellin expression by Salmonella These findings reveal a previously unrecognized immune-modulating regulatory cross-talk between endosomal TLR signaling and cytosolic NLR activation with significant implications for the establishment of infection with Salmonella.
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Affiliation(s)
| | - Shaikh M Atif
- Hybridoma Laboratory, National Institute of Immunology, 110067 New Delhi, India
| | | | - Neha Dikshit
- Hybridoma Laboratory, National Institute of Immunology, 110067 New Delhi, India
| | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT 84112
| | - Ayub Qadri
- Hybridoma Laboratory, National Institute of Immunology, 110067 New Delhi, India;
| | - Naeha Subramanian
- Institute for Systems Biology, Seattle, WA 98109;
- Department of Immunology, University of Washington, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98109
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12
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Cameron TA, Matz LM, De Lay NR. Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator. PLoS Genet 2018; 14:e1007654. [PMID: 30307990 PMCID: PMC6181284 DOI: 10.1371/journal.pgen.1007654] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Almost 60 years ago, Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase (PNPase). Although this discovery provided an important tool for deciphering the genetic code, subsequent work revealed that the predominant function of PNPase in bacteria and eukaryotes is catalyzing the reverse reaction, i.e., the release of ribonucleotides from RNA. PNPase has a crucial role in RNA metabolism in bacteria and eukaryotes mainly through its roles in processing and degrading RNAs, but additional functions in RNA metabolism have recently been reported for this enzyme. Here, we discuss these established and noncanonical functions for PNPase and the possibility that the major impact of PNPase on cell physiology is through its unorthodox roles.
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Affiliation(s)
- Todd A. Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lisa M. Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Nicholas R. De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas, United States of America
- * E-mail:
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13
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Golzarroshan B, Lin CL, Li CL, Yang WZ, Chu LY, Agrawal S, Yuan HS. Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities. Nucleic Acids Res 2018; 46:8630-8640. [PMID: 30020492 PMCID: PMC6144817 DOI: 10.1093/nar/gky642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
Human polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'-to-5' exoribonuclease principally located in mitochondria where it is responsible for RNA turnover and import. Mutations in PNPase impair structured RNA transport into mitochondria, resulting in mitochondrial dysfunction and disease. PNPase is a trimeric protein with a doughnut-shaped structure hosting a central channel for single-stranded RNA binding and degradation. Here, we show that the disease-linked human PNPase mutants, Q387R and E475G, form dimers, not trimers, and have significantly lower RNA binding and degradation activities compared to wild-type trimeric PNPase. Moreover, S1 domain-truncated PNPase binds single-stranded RNA but not the stem-loop signature motif of imported structured RNA, suggesting that the S1 domain is responsible for binding structured RNAs. We further determined the crystal structure of dimeric PNPase at a resolution of 2.8 Å and, combined with small-angle X-ray scattering, show that the RNA-binding K homology and S1 domains are relatively inaccessible in the dimeric assembly. Taken together, these results show that mutations at the interface of the trimeric PNPase tend to produce a dimeric protein with destructive RNA-binding surfaces, thus impairing both of its RNA import and degradation activities and leading to mitochondria disorders.
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Affiliation(s)
- Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Chia-Lung Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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14
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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15
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Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA. PNPase knockout results in mtDNA loss and an altered metabolic gene expression program. PLoS One 2018; 13:e0200925. [PMID: 30024931 PMCID: PMC6053217 DOI: 10.1371/journal.pone.0200925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is an essential mitochondria-localized exoribonuclease implicated in multiple biological processes and human disorders. To reveal role(s) for PNPase in mitochondria, we established PNPase knockout (PKO) systems by first shifting culture conditions to enable cell growth with defective respiration. Interestingly, PKO established in mouse embryonic fibroblasts (MEFs) resulted in the loss of mitochondrial DNA (mtDNA). The transcriptional profile of PKO cells was similar to rho0 mtDNA deleted cells, with perturbations in cholesterol (FDR = 6.35 x 10-13), lipid (FDR = 3.21 x 10-11), and secondary alcohol (FDR = 1.04x10-12) metabolic pathway gene expression compared to wild type parental (TM6) MEFs. Transcriptome analysis indicates processes related to axonogenesis (FDR = 4.49 x 10-3), axon development (FDR = 4.74 x 10-3), and axonal guidance (FDR = 4.74 x 10-3) were overrepresented in PKO cells, consistent with previous studies detailing causative PNPase mutations in delayed myelination, hearing loss, encephalomyopathy, and chorioretinal defects in humans. Overrepresentation analysis revealed alterations in metabolic pathways in both PKO and rho0 cells. Therefore, we assessed the correlation of genes implicated in cell cycle progression and total metabolism and observed a strong positive correlation between PKO cells and rho0 MEFs compared to TM6 MEFs. We quantified the normalized biomass accumulation rate of PKO clones at 1.7% (SD ± 2.0%) and 2.4% (SD ± 1.6%) per hour, which was lower than TM6 cells at 3.3% (SD ± 3.5%) per hour. Furthermore, PKO in mouse inner ear hair cells caused progressive hearing loss that parallels human familial hearing loss previously linked to mutations in PNPase. Combined, our study reports that knockout of a mitochondrial nuclease results in mtDNA loss and suggests that mtDNA maintenance could provide a unifying connection for the large number of biological activities reported for PNPase.
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Affiliation(s)
- Eriko Shimada
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Fasih M. Ahsan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mahta Nili
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dian Huang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sean Atamdede
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tara TeSlaa
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dana Case
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Benjamin J. Perrin
- Department of Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Carla M. Koehler
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael A. Teitell
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
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16
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Abstract
MicroRNAs (miRNAs or miRs) are small 19-22 nucleotide long, noncoding, single-stranded, and multifunctional RNAs that regulate a diverse assortment of gene and protein functions that impact on a vast network of pathways. Lin-4, a noncoding transcript discovered in 1993 and named miRNA, initiated the exploration of research into these intriguing molecules identified in almost all organisms. miRNAs interfere with translation or posttranscriptional regulation of their target gene and regulate multiple biological actions exerted by these target genes. In cancer, they function as both oncogenes and tumor suppressor genes displaying differential activity in various cellular contexts. Although the role of miRNAs on target gene functions has been extensively investigated, less is currently known about the upstream regulatory molecules that regulate miRNAs. This chapter focuses on the factors and processes involved in miRNA regulation.
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Affiliation(s)
- Anjan K Pradhan
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Luni Emdad
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Swadesh K Das
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Devanand Sarkar
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Paul B Fisher
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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17
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Bernhardt M, Novak D, Assenov Y, Orouji E, Knappe N, Weina K, Reith M, Larribere L, Gebhardt C, Plass C, Umansky V, Utikal J. Melanoma-Derived iPCCs Show Differential Tumorigenicity and Therapy Response. Stem Cell Reports 2017; 8:1379-1391. [PMID: 28392221 PMCID: PMC5425615 DOI: 10.1016/j.stemcr.2017.03.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 01/10/2023] Open
Abstract
A point mutation in the BRAF gene, leading to a constitutively active form of the protein, is present in 45%–60% of patients and acts as a key driver in melanoma. Shortly after therapy induction, resistance to MAPK pathway-specific inhibitors develops, indicating that pathway inhibition is circumvented by epigenetic mechanisms. Here, we mimicked epigenetic modifications in melanoma cells by reprogramming them into metastable induced pluripotent cancer cells (iPCCs) with the ability to terminally differentiate into non-tumorigenic lineages. iPCCs and their differentiated progeny were characterized by an increased resistance against targeted therapies, although the cells harbor the same oncogenic mutations and signaling activity as the parental melanoma cells. Furthermore, induction of a pluripotent state allowed the melanoma-derived cells to acquire a non-tumorigenic cell fate, further suggesting that tumorigenicity is influenced by the cell state. Human melanoma cells reprogrammed toward an iPSC-like state (iPCCs) iPCCs differentiated into neurons and fibroblasts iPCC-derived fibroblasts show no tumorigenic potential iPCCs and iPCC-derived fibroblasts lose oncogene addiction
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Affiliation(s)
- Mathias Bernhardt
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Daniel Novak
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Elias Orouji
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Nathalie Knappe
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Kasia Weina
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Maike Reith
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Lionel Larribere
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Christoffer Gebhardt
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Viktor Umansky
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany
| | - Jochen Utikal
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany.
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18
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Rajasekaran D, Siddiq A, Willoughby JLS, Biagi JM, Christadore LM, Yunes SA, Gredler R, Jariwala N, Robertson CL, Akiel MA, Shen XN, Subler MA, Windle JJ, Schaus SE, Fisher PB, Hansen U, Sarkar D. Small molecule inhibitors of Late SV40 Factor (LSF) abrogate hepatocellular carcinoma (HCC): Evaluation using an endogenous HCC model. Oncotarget 2016; 6:26266-77. [PMID: 26313006 PMCID: PMC4694900 DOI: 10.18632/oncotarget.4656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/06/2015] [Indexed: 01/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a lethal malignancy with high mortality and poor prognosis. Oncogenic transcription factor Late SV40 Factor (LSF) plays an important role in promoting HCC. A small molecule inhibitor of LSF, Factor Quinolinone Inhibitor 1 (FQI1), significantly inhibited human HCC xenografts in nude mice without harming normal cells. Here we evaluated the efficacy of FQI1 and another inhibitor, FQI2, in inhibiting endogenous hepatocarcinogenesis. HCC was induced in a transgenic mouse with hepatocyte-specific overexpression of c-myc (Alb/c-myc) by injecting N-nitrosodiethylamine (DEN) followed by FQI1 or FQI2 treatment after tumor development. LSF inhibitors markedly decreased tumor burden in Alb/c-myc mice with a corresponding decrease in proliferation and angiogenesis. Interestingly, in vitro treatment of human HCC cells with LSF inhibitors resulted in mitotic arrest with an accompanying increase in CyclinB1. Inhibition of CyclinB1 induction by Cycloheximide or CDK1 activity by Roscovitine significantly prevented FQI-induced mitotic arrest. A significant induction of apoptosis was also observed upon treatment with FQI. These effects of LSF inhibition, mitotic arrest and induction of apoptosis by FQI1s provide multiple avenues by which these inhibitors eliminate HCC cells. LSF inhibitors might be highly potent and effective therapeutics for HCC either alone or in combination with currently existing therapies.
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Affiliation(s)
- Devaraja Rajasekaran
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ayesha Siddiq
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jennifer L S Willoughby
- Department of Biology, Center for Chemical Methodology and Library Development at Boston University, Boston, MA 02215, USA.,Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Jessica M Biagi
- Department of Chemistry, Center for Chemical Methodology and Library Development at Boston University, Boston, MA 02215, USA
| | - Lisa M Christadore
- Department of Chemistry, Center for Chemical Methodology and Library Development at Boston University, Boston, MA 02215, USA
| | - Sarah A Yunes
- Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Rachel Gredler
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nidhi Jariwala
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Chadia L Robertson
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Maaged A Akiel
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Xue-Ning Shen
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mark A Subler
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jolene J Windle
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Scott E Schaus
- Department of Chemistry, Center for Chemical Methodology and Library Development at Boston University, Boston, MA 02215, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.,VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ulla Hansen
- Department of Biology, Center for Chemical Methodology and Library Development at Boston University, Boston, MA 02215, USA.,Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.,VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
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19
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Sokhi UK, Bacolod MD, Dasgupta S, Emdad L, Das SK, Dumur CI, Miles MF, Sarkar D, Fisher PB. Identification of genes potentially regulated by human polynucleotide phosphorylase (hPNPase old-35) using melanoma as a model. PLoS One 2013; 8:e76284. [PMID: 24143183 PMCID: PMC3797080 DOI: 10.1371/journal.pone.0076284] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
Human Polynucleotide Phosphorylase (hPNPaseold-35 or PNPT1) is an evolutionarily conserved 3′→5′ exoribonuclease implicated in the regulation of numerous physiological processes including maintenance of mitochondrial homeostasis, mtRNA import and aging-associated inflammation. From an RNase perspective, little is known about the RNA or miRNA species it targets for degradation or whose expression it regulates; except for c-myc and miR-221. To further elucidate the functional implications of hPNPaseold-35 in cellular physiology, we knocked-down and overexpressed hPNPaseold-35 in human melanoma cells and performed gene expression analyses to identify differentially expressed transcripts. Ingenuity Pathway Analysis indicated that knockdown of hPNPaseold-35 resulted in significant gene expression changes associated with mitochondrial dysfunction and cholesterol biosynthesis; whereas overexpression of hPNPaseold-35 caused global changes in cell-cycle related functions. Additionally, comparative gene expression analyses between our hPNPaseold-35 knockdown and overexpression datasets allowed us to identify 77 potential “direct” and 61 potential “indirect” targets of hPNPaseold-35 which formed correlated networks enriched for cell-cycle and wound healing functional association, respectively. These results provide a comprehensive database of genes responsive to hPNPaseold-35 expression levels; along with the identification new potential candidate genes offering fresh insight into cellular pathways regulated by PNPT1 and which may be used in the future for possible therapeutic intervention in mitochondrial- or inflammation-associated disease phenotypes.
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Affiliation(s)
- Upneet K. Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Manny D. Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Santanu Dasgupta
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Swadesh K. Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F. Miles
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Neurology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul B. Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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20
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Sokhi UK, Das SK, Dasgupta S, Emdad L, Shiang R, DeSalle R, Sarkar D, Fisher PB. Human polynucleotide phosphorylase (hPNPaseold-35): should I eat you or not--that is the question? Adv Cancer Res 2013; 119:161-90. [PMID: 23870512 DOI: 10.1016/b978-0-12-407190-2.00005-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RNA degradation plays a fundamental role in maintaining cellular homeostasis whether it occurs as a surveillance mechanism eliminating aberrant mRNAs or during RNA processing to generate mature transcripts. 3'-5' exoribonucleases are essential mediators of RNA decay pathways, and one such evolutionarily conserved enzyme is polynucleotide phosphorylase (PNPase). The human homologue of this fascinating enzymatic protein (hPNPaseold-35) was cloned a decade ago in the context of terminal differentiation and senescence through a novel "overlapping pathway screening" approach. Since then, significant insights have been garnered about this exoribonuclease and its repertoire of expanding functions. The objective of this review is to provide an up-to-date perspective of the recent discoveries made relating to hPNPaseold-35 and the impact they continue to have on our comprehension of its expanding and diverse array of functions.
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21
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MicroRNA turnover: when, how, and why. Trends Biochem Sci 2012; 37:436-46. [PMID: 22921610 DOI: 10.1016/j.tibs.2012.07.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are short (∼22 nucleotide) RNAs that are important for the regulation of numerous biological processes. Accordingly, the expression of miRNAs is itself tightly controlled by mechanisms acting at the level of transcription as well as processing of miRNA precursors. Recently, active degradation of mature miRNAs has been identified as another mechanism that is important for miRNA homeostasis. Here we review the molecular factors and cellular conditions that promote miRNA turnover. We also discuss what is known about the physiological relevance of miRNA decay.
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22
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Yu YL, Chou RH, Wu CH, Wang YN, Chang WJ, Tseng YJ, Chang WC, Lai CC, Lee HJ, Huo L, Chen CH, Hung MC. Nuclear EGFR suppresses ribonuclease activity of polynucleotide phosphorylase through DNAPK-mediated phosphorylation at serine 776. J Biol Chem 2012; 287:31015-26. [PMID: 22815474 DOI: 10.1074/jbc.m112.358077] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear existence of epidermal growth factor receptor (EGFR) has been documented for more than two decades. Resistance of cancer to radiotherapy is frequently correlated with elevated EGFR expression, activity, and nuclear translocation. However, the role of nuclear EGFR (nEGFR) in radioresistance of cancers remains elusive. In the current study, we identified a novel nEGFR-associated protein, polynucleotide phosphorylase (PNPase), which possesses 3' to 5' exoribonuclease activity toward c-MYC mRNA. Knockdown of PNPase increased radioresistance. Inactivation or knock-down of EGFR enhanced PNPase-mediated c-MYC mRNA degradation in breast cancer cells, and also increased its radiosensitivity. Interestingly, the association of nEGFR with PNPase and DNA-dependent protein kinase (DNAPK) increased significantly in breast cancer cells after exposure to ionizing radiation (IR). We also demonstrated that DNAPK phosphorylates PNPase at Ser-776, which is critical for its ribonuclease activity. The phospho-mimetic S776D mutant of PNPase impaired its ribonuclease activity whereas the nonphosphorylatable S776A mutant effectively degraded c-MYC mRNA. Here, we uncovered a novel role of nEGFR in radioresistance, and that is, upon ionizing radiation, nEGFR inactivates the ribonuclease activity of PNPase toward c-MYC mRNA through DNAPK-mediated Ser-776 phosphorylation, leading to increase of c-MYC mRNA, which contributes to radioresistance of cancer cells.
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Affiliation(s)
- Yung-Luen Yu
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan.
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Lin CL, Wang YT, Yang WZ, Hsiao YY, Yuan HS. Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation. Nucleic Acids Res 2011; 40:4146-57. [PMID: 22210891 PMCID: PMC3351181 DOI: 10.1093/nar/gkr1281] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human polynucleotide phosphorylase (hPNPase) is a 3′-to-5′ exoribonuclease that degrades specific mRNA and miRNA, and imports RNA into mitochondria, and thus regulates diverse physiological processes, including cellular senescence and homeostasis. However, the RNA-processing mechanism by hPNPase, particularly how RNA is bound via its various domains, remains obscure. Here, we report the crystal structure of an S1 domain-truncated hPNPase at a resolution of 2.1 Å. The trimeric hPNPase has a hexameric ring-like structure formed by six RNase PH domains, capped with a trimeric KH pore. Our biochemical and mutagenesis studies suggest that the S1 domain is not critical for RNA binding, and conversely, that the conserved GXXG motif in the KH domain directly participates in RNA binding in hPNPase. Our studies thus provide structural and functional insights into hPNPase, which uses a KH pore to trap a long RNA 3′ tail that is further delivered into an RNase PH channel for the degradation process. Structural RNA with short 3′ tails are, on the other hand, transported but not digested by hPNPase.
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Affiliation(s)
- Chia Liang Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
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Wang G, Shimada E, Koehler CM, Teitell MA. PNPASE and RNA trafficking into mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:998-1007. [PMID: 22023881 DOI: 10.1016/j.bbagrm.2011.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/26/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
The mitochondrial genome encodes a very small fraction of the macromolecular components that are required to generate functional mitochondria. Therefore, most components are encoded within the nuclear genome and are imported into mitochondria from the cytosol. Understanding how mitochondria are assembled, function, and dysfunction in diseases requires detailed knowledge of mitochondrial import mechanisms and pathways. The import of nucleus-encoded RNAs is required for mitochondrial biogenesis and function, but unlike pre-protein import, the pathways and cellular machineries of RNA import are poorly defined, especially in mammals. Recent studies have shown that mammalian polynucleotide phosphorylase (PNPASE) localizes in the mitochondrial intermembrane space (IMS) to regulate the import of RNA. The identification of PNPASE as the first component of the RNA import pathway, along with a growing list of nucleus-encoded RNAs that are imported and newly developed assay systems for RNA import studies, suggest a unique opportunity is emerging to identify the factors and mechanisms that regulate RNA import into mammalian mitochondria. Here we summarize what is known in this fascinating area of mitochondrial biogenesis, identify areas that require further investigation, and speculate on the impact unraveling RNA import mechanisms and pathways will have for the field going forward. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Geng Wang
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Human polynucleotide phosphorylase (hPNPase(old-35)): an evolutionary conserved gene with an expanding repertoire of RNA degradation functions. Oncogene 2010; 30:1733-43. [PMID: 21151174 PMCID: PMC4955827 DOI: 10.1038/onc.2010.572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human polynucleotide phosphorylase (hPNPase(old-35)) is an evolutionary conserved RNA-processing enzyme with expanding roles in regulating cellular physiology. hPNPase(old-35) was cloned using an innovative 'overlapping pathway screening' strategy designed to identify genes coordinately regulated during the processes of cellular differentiation and senescence. Although hPNPase(old-35) structurally and biochemically resembles PNPase of other species, overexpression and inhibition studies reveal that hPNPase(old-35) has evolved to serve more specialized and diversified functions in humans. Targeting specific mRNA or non-coding small microRNA, hPNPase(old-35) modulates gene expression that in turn has a pivotal role in regulating normal physiological and pathological processes. In these contexts, targeted overexpression of hPNPase(old-35) represents a novel strategy to selectively downregulate RNA expression and consequently intervene in a variety of pathophysiological conditions.
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Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells. Proc Natl Acad Sci U S A 2010; 107:11948-53. [PMID: 20547861 DOI: 10.1073/pnas.0914143107] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA), small noncoding RNAs, affect a broad range of biological processes, including tumorigenesis, by targeting gene products that directly regulate cell growth. Human polynucleotide phosphorylase (hPNPase(old-35)), a type I IFN-inducible 3'-5' exoribonuclease, degrades specific mRNAs and small noncoding RNAs. The present study examined the effect of this enzyme on miRNA expression in human melanoma cells. miRNA microarray analysis of human melanoma cells infected with empty adenovirus or with an adenovirus expressing hPNPase(old-35) identified miRNAs differentially and specifically regulated by hPNPase(old-35). One of these, miR-221, a regulator of the cyclin-dependent kinase inhibitor p27(kip1), displayed robust down-regulation with ensuing up-regulation of p27(kip1) by expression of hPNPase(old-35), which also occurred in multiple human melanoma cells upon IFN-beta treatment. Using both in vivo immunoprecipitation followed by Northern blotting and RNA degradation assays, we confirm that mature miR-221 is the target of hPNPase(old-35). Inhibition of hPNPase(old-35) by shRNA or stable overexpression of miR-221 protected melanoma cells from IFN-beta-mediated growth inhibition, accentuating the importance of hPNPase(old-35) induction and miR-221 down-regulation in mediating IFN-beta action. Moreover, we now uncover a mechanism of miRNA regulation involving selective enzymatic degradation. Targeted overexpression of hPNPase(old-35) might provide an effective therapeutic strategy for miR-221-overexpressing and IFN-resistant tumors, such as melanoma.
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Bekisz J, Baron S, Balinsky C, Morrow A, Zoon KC. Antiproliferative Properties of Type I and Type II Interferon. Pharmaceuticals (Basel) 2010; 3:994-1015. [PMID: 20664817 PMCID: PMC2907165 DOI: 10.3390/ph3040994] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 03/15/2010] [Accepted: 03/29/2010] [Indexed: 01/22/2023] Open
Abstract
The clinical possibilities of interferon (IFN) became apparent with early studies demonstrating that it was capable of inhibiting tumor cells in culture and in vivo using animal models. IFN gained the distinction of being the first recombinant cytokine to be licensed in the USA for the treatment of a malignancy in 1986, with the approval of IFN-α2a (Hoffman-La Roche) and IFN-α2b (Schering-Plough) for the treatment of Hairy Cell Leukemia. In addition to this application, other approved antitumor applications for IFN-α2a are AIDS-related Kaposi's Sarcoma and Chronic Myelogenous Leukemia (CML) and other approved antitumor applications for IFN-α2b are Malignant Melanoma, Follicular Lymphoma, and AIDS-related Kapoisi's Sarcoma. In the ensuing years, a considerable number of studies have been conducted to establish the mechanisms of the induction and action of IFN's anti-tumor activity. These include identifying the role of Interferon Regulatory Factor 9 (IRF9) as a key factor in eliciting the antiproliferative effects of IFN-α as well as identifying genes induced by IFN that are involved in recognition of tumor cells. Recent studies also show that IFN-activated human monocytes can be used to achieve >95% eradication of select tumor cells. The signaling pathways by which IFN induces apoptosis can vary. IFN treatment induces the tumor suppressor gene p53, which plays a role in apoptosis for some tumors, but it is not essential for the apoptotic response. IFN-α also activates phosphatidylinositol 3-kinase (PI3K), which is associated with cell survival. Downstream of PI3K is the mammalian target of rapamycin (mTOR) which, in conjunction with PI3K, may act in signaling induced by growth factors after IFN treatment. This paper will explore the mechanisms by which IFN acts to elicit its antiproliferative effects and more closely examine the clinical applications for the anti-tumor potential of IFN.
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Affiliation(s)
- Joseph Bekisz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Jablonska J, Leschner S, Westphal K, Lienenklaus S, Weiss S. Neutrophils responsive to endogenous IFN-beta regulate tumor angiogenesis and growth in a mouse tumor model. J Clin Invest 2010; 120:1151-64. [PMID: 20237412 DOI: 10.1172/jci37223] [Citation(s) in RCA: 429] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 01/13/2010] [Indexed: 12/12/2022] Open
Abstract
Angiogenesis is a hallmark of malignant neoplasias, as the formation of new blood vessels is required for tumors to acquire oxygen and nutrients essential for their continued growth and metastasis. However, the signaling pathways leading to tumor vascularization are not fully understood. Here, using a transplantable mouse tumor model, we have demonstrated that endogenous IFN-beta inhibits tumor angiogenesis through repression of genes encoding proangiogenic and homing factors in tumor-infiltrating neutrophils. We determined that IFN-beta-deficient mice injected with B16F10 melanoma or MCA205 fibrosarcoma cells developed faster-growing tumors with better-developed blood vessels than did syngeneic control mice. These tumors displayed enhanced infiltration by CD11b+Gr1+ neutrophils expressing elevated levels of the genes encoding the proangiogenic factors VEGF and MMP9 and the homing receptor CXCR4. They also expressed higher levels of the transcription factors c-myc and STAT3, known regulators of VEGF, MMP9, and CXCR4. In vitro, treatment of these tumor-infiltrating neutrophils with low levels of IFN-beta restored expression of proangiogenic factors to control levels. Moreover, depletion of these neutrophils inhibited tumor growth in both control and IFN-beta-deficient mice. We therefore suggest that constitutively produced endogenous IFN-beta is an important mediator of innate tumor surveillance. Further, we believe our data help to explain the therapeutic effect of IFN treatment during the early stages of cancer development.
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Affiliation(s)
- Jadwiga Jablonska
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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Van Maerken T, Sarkar D, Speleman F, Dent P, Weiss WA, Fisher PB. Adenovirus-mediated hPNPase(old-35) gene transfer as a therapeutic strategy for neuroblastoma. J Cell Physiol 2009; 219:707-15. [PMID: 19202553 DOI: 10.1002/jcp.21719] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Current treatment options for neuroblastoma fail to eradicate the disease in the majority of high-risk patients, clearly mandating development of innovative therapeutic strategies. Gene therapy represents a promising approach for reversing the neoplastic phenotype or driving tumor cells to self-destruction. We presently studied the effects of adenovirus-mediated gene transfer of human polynucleotide phosphorylase (hPNPase(old-35)), a 3',5'-exoribonuclease with growth-inhibitory properties, in neuroblastoma cells. Transgene expression was driven by either the cytomegalovirus (CMV) promoter or by a tumor-selective promoter derived from progression elevated gene-3 (PEG-3). Our data demonstrate that efficient adenoviral transduction of neuroblastoma cells and robust transgene expression are feasible objectives, that the PEG-3 promoter is capable of selectively targeting gene expression in the majority of neuroblastoma cells, and that hPNPase(old-35) induces profound growth suppression and apoptosis of malignant neuroblastoma cells, while exerting limited effects on normal neural crest-derived melanocytes. These findings support future applications of hPNPase(old-35) for targeted gene-based therapy of neuroblastoma and suggest that combination with the PEG-3 promoter holds promise for creating a potent and selective neuroblastoma therapeutic. J. Cell. Physiol. 219: 707-715, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Tom Van Maerken
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
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Staudt MR, Depass AL, Sarkar D, Fisher PB. Model cell culture system for defining the molecular and biochemical events mediating terminal differentiation of human melanoma cells. J Cell Physiol 2008; 218:304-14. [PMID: 18844238 DOI: 10.1002/jcp.21602] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cancer cells are commonly less differentiated than their normal progenitors; a phenotype that correlates with loss of specialized functions and an increased capability to self-renew. Melanoma is an ideal model to analyze cancer progression and differentiation since a well-characterized process of step-wise tumor progression has been defined. Our lab previously described a combinatorial in vitro treatment protocol to induce terminal differentiation of human melanoma cells using a low dose of the PKC activator Mezerein (Mez) combined with interferon-beta (IFN-beta), which also activates IFN-stimulated gene expression in addition to the re-differentiation program. In principle, using an alternate way to induce terminal differentiation not including IFN-beta would be more compatible with gene expression profiling. A higher concentration of Mez alone induced terminal differentiation of HO-1 human melanoma cells as measured by morphological, growth and biochemical assays. Pre-treatment with the PKC inhibitor GF109203x blocked changes associated with differentiation and inhibited the ability of Mez to force irreversible/terminal differentiation. By combining this efficient method of inducing terminal differentiation with microarray analyses we now identify potential regulators of this process and demonstrate utility of this novel in vitro model in which to study the molecular determinants and mechanisms of human melanoma differentiation.
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Affiliation(s)
- Michelle R Staudt
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
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31
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Wu J, Li Z. Human polynucleotide phosphorylase reduces oxidative RNA damage and protects HeLa cell against oxidative stress. Biochem Biophys Res Commun 2008; 372:288-92. [PMID: 18501193 DOI: 10.1016/j.bbrc.2008.05.058] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 05/14/2008] [Indexed: 11/29/2022]
Abstract
We examined HeLa cell viability and RNA oxidative damage in response to hydrogen peroxide (H2O2) treatment. The level of damaged RNA, measured by the content of 8-hydroxyguanosine (7,8-dihydro-8-oxoguanosine, 8-oxoG), increases depending on H2O2 dosage and is inversely correlated with cell viability. The elevated level of 8-oxoG in RNA decreases after removal of oxidative challenge, suggesting the existence of surveillance mechanism(s) for cleaning up oxidized RNA. Human polynucleotide phosphorylase (hPNPase), an exoribonuclease primarily located in mitochondria, has been previously shown to bind 8-oxoG-RNA with high affinity. The role of hPNPase in HeLa cell under oxidative stress conditions is examined here. Overexpression of hPNPase reduces RNA oxidation and increases cell viability against H2O2 insult. Conversely, hPNPase knockdown decreases viability and increases 8-oxoG level in HeLa cell exposed to H2O2. Our results suggest that hPNPase plays an important role in protecting cells and limiting damaged RNA under oxidative stress.
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Affiliation(s)
- Jinhua Wu
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA
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Falaleeva MV, Chetverina HV, Ugarov VI, Uzlova EA, Chetverin AB. Factors influencing RNA degradation by Thermus thermophilus polynucleotide phosphorylase. FEBS J 2008; 275:2214-26. [PMID: 18397327 DOI: 10.1111/j.1742-4658.2008.06374.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
At the optimal temperature (65 degrees C), Thermus thermophilus polynucleotide phosphorylase (Tth PNPase), produced in Escherichia coli cells and isolated to functional homogeneity, completely destroys RNAs that possess even a very stable intramolecular secondary structure, but leaves intact RNAs whose 3' end is protected by chemical modification or by hybridization with a complementary oligonucleotide. This allows individual RNAs to be isolated from heterogeneous populations by degrading unprotected species. If oligonucleotide is hybridized to an internal RNA segment, the Tth PNPase stalls eight nucleotides downstream of that segment. This allows any arbitrary 5'-terminal fragment of RNA to be prepared with a precision similar to that of run-off transcription, but without the need for a restriction site. In contrast to the high Mg(2+) requirements of mesophilic PNPases, Tth PNPase retains significant activity when the free Mg(2+) concentration is in the micromolar range. This allows minimization of the Mg(2+)-catalysed nonenzymatic hydrolysis of RNA when phosphorolysis is performed at a high temperature. This capability of Tth PNPase for fully controlled RNA phosphorolysis could be utilized in a variety of research and practical applications.
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Affiliation(s)
- Marina V Falaleeva
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Chan I, Lebedeva IV, Su ZZ, Sarkar D, Valerie K, Fisher PB. Progression elevated gene-3 promoter (PEG-Prom) confers cancer cell selectivity to human polynucleotide phosphorylase (hPNPase(old-35))-mediated growth suppression. J Cell Physiol 2008; 215:401-9. [PMID: 17960560 DOI: 10.1002/jcp.21320] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The poor prognosis of pancreatic cancer patients using currently available therapies mandates novel therapeutics that combine anti-neoplastic potency with toxicity-minimizing cancer specificity. Employing an overlapping pathway screen to identify genes exhibiting coordinated expression as a consequence of terminal cell differentiation and replicative senescence, we identified human polynucleotide phosphorylase (hPNPase(old-35)), a 3',5'-exoribonuclease that exhibits robust growth-suppressing effects in a wide spectrum of human cancers. A limitation to the anti-neoplastic efficacy of hPNPase(old-35) relates to its lack of cancer specificity. The promoter of Progression Elevated Gene-3 (PEG-Prom), discovered in our laboratory via subtraction hybridization in a transformation progression rodent tumor model functions selectively in a diverse array of human cancer cells, with limited activity in normal cells. An adenovirus constructed with the PEG-Prom driving expression of hPNPase(old-35) containing a C-terminal Hemaglutinin (HA)-tag (Ad.PEG.hPNPase(old-35)) was shown to induce robust transgene expression, growth suppression, apoptosis, and cell-cycle arrest in a broad panel of pancreatic cancer cells, with minimal effects in normal immortalized pancreatic cells. hPNPase(old-35) expression correlated with arrest in the G(2)/M phase of the cell cycle and up-regulation of the cyclin-dependent kinase inhibitors (CDKI) p21(CIP1/WAF-1/MDA-6) and p27(KIP1). In a nude mouse xenograft model, Ad.PEG.hPNPase(old-35) injections effectively inhibited growth of human pancreatic cancer cells in vivo. These findings support the potential efficacy of combining a cancer-specific promoter, such as the PEG-Prom, with a novel anti-neoplastic agent, such as hPNPase(old-35), to create a potent, targeted cancer therapeutic, especially for a devastating disease like pancreatic cancer.
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Affiliation(s)
- Isaac Chan
- College of Physicians and Surgeons, Columbia University Medical School, New York, New York, USA
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34
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Chen HW, Koehler CM, Teitell MA. Human polynucleotide phosphorylase: location matters. Trends Cell Biol 2007; 17:600-8. [DOI: 10.1016/j.tcb.2007.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 09/01/2007] [Accepted: 09/03/2007] [Indexed: 01/21/2023]
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35
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Sarkar D, Park ES, Barber GN, Fisher PB. Activation of Double-Stranded RNA–Dependent Protein Kinase, A New Pathway by Which Human Polynucleotide Phosphorylase (hPNPaseold-35) Induces Apoptosis. Cancer Res 2007; 67:7948-53. [PMID: 17804700 DOI: 10.1158/0008-5472.can-07-0872] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human polynucleotide phosphorylase (hPNPase(old-35)) is a type I IFN-inducible 3',5' exoribonuclease that mediates mRNA degradation. In melanoma cells, slow and sustained overexpression of hPNPase(old-35) induces G(1) cell cycle arrest ultimately culminating in apoptosis, whereas rapid overexpression of hPNPase(old-35) directly promotes apoptosis without cell cycle changes. These observations imply that inhibition of cell cycle progression and induction of apoptosis by hPNPase(old-35) involve multiple intracellular targets and signaling pathways. We now provide evidence that the apoptosis-inducing activity of hPNPase(old-35) is mediated by activation of double-stranded RNA-dependent protein kinase (PKR). Activation of PKR by hPNPase(old-35) precedes phosphorylation of eukaryotic initiation factor-2alpha and induction of growth arrest and DNA damage-inducible gene 153 (GADD153) that culminates in the shutdown of protein synthesis and apoptosis. Activation of PKR by hPNPase(old-35) also instigates down-regulation of the antiapoptotic protein Bcl-x(L). A dominant-negative inhibitor of PKR, as well as GADD153 antisense or bcl-x(L) overexpression, effectively inhibits apoptosis induction by hPNPase(old-35). These studies elucidate a novel pathway by which an evolutionary conserved RNA-metabolizing enzyme, hPNPase(old-35), regulates cell growth and viability.
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Affiliation(s)
- Devanand Sarkar
- Department of Urology, Herbert Irving Comprehensive Caner Center, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA.
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Rainey RN, Glavin JD, Chen HW, French SW, Teitell MA, Koehler CM. A new function in translocation for the mitochondrial i-AAA protease Yme1: import of polynucleotide phosphorylase into the intermembrane space. Mol Cell Biol 2006; 26:8488-97. [PMID: 16966379 PMCID: PMC1636789 DOI: 10.1128/mcb.01006-06] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 06/27/2006] [Accepted: 08/30/2006] [Indexed: 12/20/2022] Open
Abstract
Polynucleotide phosphorylase (PNPase) is an exoribonuclease and poly(A) polymerase postulated to function in the cytosol and mitochondrial matrix. Prior overexpression studies resulted in PNPase localization to both the cytosol and mitochondria, concurrent with cytosolic RNA degradation and pleiotropic cellular effects, including growth inhibition and apoptosis, that may not reflect a physiologic role for endogenous PNPase. We therefore conducted a mechanistic study of PNPase biogenesis in the mitochondrion. Interestingly, PNPase is localized to the intermembrane space by a novel import pathway. PNPase has a typical N-terminal targeting sequence that is cleaved by the matrix processing peptidase when PNPase engaged the TIM23 translocon at the inner membrane. The i-AAA protease Yme1 mediated translocation of PNPase into the intermembrane space but did not degrade PNPase. In a yeast strain deleted for Yme1 and expressing PNPase, nonimported PNPase accumulated in the cytosol, confirming an in vivo role for Yme1 in PNPase maturation. PNPase localization to the mitochondrial intermembrane space suggests a unique role distinct from its highly conserved function in RNA processing in chloroplasts and bacteria. Furthermore, Yme1 has a new function in protein translocation, indicating that the intermembrane space harbors diverse pathways for protein translocation.
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Affiliation(s)
- Robert N Rainey
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
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French SW, Dawson DW, Chen HW, Rainey RN, Sievers SA, Balatoni CE, Wong L, Troke JJ, Nguyen MTN, Koehler CM, Teitell MA. The TCL1 oncoprotein binds the RNase PH domains of the PNPase exoribonuclease without affecting its RNA degrading activity. Cancer Lett 2006; 248:198-210. [PMID: 16934922 DOI: 10.1016/j.canlet.2006.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/13/2006] [Indexed: 12/16/2022]
Abstract
TCL1 is an AKT kinase coactivator that, when dysregulated, initiates mature lymphocyte malignancies in humans and transgenic mice. While TCL1 augments AKT pathway signaling, additional TCL1 interacting proteins that may contribute to cellular homeostasis or transformation are lacking. Here, an exoribonuclease, PNPase, was identified in a complex with TCL1. The AKT interaction domain on TCL1 bound either RNase PH repeat domain of PNPase without influencing its RNA degrading activity, which was compatible with predicted docking models for a TCL1-PNPase complex. Our data provide a novel protein interaction for mammalian PNPase that may impact TCL1 mediated transformation.
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Affiliation(s)
- Samuel W French
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1732, USA
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