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Marshall KD, Klutho PJ, Song L, Roy R, Krenz M, Baines CP. Cardiac Myocyte-Specific Overexpression of FASTKD1 Prevents Ventricular Rupture After Myocardial Infarction. J Am Heart Assoc 2023; 12:e025867. [PMID: 36789858 PMCID: PMC10111501 DOI: 10.1161/jaha.122.025867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background The mitochondrial mRNA-binding protein FASTKD1 (Fas-activated serine/threonine [FAST] kinase domain-containing protein 1) protects myocytes from oxidative stress in vitro. However, the role of FASTKD1 in the myocardium in vivo is unknown. Therefore, we developed cardiac-specific FASTKD1 transgenic mice to test the effects of this protein on experimental myocardial infarction (MI). Methods and Results Transgenic mouse lines with cardiac myocyte-specific overexpression of FASTKD1 to varying degrees were generated. These mice displayed normal cardiac morphological features and function at the gross and microscopic levels. Isolated cardiac mitochondria from all transgenic mouse lines showed normal mitochondrial function, ATP levels, and permeability transition pore activity. Male nontransgenic and transgenic mice from the highest-expressing line were subjected to 8 weeks of permanent coronary ligation. Of nontransgenic mice, 40% underwent left ventricular free wall rupture within 7 days of MI compared with 0% of FASTKD1-overexpressing mice. At 3 days after MI, FASTKD1 overexpression did not alter infarct size. However, increased FASTKD1 resulted in decreased neutrophil and increased macrophage infiltration, elevated levels of the extracellular matrix component periostin, and enhanced antioxidant capacity compared with control mice. In contrast, markers of mitochondrial fusion/fission and apoptosis remained unaltered. Instead, transcriptomic analyses indicated activation of the integrated stress response in the FASTKD1 transgenic hearts. Conclusions Cardiac-specific overexpression of FASTKD1 results in viable mice displaying normal cardiac morphological features and function. However, these mice are resistant to MI-induced cardiac rupture and display altered inflammatory, extracellular matrix, and antioxidant responses following MI. Moreover, these protective effects were associated with enhanced activation of the integrated stress response.
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Affiliation(s)
- Kurt D Marshall
- Department of Biomedical Sciences University of Missouri Columbia MO
| | - Paula J Klutho
- Dalton Cardiovascular Research Center University of Missouri Columbia MO
| | - Lihui Song
- Dalton Cardiovascular Research Center University of Missouri Columbia MO
| | - Rajika Roy
- Dalton Cardiovascular Research Center University of Missouri Columbia MO
| | - Maike Krenz
- Department of Medical Pharmacology and Physiology University of Missouri Columbia MO.,Dalton Cardiovascular Research Center University of Missouri Columbia MO
| | - Christopher P Baines
- Department of Biomedical Sciences University of Missouri Columbia MO.,Department of Medical Pharmacology and Physiology University of Missouri Columbia MO.,Dalton Cardiovascular Research Center University of Missouri Columbia MO
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Yang Y, Fritzsching KJ, He S, McDermott AE. Zinc Alters the Supramolecular Organization of Nucleic Acid Complexes with Full-Length TIA1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525508. [PMID: 36747652 PMCID: PMC9900833 DOI: 10.1101/2023.01.25.525508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
T-Cell Intracellular Antigen-1 (TIA1) is a 43 kDa multi-domain RNA-binding protein involved in stress granule formation during eukaryotic stress response, and has been implicated in neurodegenerative diseases including Welander distal myopathy and amyotrophic lateral sclerosis. TIA1 contains three RNA recognition motifs (RRMs), which are capable of binding nucleic acids and a C-terminal Q/N-rich prion-related domain (PRD) which has been variously described as intrinsically disordered or prion inducing and is believed to play a role in promoting liquid-liquid phase separation connected with the assembly of stress granule formation. Motivated by the fact that our prior work shows RRMs 2 and 3 are well-ordered in an oligomeric full-length form, while RRM1 and the PRD appear to phase separate, the present work addresses whether the oligomeric form is functional and competent for binding, and probes the consequences of nucleic acid binding for oligomerization and protein conformation change. New SSNMR data show that ssDNA binds to full-length oligomeric TIA1 primarily at the RRM2 domain, but also weakly at the RRM3 domain, and Zn 2+ binds primarily to RRM3. Binding of Zn 2+ and DNA was reversible for the full-length wild type oligomeric form, and did not lead to formation of amyloid fibrils, despite the presence of the C-terminal prion-related domain. While TIA1:DNA complexes appear as long "daisy chained" structures, the addition of Zn 2+ caused the structures to collapse. We surmise that this points to a regulatory role for Zn 2+ . By occupying various "half" binding sites on RRM3 Zn 2+ may shift the nucleic acid binding off RRM3 and onto RRM2. More importantly, the use of different half sites on different monomers may introduce a mesh of crosslinks in the supramolecular complex rendering it compact and markedly reducing the access to the nucleic acids (including transcripts) from solution.
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Sellin M, Mack R, Rhodes MC, Zhang L, Berg S, Joshi K, Liu S, Wei W, S. J. PB, Larsen P, Taylor RE, Zhang J. Molecular mechanisms by which splice modulator GEX1A inhibits leukaemia development and progression. Br J Cancer 2022; 127:223-236. [PMID: 35422078 PMCID: PMC9296642 DOI: 10.1038/s41416-022-01796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Splice modulators have been assessed clinically in treating haematologic malignancies exhibiting splice factor mutations and acute myeloid leukaemia. However, the mechanisms by which such modulators repress leukaemia remain to be elucidated. OBJECTIVES The primary goal of this assessment was to assess the molecular mechanism by which the natural splice modulator GEX1A kills leukaemic cells in vitro and within in vivo mouse models. METHODS Using human leukaemic cell lines, we assessed the overall sensitivity these cells have to GEX1A via EC50 analysis. We subsequently analysed its effects using in vivo xenograft mouse models and examined whether cell sensitivities were correlated to genetic characteristics or protein expression levels. We also utilised RT-PCR and RNAseq analyses to determine splice change and RNA expression level differences between sensitive and resistant leukaemic cell lines. RESULTS We found that, in vitro, GEX1A induced an MCL-1 isoform shift to pro-apoptotic MCL-1S in all leukaemic cell types, though sensitivity to GEX1A-induced apoptosis was negatively associated with BCL-xL expression. In BCL-2-expressing leukaemic cells, GEX1A induced BCL-2-dependent apoptosis by converting pro-survival BCL-2 into a cell killer. Thus, GEX1A + selective BCL-xL inhibition induced synergism in killing leukaemic cells, while GEX1A + BCL-2 inhibition showed antagonism in BCL-2-expressing leukaemic cells. In addition, GEX1A sensitised FLT3-ITD+ leukaemic cells to apoptosis by inducing aberrant splicing and repressing the expression of FLT3-ITD. Consistently, in in vivo xenografts, GEX1A killed the bulk of leukaemic cells via apoptosis when combined with BCL-xL inhibition. Furthermore, GEX1A repressed leukaemia development by targeting leukaemia stem cells through inhibiting FASTK mitochondrial isoform expression across sensitive and non-sensitive leukaemia types. CONCLUSION Our study suggests that GEX1A is a potent anti-leukaemic agent in combination with BCL-xL inhibitors, which targets leukaemic blasts and leukaemia stem cells through distinct mechanisms.
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Ramasubramanian A, Paramasivam A, Ramani P. FASTK family of genes linked to cancer. Bioinformation 2022; 18:206-213. [PMID: 36518140 PMCID: PMC9722426 DOI: 10.6026/97320630018206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2024] Open
Abstract
Fas Activated Serine/Threonine Kinase (FASTK) family is a protein family encoded in the nuclear genome that spans the mitochondria and executes numerous functions, and consists of FASTK, the founding member along with 5 homologous proteins FASTKD1-5. Up regulation of FASTK family members have not only been implicated in tumour progression and invasion but also in increased resistance to chemotherapy proven by their knockdown leading to increased sensitivity to drugs. Thus, this review reports the implication of FASTK proteins in cancer and hence provides a scope to emphasise the role of these proteins in Oral Cancer.
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Affiliation(s)
- Abilasha Ramasubramanian
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
| | - A Paramasivam
- Department of Dental Research Cell- Blue Lab, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
| | - Pratibha Ramani
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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Laxmikeshav K, Kumari P, Shankaraiah N. Expedition of sulfur-containing heterocyclic derivatives as cytotoxic agents in medicinal chemistry: A decade update. Med Res Rev 2021; 42:513-575. [PMID: 34453452 DOI: 10.1002/med.21852] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 04/20/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022]
Abstract
This review article proposes a comprehensive report of the design strategies engaged in the development of various sulfur-bearing cytotoxic agents. The outcomes of various studies depict that the sulfur heterocyclic framework is a fundamental structure in diverse synthetic analogs representing a myriad scope of therapeutic activities. A number of five-, six- and seven-membered sulfur-containing heterocyclic scaffolds, such as thiazoles, thiadiazoles, thiazolidinediones, thiophenes, thiopyrans, benzothiazoles, benzothiophenes, thienopyrimidines, simple and modified phenothiazines, and thiazepines have been discussed. The subsequent studies of the derivatives unveiled their cytotoxic effects through multiple mechanisms (viz. inhibition of tyrosine kinases, topoisomerase I and II, tubulin, COX, DNA synthesis, and PI3K/Akt and Raf/MEK/ERK signaling pathways), and several others. Thus, our concise illustration explains the design strategy and anticancer potential of these five- and six-membered sulfur-containing heterocyclic molecules along with a brief outline on seven-membered sulfur heterocycles. The thorough assessment of antiproliferative activities with the reference drug allows a proficient assessment of the structure-activity relationships (SARs) of the diversely synthesized molecules of the series.
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Affiliation(s)
- Kritika Laxmikeshav
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Pooja Kumari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
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8
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Byres LP, Mufteev M, Yuki KE, Wei W, Piekna A, Wilson MD, Rodrigues DC, Ellis J. Identification of TIA1 mRNA targets during human neuronal development. Mol Biol Rep 2021; 48:6349-6361. [PMID: 34410578 PMCID: PMC8437838 DOI: 10.1007/s11033-021-06634-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Background Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in stress response and neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment under unstressed conditions is still unknown. Methods and Results To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons under unstressed conditions. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels. Conclusion Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06634-0.
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Affiliation(s)
- Loryn P Byres
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Zhang F, Wang K, Hu G, Fu F, Fan R, Li J, Yang L, Liu Y, Feng N, Gu X, Jia M, Chen X, Pei J. Genetic ablation of fas-activated serine/threonine kinase ameliorates alcoholic liver disease through modulating HuR-SIRT1 mRNA complex stability. Free Radic Biol Med 2021; 166:201-211. [PMID: 33610658 DOI: 10.1016/j.freeradbiomed.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/02/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
Chronic alcoholism often causes liver injuries characterized by hepatic steatosis, inflammation as well as oxidative stress and finally leads to advanced cirrhosis and liver cancer. Fas-activated serine/threonine kinase (FASTK) and its homologs are gradually known as multifunctional proteins involved in various biological processes; however, the role of FASTK and its family members in alcoholic liver disease (ALD) is still unexplored. Here we found that, among FASTK family members, the expression of FASTK was specifically induced both in livers of mice received chronic ethanol ingestion and in ethanol-stimulated hepatocytes. Animal studies showed that genetic deletion of FASTK attenuated chronic ethanol ingestion-induced liver damage, steatosis, and inflammation. Moreover, FASTK deficiency was associated with improved oxidative/anti-oxidative system homeostasis and reduced reactive oxygen species (ROS) generation in livers upon chronic ethanol stimulation. Importantly, FASTK ablation preserved hepatic sirtuin-1 (SIRT1) expression/activity upon chronic ethanol ingestion and SIRT1 silencing via adenovirus-mediated small interfering RNA transfer diminished FASTK deletion-elicited beneficial effects on alcohol-associated hepatic steatosis, inflammation, and oxidative stress. Mechanistically, ethanol increased the phosphorylation of human antigen R (HuR, a RNA binding protein that stabilizes SIRT1 mRNA) and triggered the dissociation of HuR-SIRT1 mRNA complex, in turn promoting SIRT1 mRNA decay. Genetic deletion of FASTK diminished ethanol-induced HuR phosphorylation and HuR-SIRT1 mRNA complex dissociation, thereby enhancing SIRT1 mRNA stability. Collectively, these findings for the first time highlight a critical role of FASTK in the pathogenesis of ALD and implicate HuR-SIRT1 mRNA complex involves in this process.
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Affiliation(s)
- Fuyang Zhang
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China; Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Kai Wang
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Guangyu Hu
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Feng Fu
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Rong Fan
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China.
| | - Jun Li
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Lu Yang
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Yali Liu
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Na Feng
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Xiaoming Gu
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Min Jia
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China
| | - Xiyao Chen
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China; Department of Geriatrics, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China.
| | - Jianming Pei
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Basic Medicine School, China.
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Hollin T, Jaroszewski L, Stajich JE, Godzik A, Le Roch KG. Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins. Microb Genom 2021; 7. [PMID: 33656416 PMCID: PMC8190603 DOI: 10.1099/mgen.0.000541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The RNA binding domain abundant in apicomplexans (RAP) is a protein domain identified in a diverse group of proteins, called RAP proteins, many of which have been shown to be involved in RNA binding. To understand the expansion and potential function of the RAP proteins, we conducted a hidden Markov model based screen among the proteomes of 54 eukaryotes, 17 bacteria and 12 archaea. We demonstrated that the domain is present in closely and distantly related organisms with particular expansions in Alveolata and Chlorophyta, and are not unique to Apicomplexa as previously believed. All RAP proteins identified can be decomposed into two parts. In the N-terminal region, the presence of variable helical repeats seems to participate in the specific targeting of diverse RNAs, while the RAP domain is mostly identified in the C-terminal region and is highly conserved across the different phylogenetic groups studied. Several conserved residues defining the signature motif could be crucial to ensure the function(s) of the RAP proteins. Modelling of RAP domains in apicomplexan parasites confirmed an ⍺/β structure of a restriction endonuclease-like fold. The phylogenetic trees generated from multiple alignment of RAP domains and full-length proteins from various distantly related eukaryotes indicated a complex evolutionary history of this family. We further discuss these results to assess the potential function of this protein family in apicomplexan parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Lukasz Jaroszewski
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Adam Godzik
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
- *Correspondence: Karine G. Le Roch,
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Hillen LM, Vandyck HLD, Leunissen DJG, de Greef BTA, Bosisio FM, zur Hausen A, van den Oord J, Winnepenninckx V. Integrative histopathological and immunophenotypical characterisation of the inflammatory microenvironment in spitzoid melanocytic neoplasms. Histopathology 2021; 78:607-626. [PMID: 32970867 PMCID: PMC7894529 DOI: 10.1111/his.14259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
AIMS The role of inflammation in conventional cutaneous melanoma has been extensively studied, whereas only little is known about the inflammatory microenvironment and immunogenic properties of spitzoid melanocytic neoplasms. The composition of infiltrating immune cells and the architectural distribution of the inflammation, in particular, are still obscure. This is the first study, to our knowledge, to systematically characterise the inflammatory patterns and the leucocyte subsets in spitzoid melanocytic lesions. METHODS AND RESULTS We examined 79 spitzoid neoplasms including banal Spitz naevi (SN, n = 50), atypical Spitz tumours (AST, n = 17) and malignant Spitz tumours (MST, n = 12) using histopathological analysis and immunohistochemistry. Spitzoid melanocytic lesions showed a high frequency (67.1%, n = 53 of 79) of inflammation. Four inflammatory patterns were identified according to architectural composition, distribution and intensity of inflammation. The majority of the inflammatory infiltrate corresponded to CD3+ /CD8+ T lymphocytes (56.1%), followed by CD3+ /CD4+ T cells (35.7%) and CD68+ histiocytes (20.3%). CD3+ /TIA-1+ cytotoxic T lymphocytes constituted 3.7% of inflammatory cells. Rarely, CD3+ / granzyme B+ cytotoxic T lymphocytes (2.7%) and CD138+ plasma cells (0.5%) were detected in the infiltrating immune cells. There was no significant difference in the inflammatory cellular composition among the spitzoid melanocytic subgroups (SN versus AST versus MST). CONCLUSION Our findings demonstrate that Spitz tumours are highly immunogenic lesions. Inflammation with the presence of lymphocytic aggregates predominated in SN, but was not distinctive for this melanocytic category. A strong and intense inflammation was suggestive of an underlying malignancy. The infiltrating cytotoxic T lymphocyte subsets in Spitz tumours deserve further investigation in larger study cohorts to elucidate prognostic and immuno-oncological therapeutic relevance.
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Affiliation(s)
- Lisa M Hillen
- Department of PathologyGROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Hendrik L D Vandyck
- Department of PathologyGROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Daphne J G Leunissen
- Department of PathologyGROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Bianca T A de Greef
- Department of Clinical Epidemiology and Medical Technology AssessmentMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Francesca M Bosisio
- Laboratory for Translational Cell and Tissue Research (TCTR)University of LeuvenKULLeuvenBelgium
| | - Axel zur Hausen
- Department of PathologyGROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Joost van den Oord
- Laboratory for Translational Cell and Tissue Research (TCTR)University of LeuvenKULLeuvenBelgium
- Department of PathologyUniversity HospitalsLeuvenBelgium
| | - Véronique Winnepenninckx
- Department of PathologyGROW School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtthe Netherlands
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Chen X, Hu G, Wang Y, Li C, Zhang F. Fas-Activated Serine/Threonine Kinase Governs Cardiac Mitochondrial Complex I Functional Integrity in Ischemia/Reperfusion Heart. Front Cell Dev Biol 2021; 8:630421. [PMID: 33585470 PMCID: PMC7876271 DOI: 10.3389/fcell.2020.630421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022] Open
Abstract
Cardiac energy homeostasis is strictly controlled by the mitochondrial complex-mediated respiration. In the heart, mitochondrial complex I is highly susceptible to functional and structural destroy after ischemia/reperfusion (I/R), thereby contributing to myocardial energy insufficiency and cardiomyocyte death. Fas-activated serine/threonine kinase (FASTK) is recently recognized as a key modulator of mitochondrial gene expression and respiration. However, the role of FASTK in cardiac I/R process is undetermined. Here, we show that FASTK expression was down-regulated in the post-I/R heart. The reactive oxygen species scavenger N-acetyl-L-cysteine reversed I/R-induced FASTK down-regulation. Genetic deletion of FASTK exacerbated I/R-induced cardiac dysfunction, enlarged myocardial infarct size, and increased cardiomyocyte apoptosis. Compared with the wild type control, the FASTK deficient heart exhibited a lower mRNA expression of NADH dehydrogenase subunit-6 (MTND6, a mitochondrial gene encoding a subunit of complex I) and was more vulnerable to I/R-associated complex I inactivation. Replenishment of FASTK expression via adenovirus-mediated gene delivery restored mitochondrial complex I activity and ameliorated cardiomyocyte death induced by I/R, whereas these beneficial effects were blocked by the co-treatment with rotenone, a specific complex I inhibitor. in vivo experiments further confirmed that cardiac overexpression of FASTK ameliorated I/R-related MTND6 down-regulation and mitochondrial complex I inactivation, thereby protecting the heart against I/R injury. Collectively, these data for the first time identify that the down-regulation of FASTK is a direct culprit behind the loss of mitochondrial complex I functional integrity and cardiac injury induced by I/R process. Targeting FASTK might be a promising and effective strategy for MI/R intervention.
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Affiliation(s)
- Xiyao Chen
- Department of Geriatrics, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Guangyu Hu
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Yuanyuan Wang
- Department of Neurology, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Congye Li
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Fuyang Zhang
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, China.,Department of Physiology and Pathophysiology, Basic Medicine School, Air Force Medical University, Xi'an, China
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13
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Oberleitner L, Poschmann G, Macorano L, Schott-Verdugo S, Gohlke H, Stühler K, Nowack ECM. The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora. Front Microbiol 2020; 11:607182. [PMID: 33329499 PMCID: PMC7729196 DOI: 10.3389/fmicb.2020.607182] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
The endosymbiotic acquisition of mitochondria and plastids more than one billion years ago was central for the evolution of eukaryotic life. However, owing to their ancient origin, these organelles provide only limited insights into the initial stages of organellogenesis. The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles-termed chromatophores-that evolved from a cyanobacterium ∼100 million years ago, independently from plastids in plants and algae. Despite the more recent origin of the chromatophore, it shows tight integration into the host cell. It imports hundreds of nucleus-encoded proteins, and diverse metabolites are continuously exchanged across the two chromatophore envelope membranes. However, the limited set of chromatophore-encoded solute transporters appears insufficient for supporting metabolic connectivity or protein import. Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. These findings imply that similar to the situation in mitochondria and plastids, also in P. chromatophora nuclear factors evolved that control metabolite exchange and gene expression in the chromatophore. Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. Thus, despite the apparent maintenance of its barrier function, canonical metabolite transporters are missing in this membrane. Instead we identified several expanded groups of short chromatophore-targeted orphan proteins. Members of one of these groups are characterized by a single transmembrane helix, and others contain amphipathic helices. We hypothesize that these proteins are involved in modulating membrane permeability. Thus, the mechanism generating metabolic connectivity of the chromatophore fundamentally differs from the one for mitochondria and plastids, but likely rather resembles the poorly understood mechanism in various bacterial endosymbionts in plants and insects. Furthermore, our mass spectrometric analysis revealed an expanded family of chromatophore-targeted helical repeat proteins. These proteins show similar domain architectures as known organelle-targeted expression regulators of the octotrico peptide repeat type in algae and plants. Apparently these chromatophore-targeted proteins evolved convergently to plastid-targeted expression regulators and are likely involved in gene expression control in the chromatophore.
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Affiliation(s)
- Linda Oberleitner
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Poschmann
- Medical Faculty, Institute for Molecular Medicine, Proteome Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luis Macorano
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Schott-Verdugo
- Department of Pharmacy, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Faculty of Engineering, Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - Holger Gohlke
- Department of Pharmacy, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Jülich Supercomputing Centre, John von Neumann Institute for Computing, Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kai Stühler
- Medical Faculty, Institute for Molecular Medicine, Proteome Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eva C. M. Nowack
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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14
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Alriyami M, Marchand L, Li Q, Du X, Olivier M, Polychronakos C. Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice. Genome Res 2019; 29:1951-1961. [PMID: 31694869 PMCID: PMC6886509 DOI: 10.1101/gr.247882.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/02/2019] [Indexed: 01/10/2023]
Abstract
Concordance for type 1 diabetes (T1D) is far from 100% in monozygotic twins and in inbred nonobese diabetic (NOD) mice, despite genetic identity and shared environment during incidence peak years. This points to stochastic determinants, such as postzygotic mutations (PZMs) in the expanding antigen-specific autoreactive T cell lineages, by analogy to their role in the expanding tumor lineage in cancer. Using comparative genomic hybridization of DNA from pancreatic lymph-node memory CD4+ T cells of 25 diabetic NOD mice, we found lymphocyte-exclusive mosaic somatic copy-number aberrations (CNAs) with highly nonrandom independent involvement of the same gene(s) across different mice, some with an autoimmunity association (e.g., Ilf3 and Dgka). We confirmed genes of interest using the gold standard approach for CNA quantification, multiplex ligation-dependent probe amplification (MLPA), as an independent method. As controls, we examined lymphocytes expanded during normal host defense (17 NOD and BALB/c mice infected with Leishmania major parasite). Here, CNAs found were fewer and significantly smaller compared to those in autoreactive cells (P = 0.0019). We determined a low T cell clonality for our samples suggesting a prethymic formation of these CNAs. In this study, we describe a novel, unexplored phenomenon of a potential causal contribution of PZMs in autoreactive T cells in T1D pathogenesis. We expect that exploration of point mutations and studies in human T cells will enable the further delineation of driver genes to target for functional studies. Our findings challenge the classical notions of autoimmunity and open conceptual avenues toward individualized prevention and therapeutics.
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Affiliation(s)
- Maha Alriyami
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada.,Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, 123, Muscat, Oman
| | - Luc Marchand
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Quan Li
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON M5G 2C1, Canada
| | - Xiaoyu Du
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Martin Olivier
- Departments of Medicine, Microbiology, and Immunology, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Constantin Polychronakos
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
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15
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García Del Río A, Delmiro A, Martín MA, Cantalapiedra R, Carretero R, Durántez C, Menegotto F, Morán M, Serrano-Lorenzo P, De la Fuente MA, Orduña A, Simarro M. The Mitochondrial Isoform of FASTK Modulates Nonopsonic Phagocytosis of Bacteria by Macrophages via Regulation of Respiratory Complex I. THE JOURNAL OF IMMUNOLOGY 2018; 201:2977-2985. [PMID: 30322967 DOI: 10.4049/jimmunol.1701075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Abstract
Phagocytosis is a pivotal process by which innate immune cells eliminate bacteria. In this study, we explore novel regulatory mechanisms of phagocytosis driven by the mitochondria. Fas-activated serine/threonine kinase (FASTK) is an RNA-binding protein with two isoforms, one localized to the mitochondria (mitoFASTK) and the other isoform to cytosol and nucleus. The mitoFASTK isoform has been reported to be necessary for the biogenesis of the mitochondrial ND6 mRNA, which encodes an essential subunit of mitochondrial respiratory complex I (CI, NADH:ubiquinone oxidoreductase). This study investigates the role and the mechanisms of action of FASTK in phagocytosis. Macrophages from FASTK─/─ mice exhibited a marked increase in nonopsonic phagocytosis of bacteria. As expected, CI activity was specifically reduced by almost 50% in those cells. To explore if decreased CI activity could underlie the phagocytic phenotype, we tested the effect of CI inhibition on phagocytosis. Indeed, treatment with CI inhibitor rotenone or short hairpin RNAs against two CI subunits (NDUFS3 and NDUFS4) resulted in a marked increase in nonopsonic phagocytosis of bacteria. Importantly, re-expression of mitoFASTK in FASTK-depleted macrophages was sufficient to rescue the phagocytic phenotype. In addition, we also report that the decrease in CI activity in FASTK─/─ macrophages is associated with an increase in phosphorylation of the energy sensor AMP-activated protein kinase (AMPK) and that its inhibition using Compound C reverted the phagocytosis phenotype. Taken together, our results clearly demonstrate for the first time, to our knowledge, that mitoFASTK plays a negative regulatory role on nonopsonic phagocytosis of bacteria in macrophages through its action on CI activity.
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Affiliation(s)
| | - Aitor Delmiro
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | - Miguel Angel Martín
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | | | - Raquel Carretero
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - Carlos Durántez
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - Fabiola Menegotto
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - María Morán
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | - Pablo Serrano-Lorenzo
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Miguel Angel De la Fuente
- Department of Cell Biology, Histology and Pharmacology, University of Valladolid, 47005 Valladolid, Spain; .,Institute of Biology and Molecular Genetics, 47003 Valladolid, Spain
| | - Antonio Orduña
- Department of Microbiology, University of Valladolid, Valladolid, Spain.,Departamento de Microbiología e Inmunología, Hospital Clínico Universitario, 47003 Valladolid, Spain; and
| | - María Simarro
- Department of Nursing, University of Valladolid, 47005 Valladolid, Spain
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16
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Khan NS, Khan P, Ansari MF, Srivastava S, Hasan GM, Husain M, Hassan MI. Thienopyrimidine-Chalcone Hybrid Molecules Inhibit Fas-Activated Serine/Threonine Kinase: An Approach To Ameliorate Antiproliferation in Human Breast Cancer Cells. Mol Pharm 2018; 15:4173-4189. [PMID: 30040903 DOI: 10.1021/acs.molpharmaceut.8b00566] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Apoptotic evasion by cancerous cells being one of the striking hallmarks of cancer has turned into a new arena of drug discovery. A large number of pathways reported that govern the apoptotic evasion have been reported. Fas-activated serine/threonine kinase (FASTK) is a member of Ser/Thr kinase family, and it has been implicated in the apoptotic evasion and, hence, the development of cancer. Keeping this in view, a series of novel thienopyrimidine-based chalcones have been synthesized and evaluated to modulate the FASTK mediated apoptotic evasion. Initial screening was done by enzyme inhibition assay and binding studies, which showed that out of 15 synthesized compounds, 3 thienopyrimidine-based chalcone derivatives possess considerably high binding affinity and enzyme inhibitory potential (nM range) for FASTK. Cell proliferation assessment of selected compounds was performed on HEK-293 and MCF-7 cells. For MCF-7 cells, compounds 2, 10, and 12 show IC50 values of 20.22 ± 1.50, 6.52 ± 0.82, and 8.20 ± 0.61 μM, respectively. Annexin-V and PI staining suggested that these molecules induce apoptosis in MCF-7 cells, arrest the cell cycle in the G0/G1 phase, and subsequently inhibit cell migration presumably by inhibiting FASTK and reactive oxygen species production. In conclusion, we have successfully designed, synthesized, and characterized thienopyrimidine-based chalcones that inhibit FASTK and induce apoptosis. These compounds may be exploited as potential anticancer agents.
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Affiliation(s)
| | | | | | | | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine , Prince Sattam Bin Abdulaziz University , Al-Kharj 11942 , Saudi Arabia
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17
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Laskowski D, Humblot P, Sirard MA, Sjunnesson Y, Jhamat N, Båge R, Andersson G. DNA methylation pattern of bovine blastocysts associated with hyperinsulinemia in vitro. Mol Reprod Dev 2018; 85:599-611. [PMID: 29745447 DOI: 10.1002/mrd.22995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 12/22/2022]
Abstract
Insulin functions as a regulator of metabolism and plays an important role in reproduction. Hyperinsulinemia is often observed in patients with obesity and diabetes type 2 and is known to impair fertility, but the underlying molecular mechanisms are only partly understood. Metabolic programming through epigenetic mechanisms such as DNA methylation during embryonic development can lead to health implications for the offspring later in life. Our aim was to study the potential effect of hyperinsulinemia on gene expression and DNA methylation of embryos by adding insulin (0.1 µg/ml = INS0.1 or 10 µg/ml = INS10) during in vitro oocyte maturation by using the EmbryoGENE DNA methylation array for a study of the bovine epigenome. Our results showed significant differences between blastocysts originating from insulin-treated oocytes compared with untreated control blastocysts. In total, 13,658 and 12,418 probes were differentially methylated (DM) in INS0.1 and INS10, respectively, with an overlap of 3,233 probes in the DM regions (DMR) for both insulin groups. Genes related to pathways such as lipid metabolism, growth and proliferation, mitochondrial function, and oxidative stress responses were influenced at both the epigenetic and transcriptomic levels. In addition, imprinted genes and genes with functions in the epigenetic machinery were among the DMRs. This study identified DMRs correlated to differential expression of genes involved in metabolic regulation and should help to improve our knowledge of the underlying molecular mechanisms of metabolic imbalance.
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Affiliation(s)
- Denise Laskowski
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Patrice Humblot
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Marc-André Sirard
- Departement des Sciences Animales, Centre de Recherche en Développement Reproduction et Santé Intergénérationnelle (CRDSI) Pavillon Des Services, University Laval, Québec, Canada
| | - Ylva Sjunnesson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Naveed Jhamat
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Renée Båge
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Göran Andersson
- The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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18
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Jourdain AA, Popow J, de la Fuente MA, Martinou JC, Anderson P, Simarro M. The FASTK family of proteins: emerging regulators of mitochondrial RNA biology. Nucleic Acids Res 2017; 45:10941-10947. [PMID: 29036396 PMCID: PMC5737537 DOI: 10.1093/nar/gkx772] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022] Open
Abstract
The FASTK family proteins have recently emerged as key post-transcriptional regulators of mitochondrial gene expression. FASTK, the founding member and its homologs FASTKD1-5 are architecturally related RNA-binding proteins, each having a different function in the regulation of mitochondrial RNA biology, from mRNA processing and maturation to ribosome assembly and translation. In this review, we outline the structure, evolution and function of these FASTK proteins and discuss the individual role that each has in mitochondrial RNA biology. In addition, we highlight the aspects of FASTK research that still require more attention.
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Affiliation(s)
- Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Johannes Popow
- Department of Cancer Cell Signalling, Boehringer-Ingelheim Regional Center Vienna, 1121 Vienna, Austria
| | - Miguel A de la Fuente
- Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | | | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Maria Simarro
- Departamento de Enfermería, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
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19
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Esnault S, Shen ZJ, Malter JS. Protein Translation and Signaling in Human Eosinophils. Front Med (Lausanne) 2017; 4:150. [PMID: 28971096 PMCID: PMC5609579 DOI: 10.3389/fmed.2017.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 01/01/2023] Open
Abstract
We have recently reported that, unlike IL-5 and GM-CSF, IL-3 induces increased translation of a subset of mRNAs. In addition, we have demonstrated that Pin1 controls the activity of mRNA binding proteins, leading to enhanced mRNA stability, GM-CSF protein production and prolonged eosinophil (EOS) survival. In this review, discussion will include an overview of cap-dependent protein translation and its regulation by intracellular signaling pathways. We will address the more general process of mRNA post-transcriptional regulation, especially regarding mRNA binding proteins, which are critical effectors of protein translation. Furthermore, we will focus on (1) the roles of IL-3-driven sustained signaling on enhanced protein translation in EOS, (2) the mechanisms regulating mRNA binding proteins activity in EOS, and (3) the potential targeting of IL-3 signaling and the signaling leading to mRNA binding activity changes to identify therapeutic targets to treat EOS-associated diseases.
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Affiliation(s)
- Stephane Esnault
- Department of Medicine, Allergy, Pulmonary, and Critical Care Medicine Division, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
| | - Zhong-Jian Shen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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20
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Srivastava S, Syed SB, Kumar V, Islam A, Ahmad F, Hassan MI. Fas-activated serine/threonine kinase: Structure and function. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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21
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Abstract
Efficient viral gene expression is threatened by cellular stress response programmes that rapidly reprioritize the translation machinery in response to varied environmental assaults, including virus infection. This results in inhibition of bulk synthesis of housekeeping proteins and causes the aggregation of messenger ribonucleoprotein complexes into cytoplasmic foci that are known as stress granules, which can entrap viral mRNAs. There is accumulating evidence for the antiviral nature of stress granules, which is supported by the discovery of many viral factors that interfere with stress granule formation and/or function. This Review focuses on recent advances in our understanding of the role of translation inhibition and stress granules in antiviral immune responses.
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22
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Rayman JB, Kandel ER. TIA-1 Is a Functional Prion-Like Protein. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a030718. [PMID: 28003185 DOI: 10.1101/cshperspect.a030718] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prions are self-propagating protein conformations that are traditionally regarded as agents of neurodegenerative disease in animals. However, it has become evident that prion-like aggregation of endogenous proteins can also occur under normal physiological conditions (e.g., during memory storage or activation of the immune response). In this review, we focus on the functional prion-related protein TIA-1, an RNA-binding protein that is involved in multiple aspects of RNA metabolism but is best understood in terms of its role in stress granule assembly during the cellular stress response. We propose that stress granule formation provides a useful conceptual framework with which to address the positive role of TIA-1 prion-like aggregation. Elucidating the function of TIA-1 prion-like aggregation will advance our understanding of how prion-based molecular switches are used in normal physiological settings.
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Affiliation(s)
- Joseph B Rayman
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, New York 10032
| | - Eric R Kandel
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, New York 10032.,Department of Psychiatry, College of Physicians and Surgeons of Columbia University, New York, New York 10032.,Howard Hughes Medical Institute at Columbia University, New York, New York 10032.,Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York 10032.,Kavli Institute for Brain Science, Columbia University, New York, New York 10032
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23
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MiR-106a: Promising biomarker for cancer. Bioorg Med Chem Lett 2016; 26:5373-5377. [PMID: 27780637 DOI: 10.1016/j.bmcl.2016.10.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/23/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs), which are characterized by highly conserved and small non-coding RNAs, have been a hot spot regarding biological processes such as cellular proliferation, apoptosis and metabolism as well as cellular differentiation, signal transduction and carcinogenesis. MiRNA-106a (miR-106a), a member of the miR-17 family, has been validated to be aberrantly regulated in the diversity of tumors. The purpose of this review is supposed to deliver an intricate overview of miR-106a, including its role in cell proliferation, apoptosis, cell cycle, invasion and metastasis, involvement in drug resistance as well as its interactions with the target proteins and signaling pathways involved.
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24
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Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-related/like protein (TIAR/TIAL1) are 2 proteins discovered in 1991 as components of cytotoxic T lymphocyte granules. They act in the nucleus as regulators of transcription and pre-mRNA splicing. In the cytoplasm, TIA1 and TIAR regulate and/or modulate the location, stability and/or translation of mRNAs. As knowledge of the different genes regulated by these proteins and the cellular/biological programs in which they are involved increases, it is evident that these antigens are key players in human physiology and pathology. This review will discuss the latest developments in the field, with physiopathological relevance, that point to novel roles for these regulators in the molecular and cell biology of higher eukaryotes.
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Affiliation(s)
- Carmen Sánchez-Jiménez
- a Centro de Biología Molecular Severo Ochoa; Consejo Superior de Investigaciones Científicas; Universidad Autónoma de Madrid (CSIC/UAM); C/Nicolás Cabrera 1 ; Madrid , Spain
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25
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Shtir C, Aldahmesh MA, Al-Dahmash S, Abboud E, Alkuraya H, Abouammoh MA, Nowailaty SR, Al-Thubaiti G, Naim EA, ALYounes B, Binhumaid FS, ALOtaibi AB, Altamimi AS, Alamer FH, Hashem M, Abouelhoda M, Monies D, Alkuraya FS. Exome-based case–control association study using extreme phenotype design reveals novel candidates with protective effect in diabetic retinopathy. Hum Genet 2015; 135:193-200. [DOI: 10.1007/s00439-015-1624-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/09/2015] [Indexed: 01/16/2023]
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26
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Roncati L, Barbolini G, Piacentini F, Piscioli F, Pusiol T, Maiorana A. Prognostic Factors for Breast Cancer: an Immunomorphological Update. Pathol Oncol Res 2015; 22:449-52. [DOI: 10.1007/s12253-015-0024-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 11/16/2015] [Indexed: 11/30/2022]
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27
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Popow J, Alleaume AM, Curk T, Schwarzl T, Sauer S, Hentze MW. FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation. RNA (NEW YORK, N.Y.) 2015; 21:1873-84. [PMID: 26370583 PMCID: PMC4604428 DOI: 10.1261/rna.052365.115] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/13/2015] [Indexed: 05/26/2023]
Abstract
Mitochondrial RNA processing is an essential step for the synthesis of the components of the electron transport chain in all eukaryotic organisms, yet several aspects of mitochondrial RNA biogenesis and regulation are not sufficiently understood. RNA interactome capture identified several disease-relevant RNA-binding proteins (RBPs) with noncanonical RNA-binding architectures, including all six members of the FASTK (FAS-activated serine/threonine kinase) family of proteins. A mutation within one of these newly assigned FASTK RBPs, FASTKD2, causes a rare form of Mendelian mitochondrial encephalomyopathy. To investigate whether RNA binding of FASTKD2 contributes to the disease phenotype, we identified the RNA targets of FASTKD2 by iCLIP. FASTKD2 interacts with a defined set of mitochondrial transcripts including 16S ribosomal RNA (RNR2) and NADH dehydrogenase subunit 6 (ND6) messenger RNA. CRISPR-mediated deletion of FASTKD2 leads to aberrant processing and expression of RNR2 and ND6 mRNA that encodes a subunit of the respiratory complex I. Metabolic phenotyping of FASTKD2-deficient cells reveals impaired cellular respiration with reduced activities of all respiratory complexes. This work identifies key aspects of the molecular network of a previously uncharacterized, disease-relevant RNA-binding protein, FASTKD2, by a combination of genomic, molecular, and metabolic analyses.
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Affiliation(s)
- Johannes Popow
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sven Sauer
- Division of Inherited Metabolic Diseases, Department of General Pediatrics, University Children's Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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Shen ZJ, Malter JS. Regulation of AU-Rich Element RNA Binding Proteins by Phosphorylation and the Prolyl Isomerase Pin1. Biomolecules 2015; 5:412-34. [PMID: 25874604 PMCID: PMC4496679 DOI: 10.3390/biom5020412] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023] Open
Abstract
The accumulation of 3' untranslated region (3'-UTR), AU-rich element (ARE) containing mRNAs, are predominantly controlled at the post-transcriptional level. Regulation appears to rely on a variable and dynamic interaction between mRNA target and ARE-specific binding proteins (AUBPs). The AUBP-ARE mRNA recognition is directed by multiple intracellular signals that are predominantly targeted at the AUBPs. These include (but are unlikely limited to) methylation, acetylation, phosphorylation, ubiquitination and isomerization. These regulatory events ultimately affect ARE mRNA location, abundance, translation and stability. In this review, we describe recent advances in our understanding of phosphorylation and its impact on conformation of the AUBPs, interaction with ARE mRNAs and highlight the role of Pin1 mediated prolyl cis-trans isomerization in these biological process.
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Affiliation(s)
- Zhong-Jian Shen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8548, USA.
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8548, USA.
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A mitochondria-specific isoform of FASTK is present in mitochondrial RNA granules and regulates gene expression and function. Cell Rep 2015; 10:1110-21. [PMID: 25704814 DOI: 10.1016/j.celrep.2015.01.063] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/10/2014] [Accepted: 01/29/2015] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome relies heavily on post-transcriptional events for its proper expression, and misregulation of this process can cause mitochondrial genetic diseases in humans. Here, we report that a novel translational variant of Fas-activated serine/threonine kinase (FASTK) co-localizes with mitochondrial RNA granules and is required for the biogenesis of ND6 mRNA, a mitochondrial-encoded subunit of the NADH dehydrogenase complex (complex I). We show that ablating FASTK expression in cultured cells and mice results specifically in loss of ND6 mRNA and reduced complex I activity in vivo. FASTK binds at multiple sites along the ND6 mRNA and its precursors and cooperates with the mitochondrial degradosome to ensure regulated ND6 mRNA biogenesis. These data provide insights into the mechanism and control of mitochondrial RNA processing within mitochondrial RNA granules.
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Das S, Yeung KT, Mahajan MA, Samuels HH. Fas Activated Serine-Threonine Kinase Domains 2 (FASTKD2) mediates apoptosis of breast and prostate cancer cells through its novel FAST2 domain. BMC Cancer 2014; 14:852. [PMID: 25409762 PMCID: PMC4256816 DOI: 10.1186/1471-2407-14-852] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/07/2014] [Indexed: 11/17/2022] Open
Abstract
Background Expression of NRIF3 (Nuclear Receptor Interacting Factor-3) rapidly and selectively leads to apoptosis of breast cancer cells. This occurs through binding of NRIF3 or its 30 amino acid Death Domain-1 (DD1) region to the transcriptional repressor, DIF-1 (DD1 Interacting Factor-1). DIF-1 acts in a wide variety of breast cancer cells but not other cell types to repress the pro-apoptotic gene, FASTKD2. Expression of NRIF3 or DD1 inactivates the DIF-1 repressor leading to rapid derepression of FASTKD2, which initiates apoptosis within 5–8 h of expression. Although FASTKD2 is an inner mitochondrial membrane protein, it does not require mitochondrial localization to initiate apoptosis. Methods Androgen dependent LNCaP cells as well as two androgen independent LNCaP cell lines (LNCaP-AI and LNCaP-abl) were studied and LNCaP-AI cells were engineered to conditionally express DD1 or the inactive DD1-S28A with 4-hydroxytamoxifen. Apoptosis was assessed by TUNEL assay. FASTKD2 is related to 4 other proteins encoded in the human genome (FASTKD1, 3, 4, 5). All contain a poorly conserved putative bipartite kinase domain designated as FAST1_FAST2. We examined whether expression of any of the other FASTKD isoforms leads to apoptosis and sought to identify the region of FASTKD2 necessary to initiate the apoptotic pathway. Results Of the FASTKD1-5 isoforms only expression of FASTKD2 leads to apoptosis. Although, the NRIF3/DD1/DIF-1 pathway does not mediate apoptosis of a wide variety of non-breast cancer cell lines, because of certain similarities and gene signatures between breast and prostate cancer we explored whether the NRIF3/DD1/DIF-1/FASTKD2 pathway mediates apoptosis of prostate cancer cells. We found that the pathway leads to apoptosis in LNCaP cells, including the two androgen-independent LNCaP cell lines that are generally resistant to apoptosis. Lastly, we identified that FASTKD2-mediated apoptosis is initiated by the 81 amino acid FAST2 region. Conclusions The NRIF3/DIF-1/FASTKD2 pathway acts as a “death switch” in breast and prostate cancer cells. Deciphering how this pathway is regulated and how FASTKD2 initiates the apoptotic response will allow for the development of therapeutic agents for the treatment of androgen-independent prostate cancer or Tamoxifen-unresponsive Estrogen Receptor negative tumors as well as metastatic breast or prostate cancer.
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Affiliation(s)
| | | | | | - Herbert H Samuels
- Department of Biochemistry and Molecular Pharmacology, PHL 814, New York University School of Medicine, 455 First Ave,, New York, NY 10016, USA.
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Huang S, Liu N, Li H, Zhao J, Su L, Zhang Y, Zhang S, Zhao B, Miao J. TIA1 interacts with annexin A7 in regulating vascular endothelial cell autophagy. Int J Biochem Cell Biol 2014; 57:115-22. [PMID: 25461769 DOI: 10.1016/j.biocel.2014.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/27/2014] [Accepted: 10/09/2014] [Indexed: 01/11/2023]
Abstract
T-cell intracellular antigen-1 (TIA1) is a DNA/RNA binding protein broadly expressed in eukaryotic cells, participating in multiple aspects of cellular metabolism. TIA1 phosphorylation was related with cell apoptosis and its RNA binding activity, however, the regulator and other functions of TIA1 phosphorylation were very little known. To find the modulator of TIA1 phosphorylation, we performed yeast two-hybrid screening and identified annexin A7 (ANXA7) as an interaction protein of TIA1. Recent study showed that a small molecule ABO could directly target ANXA7 and inhibit ANXA7 activity and its targets' phosphorylation. As a GTPase, ANXA7 was speculated to modulate TIA1 phosphorylation. Our results showed that ABO treatment promoted the interaction between TIA1 and ANXA7, and then greatly inhibited phosphorylation of TIA1 in HUVECs. Further results showed that ABO-increased interaction between ANXA7 and TIA1 significantly promoted the processing of a pro-autophagic factor FLJ11812 and the expression of ATG13. Moreover, we found that ABO increased TIA1 protein level, co-localization of ANXA7 and TIA1, and ATG13 expression in the aortic endothelium of apoE(-/-) mice. These data highlighted the new role of TIA1 phosphorylation in autophagy.
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Affiliation(s)
- Shuya Huang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ning Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Haiying Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jing Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Shandong University Qilu Hospital, Jinan 250012, China
| | - Shangli Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Baoxiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Junying Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Shandong University Qilu Hospital, Jinan 250012, China.
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Wang I, Hennig J, Jagtap PKA, Sonntag M, Valcárcel J, Sattler M. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1. Nucleic Acids Res 2014; 42:5949-66. [PMID: 24682828 PMCID: PMC4027183 DOI: 10.1093/nar/gku193] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.
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Affiliation(s)
- Iren Wang
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Miriam Sonntag
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Center for Integrated Protein Science Munich and Biomolecular NMR, Department Chemie Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
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Dinh PX, Das A, Franco R, Pattnaik AK. Heterogeneous nuclear ribonucleoprotein K supports vesicular stomatitis virus replication by regulating cell survival and cellular gene expression. J Virol 2013; 87:10059-69. [PMID: 23843646 PMCID: PMC3754001 DOI: 10.1128/jvi.01257-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/30/2013] [Indexed: 11/20/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a member of the family of hnRNPs and was recently shown in a genome-wide small interfering RNA (siRNA) screen to support vesicular stomatitis virus (VSV) growth. To decipher the role of hnRNP K in VSV infection, we conducted studies which suggest that the protein is required for VSV spreading. Virus binding to cells, entry, and nucleocapsid uncoating steps were not adversely affected in the absence of hnRNP K, whereas viral genome transcription and replication were reduced slightly. These results indicate that hnRNP K is likely involved in virus assembly and/or release from infected cells. Further studies showed that hnRNP K suppresses apoptosis of virus-infected cells, resulting in increased cell survival during VSV infection. The increased survival of the infected cells was found to be due to the suppression of proapoptotic proteins such as Bcl-XS and Bik in a cell-type-dependent manner. Additionally, depletion of hnRNP K resulted in not only significantly increased levels of T-cell-restricted intracellular antigen 1 (TIA1) but also switching of the expression of the two isoforms of the protein (TIA1a and TIA1b), both of which inhibited VSV replication. hnRNP K was also found to support expression of several cellular proteins known to be required for VSV infection. Overall, our studies demonstrate hnRNP K to be a multifunctional protein that supports VSV infection via its role(s) in suppressing apoptosis of infected cells, inhibiting the expression of antiviral proteins, and maintaining the expression of proteins required for the virus.
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Affiliation(s)
- Phat X. Dinh
- School of Veterinary Medicine and Biomedical Sciences
- Nebraska Center for Virology, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Anshuman Das
- School of Veterinary Medicine and Biomedical Sciences
- Nebraska Center for Virology, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | | | - Asit K. Pattnaik
- School of Veterinary Medicine and Biomedical Sciences
- Nebraska Center for Virology, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
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Silva-García CG, Estela Navarro R. The C. elegans TIA-1/TIAR homolog TIAR-1 is required to induce germ cell apoptosis. Genesis 2013; 51:690-707. [PMID: 23913578 DOI: 10.1002/dvg.22418] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 11/11/2022]
Abstract
In Caenorhabditis elegans, physiological germ cell apoptosis eliminates more than half of the cells in the hermaphrodite gonad to support gamete quality and germline homeostasis by a still unidentified mechanism. External factors can also affect germ cell apoptosis. The BH3-only protein EGL-1 induces germ cell apoptosis when animals are exposed to pathogens or agents that produce DNA damage. DNA damage-induced apoptosis also requires the nematode p53 homolog CEP-1. Previously, we found that heat shock, oxidative, and osmotic stresses induce germ cell apoptosis through an EGL-1 and CEP-1 independent mechanism that requires the MAPKK pathway. However, we observed that starvation increases germ cell apoptosis by an unknown pathway. Searching for proteins that participate in stress-induced apoptosis, we found the RNA-binding protein TIAR-1 (a homolog of the mammalian TIA-1/TIAR family of proteins). Here, we show that TIAR-1 in C. elegans is required to induce apoptosis in the germline under several conditions. We also show that TIAR-1 acts downstream of CED-9 (a BCL2 homolog) to induce apoptosis under stress conditions, and apparently does not seem to regulate ced-4 or ced-3 mRNAs accumulation directly. TIAR-1 is expressed ubiquitously in the cytoplasm of the soma as well as the germline, where it sometimes associates with P granules. We show that animals lacking TIAR-1 expression are temperature sensitive sterile due to oogenesis and spermatogenesis defects. Our work shows that TIAR-1 is required for proper germline function and demonstrates that this protein is important to induce germ cell apoptosis under several conditions.
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Affiliation(s)
- Carlos Giovanni Silva-García
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
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Naro C, Sette C. Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
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Zhi F, Zhou G, Shao N, Xia X, Shi Y, Wang Q, Zhang Y, Wang R, Xue L, Wang S, Wu S, Peng Y, Yang Y. miR-106a-5p inhibits the proliferation and migration of astrocytoma cells and promotes apoptosis by targeting FASTK. PLoS One 2013; 8:e72390. [PMID: 24013584 PMCID: PMC3754986 DOI: 10.1371/journal.pone.0072390] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/09/2013] [Indexed: 01/11/2023] Open
Abstract
Astrocytomas are common malignant intracranial tumors that comprise the majority of adult primary central nervous system tumors. MicroRNAs (miRNAs) are small, non-coding RNAs (20–24 nucleotides) that post-transcriptionally modulate gene expression by negatively regulating the stability or translational efficiency of their target mRNAs. In our previous studies, we found that the downregulation of miR-106a-5p in astrocytomas is associated with poor prognosis. However, its specific gene target(s) and underlying functional mechanism(s) in astrocytomas remain unclear. In this study, we used mRNA microarray experiments to measure global mRNA expression in the presence of increased or decreased miR-106a-5p levels. We then performed bioinformatics analysis based on multiple target prediction algorithms to obtain candidate target genes that were further validated by computational predictions, western blot analysis, quantitative real-time PCR, and the luciferase reporter assay. Fas-activated serine/threonine kinase (FASTK) was identified as a direct target of miR-106a-5p. In human astrocytomas, miR-106a-5p is downregulated and negatively associated with clinical staging, whereas FASTK is upregulated and positively associated with advanced clinical stages, at both the protein and mRNA levels. Furthermore, Kaplan-Meier analysis revealed that the reduced expression of miR-106a-5p or the increased expression of FASTK is significantly associated with poor survival outcome. These results further supported the finding that FASTK is a direct target gene of miR-106a-5p. Next, we explored the function of miR-106a-5p and FASTK during astrocytoma progression. Through gain-of-function and loss-of-function studies, we demonstrated that miR-106a-5p can significantly inhibit cell proliferation and migration and can promote cell apoptosis in vitro. The knockdown of FASTK induced similar effects on astrocytoma cells as those induced by the overexpression of miR-106a-5p. These observations suggest that miR-106a-5p functions as a tumor suppressor during the development of astrocytomas by targeting FASTK.
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Affiliation(s)
- Feng Zhi
- Modern Medical Research Center, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Guangxin Zhou
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Naiyuan Shao
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Xiwei Xia
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Yimin Shi
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Qiang Wang
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Yi Zhang
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Rong Wang
- Modern Medical Research Center, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Lian Xue
- Modern Medical Research Center, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Suinuan Wang
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Sujia Wu
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
- * E-mail: (YY); (YP); (SW)
| | - Ya Peng
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
- * E-mail: (YY); (YP); (SW)
| | - Yilin Yang
- Modern Medical Research Center, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
- * E-mail: (YY); (YP); (SW)
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Parmar A, Greco D, Venäläinen J, Gentile M, Dukes E, Saavalainen P. Gene Expression Profiling of Gliadin Effects on Intestinal Epithelial Cells Suggests Novel Non-Enzymatic Functions of Pepsin and Trypsin. PLoS One 2013; 8:e66307. [PMID: 23824913 PMCID: PMC3688875 DOI: 10.1371/journal.pone.0066307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/03/2013] [Indexed: 01/11/2023] Open
Abstract
Gliadin triggers T-cell mediated immunity in celiac disease, and has cytotoxic effects on enterocytes mediated through obscure mechanisms. In addition, gliadin transport mechanisms, potential cell surface receptors and gliadin-activated downstream signaling pathways are not completely understood. In order to screen for novel downstream gliadin target genes we performed a systematic whole genome expression study on intestinal epithelial cells. Undifferentiated Caco-2 cells were exposed to pepsin- and trypsin- digested gliadin (PT-G), a blank pepsin-trypsin control (PT) and to a synthetic peptide corresponding to gliadin p31-43 peptide for six hours. RNA from four different experiments was used for hybridization on Agilent one color human whole genome DNA microarray chips. The microarray data were analyzed using the Bioconductor package LIMMA. Genes with nominal p<0.01 were considered statistically significant. Compared to the untreated cells 1705, 1755 and 211 probes were affected by PT-G, PT and p31-43 respectively. 46 probes were significantly different between PT and PT-G treated cells. Among the p31-43 peptide affected probes, 10 and 21 probes were affected by PT-G and PT respectively. Only PT-G affected genes could be validated by quantitative real-time polymerase chain reaction. All the genes were, nonetheless, also affected to a comparable level by PT treated negative controls. In conclusion, we could not replicate previously reported direct effects of gliadin peptides on enterocytes. The results rather suggest that certain epitopes derived from pepsin and trypsin may also affect epithelial cell gene transcription. Our study suggests novel non-enzymatic effects of pepsin and trypsin on cells and calls for proper controls in pepsin and trypsin digested gliadin experiments. It is conceivable that gliadin effects on enterocytes are secondary mediated through oxidative stress, NFkB activation and IL-15 up-regulation.
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Affiliation(s)
- Amarjit Parmar
- Research Programs Unit, Immunobiology, and Haartman Institute, Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Department of Bioscience and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Jarkko Venäläinen
- Department of Pharmacology and Toxicology, University of Eastern Finland, Kuopio, Finland
| | | | - Emma Dukes
- Research Programs Unit, Immunobiology, and Haartman Institute, Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, and Haartman Institute, Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- * E-mail:
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Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev 2013; 253:216-36. [PMID: 23550649 PMCID: PMC3621013 DOI: 10.1111/imr.12047] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most mammalian pre-mRNAs are alternatively spliced in a manner that alters the resulting open reading frame. Consequently, alternative pre-mRNA splicing provides an important RNA-based layer of protein regulation and cellular function. The ubiquitous nature of alternative splicing coupled with the advent of technologies that allow global interrogation of the transcriptome have led to an increasing awareness of the possibility that widespread changes in splicing patterns contribute to lymphocyte function during an immune response. Indeed, a few notable examples of alternative splicing have clearly been demonstrated to regulate T-cell responses to antigen. Moreover, several proteins key to the regulation of splicing in T cells have recently been identified. However, much remains to be done to truly identify the spectrum of genes that are regulated at the level of splicing in immune cells and to determine how many of these are controlled by currently known factors and pathways versus unknown mechanisms. Here, we describe the proteins, pathways, and mechanisms that have been shown to regulate alternative splicing in human T cells and discuss what is and is not known about the genes regulated by such factors. Finally, we highlight unifying themes with regards to the mechanisms and consequences of alternative splicing in the adaptive immune system and give our view of important directions for future studies.
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Affiliation(s)
- Nicole M Martinez
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, USA
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Abstract
The number of available eukaryotic genomes has expanded to the point where we can evaluate the complete evolutionary history of many cellular processes. Such analyses for the apoptosis regulatory networks suggest that this network already existed in the ancestor of the entire animal kingdom (Metazoa) in a form more complex than in some popular animal model organisms. This supports the growing realization that regulatory networks do not necessarily evolve from simple to complex and that the relative simplicity of these networks in nematodes and insects does not represent an ancestral state, but is the result of secondary simplifications. Network evolution is not a process of monotonous increase in complexity, but a dynamic process that includes lineage-specific gene losses and expansions, protein domain reshuffling, and emergence/reemergence of similar protein architectures by parallel evolution. Studying the evolution of such networks is a challenging yet interesting subject for research and investigation, and such studies on the apoptosis networks provide us with interesting hints of how these networks, critical in so many human diseases, have developed.
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Affiliation(s)
- Christian M Zmasek
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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Daburon S, Devaud C, Costet P, Morello A, Garrigue-Antar L, Maillasson M, Hargous N, Lapaillerie D, Bonneu M, Dechanet-Merville J, Legembre P, Capone M, Moreau JF, Taupin JL. Functional characterization of a chimeric soluble Fas ligand polymer with in vivo anti-tumor activity. PLoS One 2013; 8:e54000. [PMID: 23326557 PMCID: PMC3541234 DOI: 10.1371/journal.pone.0054000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/07/2012] [Indexed: 12/21/2022] Open
Abstract
Binding of ligand FasL to its receptor Fas triggers apoptosis via the caspase cascade. FasL itself is homotrimeric, and a productive apoptotic signal requires that FasL be oligomerized beyond the homotrimeric state. We generated a series of FasL chimeras by fusing FasL to domains of the Leukemia Inhibitory Factor receptor gp190 which confer homotypic oligomerization, and analyzed the capacity of these soluble chimeras to trigger cell death. We observed that the most efficient FasL chimera, called pFasL, was also the most polymeric, as it reached the size of a dodecamer. Using a cellular model, we investigated the structure-function relationships of the FasL/Fas interactions for our chimeras, and we demonstrated that the Fas-mediated apoptotic signal did not solely rely on ligand-mediated receptor aggregation, but also required a conformational adaptation of the Fas receptor. When injected into mice, pFasL did not trigger liver injury at a dose which displayed anti-tumor activity in a model of human tumor transplanted to immunodeficient animals, suggesting a potential therapeutic use. Therefore, the optimization of the FasL conformation has to be considered for the development of efficient FasL-derived anti-cancer drugs targeting Fas.
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Affiliation(s)
- Sophie Daburon
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | - Christel Devaud
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | - Pierre Costet
- Animalerie spécialisée, Université de Bordeaux 2, Bordeaux, France
| | - Aurore Morello
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | - Laure Garrigue-Antar
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7149, Université Paris-Est Créteil, Créteil, France
| | - Mike Maillasson
- Unité Mixte de Recherche Institut National de la Santé et de la Recherche Médicale 892, Université de Nantes, Nantes, France
| | - Nathalie Hargous
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | | | - Marc Bonneu
- Centre génomique fonctionnelle, Université de Bordeaux 2, Bordeaux, France
| | - Julie Dechanet-Merville
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | - Patrick Legembre
- Equipe Associée 4427, Institut de Recherche en Santé-Environnement-Travail, Université de Rennes 1, Rennes, France
| | - Myriam Capone
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
| | - Jean-François Moreau
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
- Laboratoire d'Immunologie et immunogénétique, Centre Hospitalier et Universitaire de Bordeaux, Bordeaux, France
| | - Jean-Luc Taupin
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 5164, Université de Bordeaux 2, Bordeaux, France
- Laboratoire d'Immunologie et immunogénétique, Centre Hospitalier et Universitaire de Bordeaux, Bordeaux, France
- * E-mail:
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Li W, Ivanov P, Anderson P. Fas-activated Ser/Thr phosphoprotein (FAST) is a eukaryotic initiation factor 4E-binding protein that regulates mRNA stability and cell survival. TRANSLATION 2013; 1:e24047. [PMID: 26824015 PMCID: PMC4718062 DOI: 10.4161/trla.24047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/01/2013] [Accepted: 02/18/2013] [Indexed: 12/02/2022]
Abstract
The recognition of T cell intracellular antigen-1 (TIA-1) by Fas-activated Ser/Thr phosphoprotein (FAST) results in prolonged cell survival by inducing the expression of inhibitors of apoptosis. Here we show that the functional effects of FAST are dependent on its interactions with eukaryotic translation initiation factor 4E (eIF4E) which is the major cytosolic cap binding protein in cells. FAST binds to eIF4E via a consensus motif (428YXXXXLL433) that is also found in eIF4G, 4E-BP1/2/3, 4E-T, and cup. A point mutation within this motif at Y428 dampens the ability of FAST to recognize eIF4E. Wild-type (WT) FAST, but not its Y428G mutant, increases the expression of co-transfected cellular inhibitor of apoptosis-1 (cIAP-1) and β-gal mRNA and protein, but inhibits the Fas-induced activation of caspase-3. Increased expression of the co-transfected proteins results, in part, from stabilization of mRNA, suggesting that FAST:eIF4E interactions can inhibit mRNA decay. We propose that eIF4E:FAST:TIA-1 complexes regulate the translation and stability of specific mRNAs that encode proteins important for cell survival.
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Affiliation(s)
- Wei Li
- Department of Medicine; Division of Rheumatology, Immunology, and Allergy; Brigham and Women's Hospital; Harvard Medical School; Boston, MA USA
| | - Pavel Ivanov
- Department of Medicine; Division of Rheumatology, Immunology, and Allergy; Brigham and Women's Hospital; Harvard Medical School; Boston, MA USA
| | - Paul Anderson
- Department of Medicine; Division of Rheumatology, Immunology, and Allergy; Brigham and Women's Hospital; Harvard Medical School; Boston, MA USA
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Marshall PA, Hernandez Z, Kaneko I, Widener T, Tabacaru C, Aguayo I, Jurutka PW. Discovery of novel vitamin D receptor interacting proteins that modulate 1,25-dihydroxyvitamin D3 signaling. J Steroid Biochem Mol Biol 2012; 132:147-59. [PMID: 22626544 PMCID: PMC3408799 DOI: 10.1016/j.jsbmb.2012.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 04/03/2012] [Accepted: 05/04/2012] [Indexed: 12/24/2022]
Abstract
The nuclear vitamin D receptor (VDR) modulates gene transcription in 1,25-dihydroxyvitamin D(3) (1,25D) target tissues such as kidney, intestine, and bone. VDR is also expressed in heart, and 1,25D deficiency may play a role in the acceleration of cardiovascular disease. Employing a yeast two-hybrid system and a human heart library, using both a 1,25D-independent and 1,25D-dependent screen, we discovered six candidate VDR interacting proteins (VIPs). These novel VIPs include CXXC5, FASTK, NR4A1, TPM2, MYL3 and XIRP1. Mammalian two-hybrid assays as well as GST pull-downs were used to confirm VIP-VDR interaction, and the combination of these two assays reveals that CXXC5, XIRP1, FASTK and NR4A1 interactions with VDR may be modulated by 1,25D. The functional effects of these VIPs on 1,25D-mediated gene expression were explored in transcriptional assays employing three separate and distinct 1,25D-responsive element (VDRE)-driven luciferase reporter genes in transfected Caco-2 and HEK-293 cells, and in a C2C12 myoblast line. FASTK and TPM2 activated expression in all cell line and promoter contexts, while CXXC5 and XIRP1 exhibited differing effects depending on the cell line and promoter employed, suggesting promoter and cell-specific effects of these unique VIPs on VDR signaling. Further evaluation of the interaction between CXXC5 and VDR revealed that CXXC5 acts in a dose-dependent manner to stimulate VDR-mediated transcription on select VDREs. Identification of novel heart VIPs and their influence on VDR activity may increase our understanding of how vitamin D impacts cardiac physiology and may facilitate development of VDR/VIP drug analogs to combat heart disease.
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Affiliation(s)
- Pamela A. Marshall
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
| | - Zachary Hernandez
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
| | - Ichiro Kaneko
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
- Department of Basic Medical Sciences, The University of Arizona, College of Medicine, Phoenix, AZ, 85004, United States
| | - Tim Widener
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
- Department of Basic Medical Sciences, The University of Arizona, College of Medicine, Phoenix, AZ, 85004, United States
| | - Christa Tabacaru
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
| | - Izayadeth Aguayo
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
| | - Peter W. Jurutka
- Division of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, United States
- Department of Basic Medical Sciences, The University of Arizona, College of Medicine, Phoenix, AZ, 85004, United States
- Corresponding author at: Division of Mathematical and Natural Sciences, Arizona State University, 4701 W. Thunderbird Rd., Glendale, AZ 85306, United States, Tel. +1 602 543 6087, fax: +1 602 543 6074. (P.W. Jurutka)
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Eberhard S, Loiselay C, Drapier D, Bujaldon S, Girard-Bascou J, Kuras R, Choquet Y, Wollman FA. Dual functions of the nucleus-encoded factor TDA1 in trapping and translation activation of atpA transcripts in Chlamydomonas reinhardtii chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:1055-66. [PMID: 21623973 DOI: 10.1111/j.1365-313x.2011.04657.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
After endosymbiosis, organelles lost most of their initial genome. Moreover, expression of the few remaining genes became tightly controlled by the nucleus through trans-acting protein factors that are required for post-transcriptional expression (maturation/stability or translation) of a single (or a few) specific organelle target mRNA(s). Here, we characterize the nucleus-encoded TDA1 factor, which is specifically required for translation of the chloroplast atpA transcript that encodes subunit α of ATP synthase in Chlamydomonas reinhardtii. The sequence of TDA1 contains eight copies of a degenerate 38-residue motif, that we named octotrico peptide repeat (OPR), which has been previously described in a few other trans-acting factors targeted to the C. reinhardtii chloroplast. Interestingly, a proportion of the untranslated atpA transcripts are sequestered into high-density, non-polysomic, ribonucleoprotein complexes. Our results suggest that TDA1 has a dual function: (i) trapping a subset of untranslated atpA transcripts into non-polysomic complexes, and (ii) translational activation of these transcripts. We discuss these results in light of our previous observation that only a proportion of atpA transcripts are translated at any given time in the chloroplast of C. reinhardtii.
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Affiliation(s)
- Stephan Eberhard
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Université Pierre et Marie Curie (UPMC - Paris 06), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.
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Zheng D, Chen CYA, Shyu AB. Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation. RNA (NEW YORK, N.Y.) 2011; 17:1619-34. [PMID: 21750099 PMCID: PMC3162328 DOI: 10.1261/rna.2789611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cellular factors involved in mRNA degradation and translation repression can aggregate into cytoplasmic domains known as GW bodies or mRNA processing bodies (P-bodies). However, current understanding of P-bodies, especially the regulatory aspect, remains relatively fragmentary. To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance, and disassembly, we compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are not recognized as P-body components. The observation suggests that these other cellular proteins may play important roles in regulating P-body dynamics and functions. We further used siRNA-mediated gene knockdown and immunofluorescence microscopy to demonstrate the validity of our in silico analyses. Our combined approach identifies new P-body components and suggests that protein ubiquitination and protein phosphorylation involving 14-3-3 proteins may play critical roles for post-translational modifications of P-body components in regulating P-body dynamics. Our analyses provide not only a global view of human P-body components and their physical interactions but also a wealth of hypotheses to help guide future research on the regulation and function of human P-bodies.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Chyi-Ying A. Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
- Corresponding author.E-mail .
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A novel transcription complex that selectively modulates apoptosis of breast cancer cells through regulation of FASTKD2. Mol Cell Biol 2011; 31:2287-98. [PMID: 21444724 DOI: 10.1128/mcb.01381-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We previously reported that expression of NRIF3 (nuclear receptor interacting factor-3) rapidly and selectively leads to apoptosis of breast cancer cells. DIF-1 (also known as interferon regulatory factor-2 binding protein 2 [IRF-2BP2]), the cellular target of NRIF3, was identified as a transcriptional repressor, and DIF-1 knockdown leads to apoptosis of breast cancer cells but not other cell types. Here, we identify IRF-2BP1 and EAP1 (enhanced at puberty 1) as important components of the DIF-1 complex mediating both complex stability and transcriptional repression. This interaction of DIF-1, IRF-2BP1, and EAP1 occurs through the conserved C4 zinc fingers of these proteins. Microarray studies were carried out in breast cancer cell lines engineered to conditionally and rapidly increase the levels of the death domain (DD1) region of NRIF3. The DIF-1 complex was found to repress FASTKD2, a putative proapoptotic gene, in breast cancer cells and to bind to the FASTKD2 gene by chromatin immunoprecipitation. FASTKD2 knockdown prevents apoptosis of breast cancer cells from NRIF3 expression or DIF-1 knockdown, while expression of FASTKD2 leads to apoptosis of both breast and nonbreast cancer cells. Thus, regulation of FASTKD2 by NRIF3 and the DIF-1 complex acts as a novel death switch that selectively modulates apoptosis in breast cancer.
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Wu CY, Whye D, Glazewski L, Choe L, Kerr D, Lee KH, Mason RW, Wang W. Proteomic assessment of a cell model of spinal muscular atrophy. BMC Neurosci 2011; 12:25. [PMID: 21385431 PMCID: PMC3063191 DOI: 10.1186/1471-2202-12-25] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 03/08/2011] [Indexed: 12/29/2022] Open
Abstract
Background Deletion or mutation(s) of the survival motor neuron 1 (SMN1) gene causes spinal muscular atrophy (SMA), a neuromuscular disease characterized by spinal motor neuron death and muscle paralysis. Complete loss of the SMN protein is embryonically lethal, yet reduced levels of this protein result in selective death of motor neurons. Why motor neurons are specifically targeted by SMN deficiency remains to be determined. In this study, embryonic stem (ES) cells derived from a severe SMA mouse model were differentiated into motor neurons in vitro by addition of retinoic acid and sonic hedgehog agonist. Proteomic and western blot analyses were used to probe protein expression alterations in this cell-culture model of SMA that could be relevant to the disease. Results When ES cells were primed with Noggin/fibroblast growth factors (bFGF and FGF-8) in a more robust neural differentiation medium for 2 days before differentiation induction, the efficiency of in vitro motor neuron differentiation was improved from ~25% to ~50%. The differentiated ES cells expressed a pan-neuronal marker (neurofilament) and motor neuron markers (Hb9, Islet-1, and ChAT). Even though SMN-deficient ES cells had marked reduced levels of SMN (~20% of that in control ES cells), the morphology and differentiation efficiency for these cells are comparable to those for control samples. However, proteomics in conjunction with western blot analyses revealed 6 down-regulated and 14 up-regulated proteins with most of them involved in energy metabolism, cell stress-response, protein degradation, and cytoskeleton stability. Some of these activated cellular pathways showed specificity for either undifferentiated or differentiated cells. Increased p21 protein expression indicated that SMA ES cells were responding to cellular stress. Up-regulation of p21 was confirmed in spinal cord tissues from the same SMA mouse model from which the ES cells were derived. Conclusion SMN-deficient ES cells provide a cell-culture model for SMA. SMN deficiency activates cellular stress pathways, causing a dysregulation of energy metabolism, protein degradation, and cytoskeleton stability.
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Affiliation(s)
- Chia-Yen Wu
- Department of Biological Science, University of Delaware, Newark, DE, USA
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Yoon J, Kim ES, Lee SJ, Park CW, Cha HJ, Hong BH, Choi KY. Apoptosis-related mRNA expression profiles of ovarian cancer cell lines following cisplatin treatment. J Gynecol Oncol 2010; 21:255-61. [PMID: 21278888 DOI: 10.3802/jgo.2010.21.4.255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/11/2010] [Accepted: 11/18/2010] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE The aim of this study was to identify apoptosis-related genes of ovarian cancer cell lines following cisplatin treatment. METHODS We used IC(50) values and fluorescence-activated cell sorting analysis to compare cell death in 2 ovarian cancer cell lines, namely, SKOV-3 and OVCAR-3, upon treatment with cisplatin. Moreover, the change in transcriptional levels of apoptosis-associated genes was measured with a dendron-modified DNA microarray. RESULTS The protein levels for the up-regulated genes in each cell line were validated to identify the molecules that may determine the cellular behavior of cisplatin resistance. Eight genes were over-expressed in the 2 cell lines. The cisplatin-induced up-regulation of DAD1 in transcriptional and protein levels contributed to the cisplatin resistance of OVCAR-3, and the up-regulation of FASTK and TNFRSF11A in SKOV-3 resulted in its higher sensitivity to cisplatin than that of OVCAR-3. CONCLUSION In the present study, we have identified a set of genes responsible for apoptosis following cisplatin treatment in ovarian cancer cell lines. These genes may give information about the understanding of cisplatin-induced apoptosis in ovarian cancer.
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Affiliation(s)
- Joohee Yoon
- Department of Obstetrics and Gynecology, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea
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Simarro M, Gimenez-Cassina A, Kedersha N, Lazaro JB, Adelmant GO, Marto JA, Rhee K, Tisdale S, Danial N, Benarafa C, Orduña A, Anderson P. Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration. Biochem Biophys Res Commun 2010; 401:440-6. [PMID: 20869947 DOI: 10.1016/j.bbrc.2010.09.075] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 09/18/2010] [Indexed: 01/23/2023]
Abstract
Fas-activated serine/threonine phosphoprotein (FAST) is the founding member of the FAST kinase domain-containing protein (FASTKD) family that includes FASTKD1-5. FAST is a sensor of mitochondrial stress that modulates protein translation to promote the survival of cells exposed to adverse conditions. Mutations in FASTKD2 have been linked to a mitochondrial encephalomyopathy that is associated with reduced cytochrome c oxidase activity, an essential component of the mitochondrial electron transport chain. We have confirmed the mitochondrial localization of FASTKD2 and shown that all FASTKD family members are found in mitochondria. Although human and mouse FASTKD1-5 genes are expressed ubiquitously, some of them are most abundantly expressed in mitochondria-enriched tissues. We have found that RNA interference-mediated knockdown of FASTKD3 severely blunts basal and stress-induced mitochondrial oxygen consumption without disrupting the assembly of respiratory chain complexes. Tandem affinity purification reveals that FASTKD3 interacts with components of mitochondrial respiratory and translation machineries. Our results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration.
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Affiliation(s)
- Maria Simarro
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
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Duffau P, Seneschal J, Nicco C, Richez C, Lazaro E, Douchet I, Bordes C, Viallard JF, Goulvestre C, Pellegrin JL, Weil B, Moreau JF, Batteux F, Blanco P. Platelet CD154 Potentiates Interferon- Secretion by Plasmacytoid Dendritic Cells in Systemic Lupus Erythematosus. Sci Transl Med 2010; 2:47ra63. [DOI: 10.1126/scitranslmed.3001001] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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50
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Alcaraz-Estrada SL, Yocupicio-Monroy M, del Angel RM. Insights into dengue virus genome replication. Future Virol 2010. [DOI: 10.2217/fvl.10.49] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since many antiviral drugs are designed to interfere with viral genome replication, understanding this step in the viral replicative cycle has gained importance in recent years. Replication for many RNA viruses occurs in cellular compartments mainly originated from the production and reorganization of virus-induced membranes. Dengue virus translates, replicates and assembles new viral particles within virus-induced membranes from endoplasmic reticulum. In these compartments, all of the components required for replication are recruited, making the process efficient. In addition, membranes protect replication complexes from RNAases and proteases, and ultimately make them less visible to cellular defense sensors. Although several aspects in dengue virus replication are known, many others are yet to be understood. This article aims to summarize the advances in the understanding of dengue virus genome replication, highlighting the cis as well as trans elements that may have key roles in this process.
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Affiliation(s)
- Sofia Lizeth Alcaraz-Estrada
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508. Col. San Pedro Zacatenco, México, D.F. C.P. 07360
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México, D.F. México
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