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Muazzen Z, Moghrabi W, Bakheet T, Mahmoud L, Al-Saif M, Khabar KSA, Hitti EG. Global analysis of the abundance of AU-rich mRNAs in response to glucocorticoid treatment. Sci Rep 2024; 14:913. [PMID: 38195703 PMCID: PMC10776588 DOI: 10.1038/s41598-024-51301-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Glucocorticoids (GC) like dexamethasone (Dex) are potent anti-inflammatory agents with diverse cellular functions including the potentiation of the activity of AU-rich elements (AREs). AREs are cis-acting instability sequence elements located in the 3'UTRs of many inflammatory mediator mRNAs. Here, available RNA-seq data were used to investigate the effect of GCs on the ARE-mRNA-transcriptome. At a global scale, ARE-mRNAs had a tendency to be downregulated after GC-treatment of the A549 lung cancer cell-line, but with notable cases of upregulation. mRNA stability experiments indicated that not only the downregulated, but also the upregulated ARE-mRNAs are destabilized by Dex-treatment. Several of the most upregulated ARE-mRNAs code for anti-inflammatory mediators including the established GC targets DUSP1 and ZFP36; both code for proteins that target ARE-containing mRNAs for destruction. GCs are widely used in the treatment of COVID-19 patients; we show that ARE-mRNAs are more likely to regulate in opposite directions between Dex-treatment and SARS-CoV-2 infections compared to non-ARE mRNAs. The effect of GC treatment on ARE-mRNA abundance was also investigated in blood monocytes of COVID-19 patients. The results were heterogeneous; however, in agreement with in vitro observations, ZFP36 and DUSP1 were often amongst the most differentially expressed mRNAs. The results of this study propose a universal destabilization of ARE-mRNAs by GCs, but a diverse overall outcome in vitro likely due to induced transcription or due to the heterogeneity of COVID-19 patient's responses in vivo.
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Affiliation(s)
- Zeyad Muazzen
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Walid Moghrabi
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Tala Bakheet
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Linah Mahmoud
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Edward G Hitti
- Molecular BioMedicine Department, Research and Innovation, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia.
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2
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Al-Yahya S, Al-Saif M, Al-Ghamdi M, Moghrabi W, Khabar KS, Al-Souhibani N. Post-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin. RNA Biol 2024; 21:1-15. [PMID: 38111129 PMCID: PMC10761079 DOI: 10.1080/15476286.2023.2286101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 12/20/2023] Open
Abstract
Inhibition of apoptosis is one of the hallmarks of cancer and is a target of various therapeutic interventions. BIRC5 is an inhibitor of apoptosis that is aberrantly expressed in cancer leading to sustained growth of tumours. Post-transcriptional control mechanisms involving RNA-binding proteins and AU-rich elements (AREs) are fundamental to many cellular processes and changes in the expression or function of these proteins can promote an aberrant and pathological phenotype. BIRC5 mRNA has an ARE in its 3' UTR making it a candidate for regulation by the RNA binding proteins tristetraprolin (TTP) and HuR (ELAVL1). In this study, we investigated the binding of TTP and HuR by RNA-immunoprecipitation assays and found that these proteins were associated with BIRC5 mRNA to varying extents. Consequently, BIRC5 expression decreased when TTP was overexpressed and apoptosis was induced. In the absence of TTP, BIRC5 mRNA was stabilized, protein expression increased and the number of apoptotic cells declined. As an ARE-mRNA stabilizing protein, recombinant HuR led to upregulation of BIRC5 expression, whereas HuR silencing was concomitant with downregulation of BIRC5 mRNA and protein and increased cell death. Survival analyses demonstrated that increased TTP and low BIRC5 expression predicted an overall better prognosis compared to dysregulated TTP and high BIRC5. Thus, the results present a novel target of ARE-mediated post-transcriptional regulation.
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Affiliation(s)
- Suhad Al-Yahya
- Molecular Biomedicine Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular Biomedicine Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Al-Ghamdi
- Biomedical Physics Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Walid Moghrabi
- Molecular Biomedicine Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S.A. Khabar
- Molecular Biomedicine Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Norah Al-Souhibani
- Molecular Biomedicine Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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3
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Al-Matouq J, Al-Haj L, Al-Saif M, Khabar KSA. Post-transcriptional screen of cancer amplified genes identifies ERBB2/Her2 signaling as AU-rich mRNA stability-promoting pathway. Oncogenesis 2021; 10:61. [PMID: 34535639 PMCID: PMC8448767 DOI: 10.1038/s41389-021-00351-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Amplification of specific cancer genes leads to their over-expression contributing to tumor growth, spread, and drug resistance. Little is known about the ability of these amplified oncogenes to augment the expression of cancer genes through post-transcriptional control. The AU-rich elements (ARE)-mediated mRNA decay is compromised for many key cancer genes leading to their increased abundance and effects. Here, we performed a post-transcriptional screen for frequently amplified cancer genes demonstrating that ERBB2/Her2 overexpression was able to augment the post-transcriptional effects. The ERBB1/2 inhibitor, lapatinib, led to the reversal of the aberrant ARE-mediated process in ERBB2-amplified breast cancer cells. The intersection of overexpressed genes associated with ERBB2 amplification in TCGA datasets with ARE database (ARED) identified ERBB2-associated gene cluster. Many of these genes were over-expressed in the ERBB2-positive SKBR3 cells compared to MCF10A normal-like cells, and were under-expressed due to ERBB2 siRNA treatment. Lapatinib accelerated the ARE-mRNA decay for several ERBB2-regulated genes. The ERBB2 inhibitor decreased both the abundance and stability of the phosphorylated inactive form of the mRNA decay-promoting protein, tristetraprolin (ZFP36/TTP). The ERBB2 siRNA was also able to reduce the phosphorylated ZFP36/TTP form. In contrast, ectopic expression of ERBB2 in MCF10A or HEK293 cells led to increased abundance of the phosphorylated ZFP36/TTP. The effect of ERBB2 on TTP phosphorylation appeared to be mediated via the MAPK-MK2 pathway. Screening for the impact of other amplified cancer genes in HEK293 cells also demonstrated that EGFR, AKT2, CCND1, CCNE1, SKP2, and FGFR3 caused both increased abundance of phosphorylated ZFP36/TTP and ARE-post-transcriptional reporter activity. Thus, specific amplified oncogenes dysregulate post-transcriptional ARE-mediated effects, and targeting the ARE-mediated pathway itself may provide alternative therapeutic approaches.
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Affiliation(s)
- Jenan Al-Matouq
- grid.415310.20000 0001 2191 4301Molecular BioMedicine Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211 Saudi Arabia ,Present Address: Mohammed Al-Mana College for Medical Science, Dammam, Saudi Arabia
| | - Latifa Al-Haj
- grid.415310.20000 0001 2191 4301Molecular BioMedicine Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211 Saudi Arabia
| | - Maher Al-Saif
- grid.415310.20000 0001 2191 4301Molecular BioMedicine Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211 Saudi Arabia
| | - Khalid S. A. Khabar
- grid.415310.20000 0001 2191 4301Molecular BioMedicine Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211 Saudi Arabia
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4
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Al-Ansari MM, Al-Saif M, Arafah M, Eldali AM, Tulbah A, Al-Tweigeri T, Semlali A, Khabar KS, Aboussekhra A. Clinical and functional significance of tumor/stromal ATR expression in breast cancer patients. Breast Cancer Res 2020; 22:49. [PMID: 32414408 PMCID: PMC7229635 DOI: 10.1186/s13058-020-01289-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 05/06/2020] [Indexed: 12/28/2022] Open
Abstract
Background Most breast cancer-associated fibroblasts (CAFs) are active and important cancer-promoting cells, with significant impact on patient prognosis. Therefore, we investigated here the role of the protein kinase ATR in breast stromal fibroblasts in the prognosis of locally advanced breast cancer patients. Methods We have used immunohistochemistry to assess the level of ATR in breast cancer tissues and their adjacent normal tissues. Immunoblotting as well as quantitative RT-PCR were utilized to show the role of breast cancer cells and IL-6 as well as AUF-1 in downregulating ATR in breast stromal fibroblasts. Engineered human breast tissue model was also used to show that ATR-deficient breast stromal fibroblasts enhance the growth of breast cancer cells. Results We have shown that the protein kinase ATR is downregulated in cancer cells and their neighboring CAFs in breast cancer tissues as compared to their respective adjacent normal tissues. The implication of cancer cells in ATR knockdown in CAFs has been proven in vitro by showing that breast cancer cells downregulate ATR in breast fibroblasts in an IL-6/STAT3-dependent manner and via AUF-1. In another cohort of 103 tumors from locally advanced breast cancer patients, we have shown that absence or reduced ATR expression in tumoral cells and their adjacent stromal fibroblasts is correlated with poor overall survival as well as disease-free survival. Furthermore, ATR expression in CAFs was inversely correlated with tumor recurrence and progression. Conclusion ATR downregulation in breast CAFs is frequent, procarcinogenic, and correlated with poor patient survival.
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Affiliation(s)
- Mysoon M Al-Ansari
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, MBC#03, Riyadh, 11211, Saudi Arabia.,Department of Microbiology, Faculty of Science and Medical Studies, King Saud University, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular BioMedicine Program, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Maria Arafah
- Department of Pathology, King Saud University, PO BOX 2925, Riyadh, 11461, Saudi Arabia
| | - Abdelmonneim M Eldali
- Department of Biostatistics, Epidemiology and Scientific computing, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Taher Al-Tweigeri
- Department of Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval Québec, Local 1758, 2420 rue de la terrasse, Québec, G1V 0A6, Canada
| | - Khalid S Khabar
- Molecular BioMedicine Program, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Abdelilah Aboussekhra
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, MBC#03, Riyadh, 11211, Saudi Arabia.
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5
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Patel N, Khan AO, Al-Saif M, Moghrabi WN, AlMaarik BM, Ibrahim N, Abdulwahab F, Hashem M, Alshidi T, Alobeid E, Alomar RA, Al-Harbi S, Abouelhoda M, Khabar KSA, Alkuraya FS. A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation. Genome Biol 2017; 18:144. [PMID: 28754144 PMCID: PMC5534118 DOI: 10.1186/s13059-017-1274-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/06/2017] [Indexed: 01/09/2023] Open
Abstract
Background Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations associated with the multisystem disorder linked to the gene. This remains an incompletely understood phenomenon with proposed mechanisms ranging from allele-specific to stochastic. Results We report three consanguineous families in which an isolated ocular phenotype is linked to a novel 3′ UTR mutation in SLC4A4, a gene known to be mutated in a syndromic form of intellectual disability with renal and ocular involvement. Although SLC4A4 is normally devoid of AU-rich elements (AREs), a 3′ UTR motif that mediates post-transcriptional control of a subset of genes, the mutation we describe creates a functional ARE. We observe a marked reduction in the transcript level of SLC4A4 in patient cells. Experimental confirmation of the ARE-creating mutation is shown using a post-transcriptional reporter system that reveals consistent reduction in the mRNA-half life and reporter activity. Moreover, the neo-ARE binds and responds to the zinc finger protein ZFP36/TTP, an ARE-mRNA decay-promoting protein. Conclusions This novel mutational mechanism for a Mendelian disease expands the potential mechanisms that underlie variable phenotypic expressivity in humans to also include 3′ UTR mutations with tissue-specific pathology.
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Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, 112412, United Arab Emirates
| | - Maher Al-Saif
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Walid N Moghrabi
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Balsam M AlMaarik
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana A Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saad Al-Harbi
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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6
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Hitti E, Bakheet T, Al-Souhibani N, Moghrabi W, Al-Yahya S, Al-Ghamdi M, Al-Saif M, Shoukri MM, Lánczky A, Grépin R, Győrffy B, Pagès G, Khabar KSA. Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins. Cancer Res 2016; 76:4068-80. [PMID: 27197193 DOI: 10.1158/0008-5472.can-15-3110] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
Abstract
Defects in AU-rich elements (ARE)-mediated posttranscriptional control can lead to several abnormal processes that underlie carcinogenesis. Here, we performed a systematic analysis of ARE-mRNA expression across multiple cancer types. First, the ARE database (ARED) was intersected with The Cancer Genome Atlas databases and others. A large set of ARE-mRNAs was over-represented in cancer and, unlike non-ARE-mRNAs, correlated with the reversed balance in the expression of the RNA-binding proteins tristetraprolin (TTP, ZFP36) and HuR (ELAVL1). Serial statistical and functional enrichment clustering identified a cluster of 11 overexpressed ARE-mRNAs (CDC6, KIF11, PRC1, NEK2, NCAPG, CENPA, NUF2, KIF18A, CENPE, PBK, TOP2A) that negatively correlated with TTP/HuR mRNA ratios and was involved in the mitotic cell cycle. This cluster was upregulated in a number of solid cancers. Experimentally, we demonstrated that the ARE-mRNA cluster is upregulated in a number of tumor breast cell lines when compared with noninvasive and normal-like breast cancer cells. RNA-IP demonstrated the association of the ARE-mRNAs with TTP and HuR. Experimental modulation of TTP or HuR expression led to changes in the mitosis ARE-mRNAs. Posttranscriptional reporter assays confirmed the functionality of AREs. Moreover, TTP augmented mitotic cell-cycle arrest as demonstrated by flow cytometry and histone H3 phosphorylation. We found that poor breast cancer patient survival was significantly associated with low TTP/HuR mRNA ratios and correlated with high levels of the mitotic ARE-mRNA signature. These results significantly broaden the role of AREs and their binding proteins in cancer, and demonstrate that TTP induces an antimitotic pathway that is diminished in cancer. Cancer Res; 76(14); 4068-80. ©2016 AACR.
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Affiliation(s)
- Edward Hitti
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Tala Bakheet
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Norah Al-Souhibani
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Walid Moghrabi
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Suhad Al-Yahya
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Maha Al-Ghamdi
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Mohamed M Shoukri
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - András Lánczky
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary
| | - Renaud Grépin
- Centre Scientifique de Monaco Biomedical Department, Monaco, Principality of Monaco
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary. 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Gilles Pagès
- University of Nice, Institute for research on cancer and aging of Nice (IRCAN), Nice, France
| | - Khalid S A Khabar
- Molecular BioMedicine Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.
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7
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Abstract
The mRNAs of most inflammatory mediators are short-lived due to AU-rich elements (AREs) in their 3'-untranslated regions. AREs ensure a low basal level of expression during homeostasis and a transient nature of expression during the inflammatory response. Here, we report that the mRNA of the pro-inflammatory chemokine IL-8, which contains an archetypal ARE, is unexpectedly constitutively abundant and highly stable in primary human monocytes and macrophages. Using the pre-monocyte-like THP-1 cell line that can differentiate into macrophage-like cells, we show that a low level of unstable IL-8 mRNA in undifferentiated cells (half-life<30 min) becomes constitutively elevated and the mRNA is dramatically stabilized in differentiated THP-1 cells with a half-life of more than 15 h similar to primary monocytes and macrophages. In contrast, the level and stability of TNF-α mRNA also containing an ARE is only slightly affected by differentiation; it remains low and unstable in primary macrophages and differentiated THP-1 cells with an estimated half-life of less than 20 min. This differentiation-dependent stabilization of IL-8 mRNA is p38 MAPK-independent and is probably coupled with reduced protein translation. Reporter assays in THP-1 cells suggest that the ARE alone is not sufficient for the constitutive stabilization in macrophage-like cells and imply an effect of the natural biogenesis of the transcript on the stabilization of the mature form. We present a novel, cell type-dependent sustained stabilization of an ARE-containing mRNA with similarities to situations found in disease.
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Affiliation(s)
- Linah Mahmoud
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Fatma Al-Enezi
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia; Department of Biochemistry; King Saud University; Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Arjumand Warsy
- Department of Biochemistry; King Saud University; Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Edward G Hitti
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
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8
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Doucette KE, Al-Saif M, Kneteman N, Chui L, Tyrrell GJ, Kumar D, Humar A. Donor-derived bacteremia in liver transplant recipients despite antibiotic prophylaxis. Am J Transplant 2013; 13:1080-1083. [PMID: 23398841 DOI: 10.1111/ajt.12133] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/03/2012] [Accepted: 12/07/2012] [Indexed: 02/06/2023]
Abstract
As the disparity between the number of candidates listed for transplant and the number of donors continues to grow, marginal organ donors are increasingly utilized. This includes bacteremic donors which may carry an increased risk of transmission of infection. It is recommended that recipients of organs from bacteremic donors receive antibiotic prophylaxis based on the susceptibilities of the donor isolate to prevent transmission. Here, we present four cases of donor-derived bacteremia, despite appropriate antimicrobial prophylaxis, in four liver transplant recipients. Transmitted pathogens included Staphylococcus aureus in two cases, and Escherichia coli and Group B Streptococcus each in one case. Interestingly, none of the nonhepatic organs (n=10) utilized from these bacteremic donors resulted in transmissions. These cases highlight the fact that risk of transmission from bacteremic donors is not eliminated with antimicrobial therapy in the donor and recipient. As no transmissions occurred in recipients of nonhepatic organs from these donors, these cases also suggest that liver recipients may be at higher risk of donor transmitted bacteremia.
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Affiliation(s)
- K E Doucette
- Transplant Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - M Al-Saif
- Transplant Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - N Kneteman
- Division of Transplantation, Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - L Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, Alberta, Canada
| | - G J Tyrrell
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, Alberta, Canada
| | - D Kumar
- Transplant Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - A Humar
- Transplant Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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9
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Mahmoud L, Al-Saif M, Amer HM, Sheikh M, Almajhdi FN, Khabar KS. PS1-117 GFP reporter system with transcriptional sequence heterogeneity for monitoring interferon response. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Hitti E, Mahmoud L, Al-Saif M, Khabar KS. PS1-004. Differentiation-dependent stabilization of chemokine mRNA in human macrophages. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Al-Khalaf HH, Colak D, Al-Saif M, Al-Bakheet A, Hendrayani SF, Al-Yousef N, Kaya N, Khabar KS, Aboussekhra A. p16( INK4a) positively regulates cyclin D1 and E2F1 through negative control of AUF1. PLoS One 2011; 6:e21111. [PMID: 21799732 PMCID: PMC3140473 DOI: 10.1371/journal.pone.0021111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/19/2011] [Indexed: 11/23/2022] Open
Abstract
Background The cyclin-D/CDK4,6/p16INK4a/pRB/E2F pathway, a key regulator of the critical G1 to S phase transition of the cell cycle, is universally disrupted in human cancer. However, the precise function of the different members of this pathway and their functional interplay are still not well defined. Methodology/Principal Findings We have shown here that the tumor suppressor p16INK4a protein positively controls the expression of cyclin D1 and E2F1 in both human and mouse cells. p16INK4a stabilizes the mRNAs of the corresponding genes through negative regulation of the mRNA decay-promoting AUF1 protein. Immunoprecipitation of AUF1-associated RNAs followed by RT-PCR indicated that endogenous AUF1 binds to the cyclin D1 and E2F1 mRNAs. Furthermore, AUF1 down-regulation increased the expression levels of these genes, while concurrent silencing of AUF1 and p16INK4a, using specific siRNAs, restored normal expression of both cyclinD1 and E2F1. Besides, we have shown the presence of functional AU-rich elements in the E2F1 3′UTR, which contributed to p16/AUF1-mediated regulation of E2F1 post-transcriptional events in vivo. Importantly, genome-wide gene expression microarray analysis revealed the presence of a large number of genes differentially expressed in a p16INK4a -dependent manner, and several of these genes are also members of the AUF1 and E2F1 regulons. We also present evidence that E2F1 mediates p16-dependent regulation of several pro- and anti-apoptotic proteins, and the consequent induction of spontaneous as well as doxorubicin-induced apoptosis. Conclusion/Significance These findings show that the cyclin-dependent kinase inhibitor p16 INK4a is also a modulator of transcription and apoptosis through controlling the expression of two major transcription regulators, AUF1 and E2F1.
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Affiliation(s)
- Huda H. Al-Khalaf
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Albandary Al-Bakheet
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Siti-Faujiah Hendrayani
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nujoud Al-Yousef
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S. Khabar
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdelilah Aboussekhra
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- * E-mail:
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Halees AS, Hitti E, Al-Saif M, Mahmoud L, Vlasova-St Louis IA, Beisang DJ, Bohjanen PR, Khabar K. Global assessment of GU-rich regulatory content and function in the human transcriptome. RNA Biol 2011; 8:681-91. [PMID: 21691152 DOI: 10.4161/rna.8.4.16283] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Unlike AU-rich elements (AREs) that are largely present in the 3'UTRs of many unstable mammalian mRNAs, the function and abundance of GU-rich elements (GREs) are poorly understood. We performed a genome-wide analysis and found that at least 5% of human genes contain GREs in their 3'UTRs with functional over-representation in genes involved in transcription, nucleic acid metabolism, developmental processes, and neurogenesis. GREs have similar sequence clustering patterns with AREs such as overlapping GUUUG pentamers and enrichment in 3'UTRs. Functional analysis using T-cell mRNA expression microarray data confirms correlation with mRNA destabilization. Reporter assays show that compared to AREs the ability of GREs to destabilize mRNA is modest and does not increase with the increasing number of overlapping pentamers. Naturally occurring GREs within U-rich contexts were more potent in destabilizing GFP reporter mRNAs than synthetic GREs with perfectly overlapping pentamers. Overall, we find that GREs bear a resemblance to AREs in sequence patterns but they regulate a different repertoire of genes and have different dynamics of mRNA decay. A dedicated resource on all GRE-containing genes of the human, mouse and rat genomes can be found at brp.kfshrc.edu.sa/GredOrg.
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Affiliation(s)
- Anason S Halees
- The BioMolecular Research Program at King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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Hitti E, Al-Yahya S, Al-Saif M, Mohideen P, Mahmoud L, Polyak SJ, Khabar KSA. A versatile ribosomal protein promoter-based reporter system for selective assessment of RNA stability and post-transcriptional control. RNA 2010; 16:1245-55. [PMID: 20418359 PMCID: PMC2874176 DOI: 10.1261/rna.2026310] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Assessment of post-transcriptional control relies on use of transcriptional inhibitors and is masked by copious and cryptic transcriptional induction. We screened several cellular promoters that are constitutively active yet noninducible to external stimuli. The ribosomal protein RPS30 promoter was chosen; its TATA signal and sp1 site location were optimized. The modified promoter (RPS30M) is selective to post-transcriptional effects of AU-rich elements (ARE) in the 3'UTR, while it is not transcriptionally responsive to a wide variety of agents including pro-inflammatory cytokines and RNA-binding proteins. Specific cis-acting elements can be appended to RPS30M by a cloning-free approach to allow coupled transcriptional/post-transcriptional assessment, as demonstrated with NF-kappaB and beta-catenin/wnt signaling experiments. Moreover, efficient tetracycline-regulated RPS30M was created for quantitative assessment of the half-lives of mRNAs containing AREs. The described approach provides enhanced versatility and suitability for selective post-transcriptional assessment with or without transcriptional induction.
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Affiliation(s)
- Edward Hitti
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia 11211
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Hitti E, Al-Yahya S, Al-Saif M, Mohideen P, Omar L, Khabar KS. Ribosomal protein gene promoter-based system for selective assessment of post-transcriptional regulation of cytokine genes. Cytokine 2009. [DOI: 10.1016/j.cyto.2009.07.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Al-Haj L, Al-Ahamdi W, Al-Ghamdi M, Al-Saif M, Hitti E, Silverman RH, Khabar KS. The wild type RNase L but not mutant laboratory and natural variants suppresses the RNA binding protein, HUR: Effects on cytokine 3′ UTR. Cytokine 2009. [DOI: 10.1016/j.cyto.2009.07.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Al-Ahmadi W, Al-Ghamdi M, Al-Haj L, Al-Saif M, Khabar KSA. Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation. Nucleic Acids Res 2009; 37:3612-24. [PMID: 19359363 PMCID: PMC2699509 DOI: 10.1093/nar/gkp223] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The RNA-binding protein, HuR, is involved in the stabilization of AU-rich element-containing mRNAs with products that are involved in cell-cycle progression, cell differentiation and inflammation. We show that there are multiple polyadenylation variants of HuR mRNA that differ in their abundance, using both bioinformatics and experimental approaches. A polyadenylation variant with distal poly(A) signal is a rare transcript that harbors functional AU-rich elements (ARE) in the 3′UTR. A minimal 60-nt region, but not a mutant form, fused to reporter-3′UTR constructs was able to downregulate the reporter activity. The most predominant and alternatively polyadenylated mature transcript does not contain the ARE. HuR itself binds HuR mRNA, and upregulated the activity of reporter from constructs fused with ARE-isoform and the HuR ARE. Wild-type tristetraprolin (TTP), but not the zinc finger mutant TTP, competes for HuR binding and upregulation of HuR mRNA. The study shows that the HuR gene codes for several polyadenylation variants differentially regulated by AU-rich elements, and demonstrates an auto-regulatory role of HuR.
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Affiliation(s)
- Wijdan Al-Ahmadi
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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al-Haj L, Al-Ahmadi W, Al-Saif M, Demirkaya O, Khabar KSA. Cloning-free regulated monitoring of reporter and gene expression. BMC Mol Biol 2009; 10:20. [PMID: 19267938 PMCID: PMC2662838 DOI: 10.1186/1471-2199-10-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 03/08/2009] [Indexed: 11/10/2022] Open
Abstract
Background The majority of the promoters, their regulatory elements, and their variations in the human genome remain unknown. Reporter gene technology for transcriptional activity is a widely used tool for the study of promoter structure, gene regulation, and signaling pathways. Construction of transcriptional reporter vectors, including use of cis-acting sequences, requires cloning and time-demanding manipulations, particularly with introduced mutations. Results In this report, we describe a cloning-free strategy to generate transcriptionally-controllable linear reporter constructs. This approach was applied in common transcriptional models of inflammatory response and the interferon system. In addition, it was used to delineate minimal transcriptional activity of selected ribosomal protein promoters. The approach was tested for conversion of genes into TetO-inducible/repressible expression cassettes. Conclusion The simple introduction and tuning of any transcriptional control in the linear DNA product renders promoter activation and regulated gene studies simple and versatile.
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Affiliation(s)
- Latifa al-Haj
- Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.
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