1
|
Todorovski I, Tsang MJ, Feran B, Fan Z, Gadipally S, Yoannidis D, Kong I, Bjelosevic S, Rivera S, Voulgaris O, Zethoven M, Hawkins E, Simpson K, Arnau GM, Papenfuss A, Johnstone R, Vervoort S. RNA kinetics influence the response to transcriptional perturbation in leukaemia cell lines. NAR Cancer 2024; 6:zcae039. [PMID: 39372038 PMCID: PMC11447529 DOI: 10.1093/narcan/zcae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/30/2024] [Accepted: 09/13/2024] [Indexed: 10/08/2024] Open
Abstract
Therapeutic targeting of dysregulated transcription has emerged as a promising strategy for the treatment of cancers, such as leukaemias. The therapeutic response to small molecule inhibitors of Bromodomain-Containing Proteins (BRD), such as BRD2 and BRD4, P300/cAMP-response element binding protein (CBP) and Cyclin Dependent Kinases (CDKs), is generally attributed to the selective disruption of oncogenic gene expression driven by enhancers, super-enhancers (SEs) and lineage-specific transcription factors (TFs), including the c-MYC oncogene. The selectivity of compounds targeting the transcriptional machinery may be further shaped by post-transcriptional processes. To quantitatively assess the contribution of post-transcriptional regulation in responses to transcription inhibition, we performed multi-omics analyses to accurately measure mRNA production and decay kinetics. We demonstrate that it is not only the selective disruption of mRNA production, but rather mRNA decay rates that largely influence the selectivity associated with transcriptional inhibition. Accordingly, genes down-regulated with transcriptional inhibitors are largely characterized by extremely rapid mRNA production and turnover. In line with this notion, stabilization of the c-MYC transcript through swapping of its 3' untranslated region (UTR) rendered c-MYC insensitive to transcriptional targeting. This failed to negate the impact on c-MYC downstream targets and did not abrogate therapeutic responses. Finally, we provide evidence that modulating post-transcriptional pathways, such as through ELAVL1 targeting, can sensitize long-lived mRNAs to transcriptional inhibition and be considered as a combination therapy approach in leukaemia. Taken together, these data demonstrate that mRNA kinetics influence the therapeutic response to transcriptional perturbation and can be modulated for novel therapeutic outcomes using transcriptional agents in leukaemia.
Collapse
Affiliation(s)
- Izabela Todorovski
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Mary-Jane Tsang
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Breon Feran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Zheng Fan
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Sreeja Gadipally
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - David Yoannidis
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Stefan Bjelosevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Sarahi Rivera
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Olivia Voulgaris
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Magnus Zethoven
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Edwin D Hawkins
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Kaylene J Simpson
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Gisela Mir Arnau
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Anthony T Papenfuss
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Stephin J Vervoort
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| |
Collapse
|
2
|
Supe S, Dighe V, Upadhya A, Singh K. Analysis of RNA Interference Targeted Against Human Antigen R (HuR) to Reduce Vascular Endothelial Growth Factor (VEGF) Protein Expression in Human Retinal Pigment Epithelial Cells. Mol Biotechnol 2024; 66:2972-2984. [PMID: 37856012 DOI: 10.1007/s12033-023-00913-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023]
Abstract
VEGF-A or vascular endothelial growth factor-A is an important factor in enabling neovascularization and angiogenesis. VEGF-A is regulated transcriptionally as well as post transcriptionally. Human antigen R (HuR) belonging to the embryonic lethal abnormal vision (ELAV) family is a key regulator promoting stabilization of VEGF-A mRNA. In this research we investigate, whether HuR targeted RNA interference would enable the reduction of the VEGF-A protein in human retinal pigment epithelial cells (ARPE-19) in-vitro, in normoxic conditions. Three siRNA molecules with sequences complementary to three regions of the HuR mRNA were designed. The three designed siRNA molecules were individually transfected in ARPE-19 cells using Lipofectamine™2000 reagent. Post-transfection (24 h, 48 h, 72 h), downregulation of HuR mRNA was estimated by real-time polymerase reaction, while HuR protein and VEGF-A protein levels were semi-quantitatively determined by western blotting techniques. VEGF-A protein levels were additionally quantified using ELISA techniques. All experiments were done in triplicate. The designed siRNA could successfully downregulate HuR mRNA with concomitant decreases in HuR and VEGF-A protein. The study reveals that HuR downregulation can prominently downregulate VEGF-A, making the protein a target for therapy against pathological angiogenesis conditions such as diabetic retinopathy.
Collapse
Affiliation(s)
- Shibani Supe
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Vile Parle (W), Mumbai, Maharashtra, 400056, India
| | - Vikas Dighe
- National Centre for Preclinical Reproductive and Genetic Toxicology, ICMR-National Institute for Research in Reproductive and Child Health, J.M. Street, Parel, Mumbai, Maharashtra, 400012, India
| | - Archana Upadhya
- Maharashtra Educational Society's H. K. College of Pharmacy, H. K. College Campus, Oshiwara, Jogeshwari (W), Mumbai, Maharashtra, 400102, India.
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Vile Parle (W), Mumbai, Maharashtra, 400056, India.
| |
Collapse
|
3
|
Zhang S, Sun S, Zhang Y, Liu J, Wu Y, Zhang X. Comprehensive Analysis of N6-Methyladenosine RNA Methylation Regulators in the Diagnosis and Subtype Classification of Rheumatoid Arthritis. Biochem Genet 2024; 62:3467-3484. [PMID: 38112894 DOI: 10.1007/s10528-023-10610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
m6A modification is the most abundant mRNA modifications and plays an integral role in various biological processes in eukaryotes. However, the role of m6A regulators in rheumatoid arthritis remains unknown. To determine the expression of m6A RNA methylation regulators in rheumatoid arthritis and their possible functional and prognostic value. In this study, we performed differential analysis in the comprehensive gene expression database GSE93272 dataset between non-rheumatoid arthritis patients and rheumatoid arthritis patients to obtain 15 important m6A regulators. A random forest model and lasso regression were used to screen the five most important m6A regulators to predict the risk of developing rheumatoid arthritis. After further validation using in vitro qPCR experiments, a nomogram model was developed based on the four most important m6A regulators (ELAVL1, WTAP, YTHDF1, and ALKBH5). Immuno-infiltration analysis and consensus clustering analysis were then performed. An analysis of the decision curve showed that the nomogram model could be beneficial to patients. According to selected important m6A regulators, patients with rheumatoid arthritis were classified into two m6A models (ClusterA and ClusterB) via consensus approach. Activated B cells, CD56dim natural killer cells, immature B cells, monocytes, natural killer T cells, and T lymphocytes were associated with ClusterA in immune infiltration analysis. Importantly, immune infiltration in patients with high ELAVL1 expression was strikingly similar to ClusterA. m6A regulators play a non-negligible role in the development of rheumatoid arthritis. A study of m6A patterns may provide future therapeutic options for rheumatoid arthritis.
Collapse
Affiliation(s)
- Shaoxiong Zhang
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Shuo Sun
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | | | - Jianping Liu
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Yuhuai Wu
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China.
| | - Xiguang Zhang
- The 6th Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China.
| |
Collapse
|
4
|
McQuarrie DWJ, Soller M. Phylogenomic instructed target analysis reveals ELAV complex binding to multiple optimally spaced U-rich motifs. Nucleic Acids Res 2024:gkae826. [PMID: 39319593 DOI: 10.1093/nar/gkae826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/04/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024] Open
Abstract
ELAV/Hu RNA-binding proteins are gene-specific regulators of alternative pre-mRNA processing. ELAV/Hu family proteins bind to short AU-rich motifs which are abundant in pre-mRNA, making it unclear how they achieve gene specificity. ELAV/Hu proteins multimerize, but how multimerization contributes to decode degenerate sequence environments remains uncertain. Here, we show that ELAV forms a saturable complex on extended RNA. Through phylogenomic instructed target analysis we identify the core binding motif U5N2U3, which is repeated in an extended binding site. Optimally spaced short U5N2U3 binding motifs are key for high-affinity binding in this minimal binding element. Binding strength correlates with ELAV-regulated alternative poly(A) site choice, which is physiologically relevant through regulation of the major ELAV target ewg in determining synapse numbers. We further identify a stem-loop secondary structure in the ewg binding site unwound upon ELAV binding at three distal U motifs. Base-pairing of U motifs prevents ELAV binding, but N6-methyladenosine (m6A) has little effect. Further, stem-loops are enriched in ELAV-regulated poly(A) sites. Additionally, ELAV can nucleate preferentially from 3' to 5'. Hence, we identify a decisive mechanism for ELAV complex formation, addressing a fundamental gap in understanding how ELAV/Hu family proteins decode degenerate sequence spaces for gene-specific mRNA processing.
Collapse
Affiliation(s)
- David W J McQuarrie
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| |
Collapse
|
5
|
Parsha R, Kota SK. Elavl1 is dispensable for appendicular skeletal development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.23.614008. [PMID: 39386561 PMCID: PMC11463591 DOI: 10.1101/2024.09.23.614008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Elavl1/HuR is a RNA binding protein implicated in multiple developmental processes with pleiotropic roles in RNA life cycle. Loss of Elavl1 is incompatible with life with early embryonic loss of Elavl1 in epiblast cells being lethal with defects in placental branching and embryonic tissue growth. Postnatal global deletion of Elavl1/HuR results in lethality with atrophy in multiple tissues mainly due to loss of progenitor cells. However, roles of Elavl1 specifically during embryonic limb development is not well understood. Here we report that deletion of Elavl1 in limb bud mesenchyme in mouse did not reveal any abnormalities during embryonic development with normal development in pre- and postnatal limb skeleton. Analyses of skeletal patterning, morphogenesis and skeletal maturation including skeletal elements in stylopod, zeugopod and autopod during development did not reveal any significant differences between long bones from control and Elavl1 conditional knockout animals. Our study indicates differential dependency and susceptibility to loss of Elavl1 in different stem cell lineages with its functions being dispensable during limb development.
Collapse
|
6
|
Yadav V, Singh T, Sharma D, Garg VK, Chakraborty P, Ghatak S, Satapathy SR. Unraveling the Regulatory Role of HuR/microRNA Axis in Colorectal Cancer Tumorigenesis. Cancers (Basel) 2024; 16:3183. [PMID: 39335155 PMCID: PMC11430344 DOI: 10.3390/cancers16183183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
Colorectal cancer (CRC) remains a significant global health burden with high incidence and mortality. MicroRNAs (miRNAs) are small non-protein coding transcripts, conserved throughout evolution, with an important role in CRC tumorigenesis, and are either upregulated or downregulated in various cancers. RNA-binding proteins (RBPs) are known as essential regulators of miRNA activity. Human antigen R (HuR) is a prominent RBP known to drive tumorigenesis with a pivotal role in CRC. In this review, we discuss the regulatory role of the HuR/miRNA axis in CRC. Interestingly, miRNAs can directly target HuR, altering its expression and activity. However, HuR can also stabilize or degrade miRNAs, forming complex feedback loops that either activate or block CRC-associated signaling pathways. Dysregulation of the HuR/miRNA axis contributes to CRC initiation and progression. Additionally, HuR-miRNA regulation by other small non-coding RNAs, circular RNA (circRNAs), or long-non-coding RNAs (lncRNAs) is also explored here. Understanding this HuR-miRNA interplay could reveal novel biomarkers with better diagnostic or prognostic accuracy.
Collapse
Affiliation(s)
- Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Lund University, 221 00 Malmö, Sweden;
| | - Tejveer Singh
- Translational Oncology Laboratory, Department of Zoology, Hansraj College, University of Delhi, New Delhi 110021, India; (T.S.); (D.S.)
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS-DRDO), New Delhi 110054, India
| | - Deepika Sharma
- Translational Oncology Laboratory, Department of Zoology, Hansraj College, University of Delhi, New Delhi 110021, India; (T.S.); (D.S.)
| | - Vivek Kumar Garg
- Department of Medical Lab Technology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India;
| | - Payel Chakraborty
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, West Bengal, India; (P.C.); (S.G.)
| | - Souvik Ghatak
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, West Bengal, India; (P.C.); (S.G.)
| | - Shakti Ranjan Satapathy
- Department of Translational Medicine, Clinical Research Centre, Lund University, 221 00 Malmö, Sweden;
| |
Collapse
|
7
|
Papadimitriou E, Thomaidou D. Post-transcriptional mechanisms controlling neurogenesis and direct neuronal reprogramming. Neural Regen Res 2024; 19:1929-1939. [PMID: 38227517 DOI: 10.4103/1673-5374.390976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 01/17/2024] Open
Abstract
Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches. A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic, transcriptional, and post-transcriptional regulation. Understanding these neurogenic mechanisms is of major importance, not only for shedding light on very complex and crucial developmental processes, but also for the identification of putative reprogramming factors, that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate. The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors, as well as repressor complexes, have been identified and employed in direct reprogramming protocols to convert non-neuronal cells, into functional neurons. The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer, strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function. In particular, recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis, such as alternative splicing, polyadenylation, stability, and translation. Apart from the RNA binding proteins, microRNAs, a class of small non-coding RNAs that block the translation of their target mRNAs, have also been shown to play crucial roles in all the stages of the neurogenic process, from neural stem/progenitor cell proliferation, neuronal differentiation and migration, to functional maturation. Here, we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process, giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs. Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming, we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors, highlighting the so far known mechanisms of their reprogramming action.
Collapse
|
8
|
Kaur M, Mehta R, Muthuswami R, Mallick BN. Noradrenaline enhances Na-K ATPase subunit expression by HuR-induced mRNA stabilization and their transportation to the cell surface through PLC and PKC mediated pathway: Implications with REMS-loss associated disorders. J Neurochem 2024; 168:2561-2576. [PMID: 38676340 DOI: 10.1111/jnc.16116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/08/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Rapid eye movement sleep (REMS) maintains brain excitability at least by regulating Na-K ATPase activity. Although REMS deprivation (REMSD)-associated elevated noradrenaline (NA) increases Na-K ATPase protein expression, its mRNA transcription did not increase. We hypothesized and confirmed both in vivo as well as in vitro that elevated mRNA stability explains the apparent puzzle. The mRNA stability was measured in control and REMSD rat brain with or without in vivo treatment with α1-adrenoceptor (AR) antagonist, prazosin (PRZ). Upon REMSD, Na-K ATPase α1-, and α2-mRNA stability increased significantly, which was prevented by PRZ. To decipher the molecular mechanism of action, we estimated NA-induced Na-K ATPase mRNA stability in Neuro-2a cells under controlled conditions and by transcription blockage using Actinomycin D (Act-D). NA increased Na-K ATPase mRNA stability, which was prevented by PRZ and propranolol (PRP, β-AR antagonist). The knockdown assay confirmed that the increased mRNA stabilization was induced by elevated cytoplasmic abundance of Human antigen R (HuR) and involving (Phospholipase C) PLC-mediated activation of Protein Kinase C (PKC). Additionally, using cell-impermeable Enz-link sulfo NHS-SS-Biotin, we observed that NA increased Na-K ATPase α1-subunits on the Neuro-2a cell surface. We conclude that REMSD-associated elevated NA, acting on α1- and β-AR, increases nucleocytoplasmic translocation of HuR and increases Na-K ATPase mRNA stability, resulting in increased Na-K ATPase protein expression. The latter then gets translocated to the neuronal membrane surface involving both PKC and (Protein Kinase A) PKA-mediated pathways. These findings may be exploited for the amelioration of REMSD-associated chronic disorders and symptoms.
Collapse
Affiliation(s)
- Manjeet Kaur
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rachna Mehta
- AMITY Institute of Neuropsychology and Neurosciences, AMITY University Uttar Pradesh, Noida, UP, India
| | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Birendra Nath Mallick
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- AMITY Institute of Neuropsychology and Neurosciences, AMITY University Uttar Pradesh, Noida, UP, India
| |
Collapse
|
9
|
Baños-Jaime B, Corrales-Guerrero L, Pérez-Mejías G, Rejano-Gordillo CM, Velázquez-Campoy A, Martínez-Cruz LA, Martínez-Chantar ML, De la Rosa MA, Díaz-Moreno I. Phosphorylation at the disordered N-end makes HuR accumulate and dimerize in the cytoplasm. Nucleic Acids Res 2024; 52:8552-8565. [PMID: 38966993 PMCID: PMC11317137 DOI: 10.1093/nar/gkae564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/30/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024] Open
Abstract
Human antigen R (HuR) is an RNA binding protein mainly involved in maintaining the stability and controlling the translation of mRNAs, critical for immune response, cell survival, proliferation and apoptosis. Although HuR is a nuclear protein, its mRNA translational-related function occurs at the cytoplasm, where the oligomeric form of HuR is more abundant. However, the regulation of nucleo-cytoplasmic transport of HuR and its connection with protein oligomerization remain unclear. In this work, we describe the phosphorylation of Tyr5 as a new hallmark for HuR activation. Our biophysical, structural and computational assays using phosphorylated and phosphomimetic HuR proteins demonstrate that phosphorylation of Tyr5 at the disordered N-end stretch induces global changes on HuR dynamics and conformation, modifying the solvent accessible surface of the HuR nucleo-cytoplasmic shuttling (HNS) sequence and releasing regions implicated in HuR dimerization. These findings explain the preferential cytoplasmic accumulation of phosphorylated HuR in HeLa cells, aiding to comprehend the mechanisms underlying HuR nucleus-cytoplasm shuttling and its later dimerization, both of which are relevant in HuR-related pathogenesis.
Collapse
Affiliation(s)
- Blanca Baños-Jaime
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Laura Corrales-Guerrero
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Gonzalo Pérez-Mejías
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Claudia M Rejano-Gordillo
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura; University Institute of Biosanitary Research of Extremadura (INUBE), Badajoz 06071, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, Zaragoza 50018, Spain
- Departament of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza 50009, Spain
- Institute for Health Research of Aragón (IIS Aragon), Zaragoza 50009, Spain
| | - Luis Alfonso Martínez-Cruz
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - María Luz Martínez-Chantar
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - Miguel A De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| |
Collapse
|
10
|
Zhong X, Wang K, Wang Y, Wang L, Wang S, Huang W, Jia Z, Dai SS, Huang Z. Angiotension II directly bind P2X7 receptor to induce myocardial ferroptosis and remodeling by activating human antigen R. Redox Biol 2024; 72:103154. [PMID: 38626575 PMCID: PMC11035111 DOI: 10.1016/j.redox.2024.103154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/24/2024] [Accepted: 04/07/2024] [Indexed: 04/18/2024] Open
Abstract
Continuous remodeling of the heart can result in adverse events such as reduced myocardial function and heart failure. Available evidence indicates that ferroptosis is a key process in the emergence of cardiac disease. P2 family purinergic receptor P2X7 receptor (P2X7R) activation plays a crucial role in numerous aspects of cardiovascular disease. The aim of this study was to elucidate any potential interactions between P2X7R and ferroptosis in cardiac remodeling stimulated by angiotensin II (Ang II), and P2X7R knockout mice were utilized to explore the role of P2X7R and elucidate its underlying mechanism through molecular biological methods. Ferroptosis is involved in cardiac remodeling, and P2X7R deficiency significantly alleviates cardiac dysfunction, remodeling, and ferroptosis induced by Ang II. Mechanistically, Ang II interacts with P2X7R directly, and LYS-66 and MET-212 in the in the ATP binding pocket form a binding complex with Ang II. P2X7R blockade influences HuR-targeted GPX4 and HO-1 mRNA stability by affecting the shuttling of HuR from the nucleus to the cytoplasm and its expression. These results suggest that focusing on P2X7R could be a possible therapeutic approach for the management of hypertensive heart failure.
Collapse
Affiliation(s)
- Xin Zhong
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, The First Affiliated Hospital of WenZhou Medical University, WenZhou, ZheJiang, China
| | - Kangwei Wang
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, The First Affiliated Hospital of WenZhou Medical University, WenZhou, ZheJiang, China
| | - Yonghua Wang
- Department of Physical Education, WenZhou Medical University, WenZhou, ZheJiang, China
| | - Luya Wang
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, The First Affiliated Hospital of WenZhou Medical University, WenZhou, ZheJiang, China
| | - Sudan Wang
- Department of Respiratory, Wenzhou People's Hospital of Zhejiang Province, WenZhou, ZheJiang, China
| | - Weijian Huang
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, The First Affiliated Hospital of WenZhou Medical University, WenZhou, ZheJiang, China
| | - Zhuyin Jia
- Department of Cardiology, Wenzhou Central Hospital, The Second Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China.
| | - Shan-Shan Dai
- Department of Emergency, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, Zhejiang, China.
| | - Zhouqing Huang
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, The First Affiliated Hospital of WenZhou Medical University, WenZhou, ZheJiang, China.
| |
Collapse
|
11
|
O'Reilly ME, Ho S, Coronel J, Zhu L, Liu W, Xue C, Kim E, Cynn E, Matias CV, Soni RK, Wang C, Ionita-Laza I, Bauer RC, Ross L, Zhang Y, Corvera S, Fried SK, Reilly MP. linc-ADAIN, a human adipose lincRNA, regulates adipogenesis by modulating KLF5 and IL-8 mRNA stability. Cell Rep 2024; 43:114240. [PMID: 38753486 PMCID: PMC11334222 DOI: 10.1016/j.celrep.2024.114240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 03/01/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Adipose tissue remodeling and dysfunction, characterized by elevated inflammation and insulin resistance, play a central role in obesity-related development of type 2 diabetes (T2D) and cardiovascular diseases. Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular functions. Here, we describe the functions of linc-ADAIN (adipose anti-inflammatory), an adipose lincRNA that is downregulated in white adipose tissue of obese humans. We demonstrate that linc-ADAIN knockdown (KD) increases KLF5 and interleukin-8 (IL-8) mRNA stability and translation by interacting with IGF2BP2. Upregulation of KLF5 and IL-8, via linc-ADAIN KD, leads to an enhanced adipogenic program and adipose tissue inflammation, mirroring the obese state, in vitro and in vivo. KD of linc-ADAIN in human adipose stromal cell (ASC) hTERT adipocytes implanted into mice increases adipocyte size and macrophage infiltration compared to implanted control adipocytes, mimicking hallmark features of obesity-induced adipose tissue remodeling. linc-ADAIN is an anti-inflammatory lincRNA that limits adipose tissue expansion and lipid storage.
Collapse
Affiliation(s)
- Marcella E O'Reilly
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Sebastian Ho
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Johana Coronel
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Lucie Zhu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Wen Liu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Chenyi Xue
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Eunyoung Kim
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Esther Cynn
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Caio V Matias
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Chen Wang
- Department of Statistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Statistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Robert C Bauer
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Leila Ross
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Yiying Zhang
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Susan K Fried
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Muredach P Reilly
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
12
|
Magg V, Manetto A, Kopp K, Wu CC, Naghizadeh M, Lindner D, Eke L, Welsch J, Kallenberger SM, Schott J, Haucke V, Locker N, Stoecklin G, Ruggieri A. Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress. Cell Rep 2024; 43:114069. [PMID: 38602876 DOI: 10.1016/j.celrep.2024.114069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of growth arrest and DNA damage-inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We establish that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element (ARE) recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a component of the transient ISR memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.
Collapse
Affiliation(s)
- Vera Magg
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Alessandro Manetto
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Katja Kopp
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Chia Ching Wu
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Mohsen Naghizadeh
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Doris Lindner
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Lucy Eke
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Julia Welsch
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Stefan M Kallenberger
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, 10178 Berlin, Germany; Medical Oncology, National Center for Tumor Diseases, Heidelberg University, 69120 Heidelberg, Germany
| | - Johanna Schott
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, and Pharmacy, 14195 Berlin, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK; The Pirbright Institute, GU24 0NF Pirbright, UK
| | - Georg Stoecklin
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Alessia Ruggieri
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany.
| |
Collapse
|
13
|
Schall PZ, Latham KE. Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation. Physiol Genomics 2024; 56:9-31. [PMID: 37842744 PMCID: PMC11281819 DOI: 10.1152/physiolgenomics.00048.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/26/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023] Open
Abstract
Oocyte maturation is accompanied by changes in abundances of thousands of mRNAs, many degraded and many preferentially stabilized. mRNA stability can be regulated by diverse features including GC content, codon bias, and motifs within the 3'-untranslated region (UTR) interacting with RNA binding proteins (RBPs) and miRNAs. Many studies have identified factors participating in mRNA splicing, bulk mRNA storage, and translational recruitment in mammalian oocytes, but the roles of potentially hundreds of expressed factors, how they regulate cohorts of thousands of mRNAs, and to what extent their functions are conserved across species has not been determined. We performed an extensive in silico cross-species analysis of features associated with mRNAs of different stability classes during oocyte maturation (stable, moderately degraded, and highly degraded) for five mammalian species. Using publicly available RNA sequencing data for germinal vesicle (GV) and MII oocyte transcriptomes, we determined that 3'-UTR length and synonymous codon usage are positively associated with stability, while greater GC content is negatively associated with stability. By applying machine learning and feature selection strategies, we identified RBPs and miRNAs that are predictive of mRNA stability, including some across multiple species and others more species-restricted. The results provide new insight into the mechanisms regulating maternal mRNA stabilization or degradation.NEW & NOTEWORTHY Conservation across species of mRNA features regulating maternal mRNA stability during mammalian oocyte maturation was analyzed. 3'-Untranslated region length and synonymous codon usage are positively associated with stability, while GC content is negatively associated. Just three RNA binding protein motifs were predicted to regulate mRNA stability across all five species examined, but associated pathways and functions are shared, indicating oocytes of different species arrive at comparable physiological destinations via different routes.
Collapse
Affiliation(s)
- Peter Z Schall
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, United States
- Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, Michigan, United States
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, United States
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, Michigan, United States
| |
Collapse
|
14
|
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] [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.
Collapse
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
| |
Collapse
|
15
|
Abedeera SM, Davila-Calderon J, Haddad C, Henry B, King J, Penumutchu S, Tolbert BS. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses 2023; 16:75. [PMID: 38257775 PMCID: PMC10821071 DOI: 10.3390/v16010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Viruses pose a great threat to people's lives. Enterovirus A71 (EV-A71) infects children and infants all over the world with no FDA-approved treatment to date. Understanding the basic mechanisms of viral processes aids in selecting more efficient drug targets and designing more effective antivirals to thwart this virus. The 5'-untranslated region (5'-UTR) of the viral RNA genome is composed of a cloverleaf structure and an internal ribosome entry site (IRES). Cellular proteins that bind to the cloverleaf structure regulate viral RNA synthesis, while those that bind to the IRES also known as IRES trans-acting factors (ITAFs) regulate viral translation. In this review, we survey the cellular proteins currently known to bind the 5'-UTR and influence viral gene expression with emphasis on comparing proteins' functions and localizations pre- and post-(EV-A71) infection. A comprehensive understanding of how the host cell's machinery is hijacked and reprogrammed by the virus to facilitate its replication is crucial for developing effective antivirals.
Collapse
Affiliation(s)
- Sudeshi M. Abedeera
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Jesse Davila-Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Barrington Henry
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
16
|
Nelson EV, Ross SJ, Olejnik J, Hume AJ, Deeney DJ, King E, Grimins AO, Lyons SM, Cifuentes D, Mühlberger E. The 3' Untranslated Regions of Ebola Virus mRNAs Contain AU-Rich Elements Involved in Posttranscriptional Stabilization and Decay. J Infect Dis 2023; 228:S488-S497. [PMID: 37551415 PMCID: PMC10651315 DOI: 10.1093/infdis/jiad312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
The 3' untranslated regions (UTRs) of Ebola virus (EBOV) mRNAs are enriched in their AU content and therefore represent potential targets for RNA binding proteins targeting AU-rich elements (ARE-BPs). ARE-BPs are known to fine-tune RNA turnover and translational activity. We identified putative AREs within EBOV mRNA 3' UTRs and assessed whether they might modulate mRNA stability. Using mammalian and zebrafish embryo reporter assays, we show a conserved, ARE-BP-mediated stabilizing effect and increased reporter activity with the tested EBOV 3' UTRs. When coexpressed with the prototypic ARE-BP tristetraprolin (TTP, ZFP36) that mainly destabilizes its target mRNAs, the EBOV nucleoprotein (NP) 3' UTR resulted in decreased reporter gene activity. Coexpression of NP with TTP led to reduced NP protein expression and diminished EBOV minigenome activity. In conclusion, the enrichment of AU residues in EBOV 3' UTRs makes them possible targets for cellular ARE-BPs, leading to modulation of RNA stability and translational activity.
Collapse
Affiliation(s)
- Emily V Nelson
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Stephen J Ross
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Judith Olejnik
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Adam J Hume
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Dylan J Deeney
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Emily King
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Autumn O Grimins
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Shawn M Lyons
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Daniel Cifuentes
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Elke Mühlberger
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
17
|
Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
Collapse
Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
| |
Collapse
|
18
|
Li J, Dong X, Kong X, Wang Y, Li Y, Tong Y, Zhao W, Duan W, Li P, Wang Y, Wang C. Circular RNA hsa_circ_0067842 facilitates tumor metastasis and immune escape in breast cancer through HuR/CMTM6/PD-L1 axis. Biol Direct 2023; 18:48. [PMID: 37592296 PMCID: PMC10436663 DOI: 10.1186/s13062-023-00397-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) have been shown to play diverse biological functions in the progression of multiple diseases. However, the impacts of circRNAs on breast cancer (BC) progression remains unclear. Therefore, the objective of this paper is to investigate the role and mechanisms of a functional circRNA in BC metastasis and immune escape. METHODS This study used a circRNA microarray and identified a novel circRNA hsa_circ_0067842. The validation and characteristics of hsa_circ_0067842 were investigated using qRT-PCR, sanger sequencing, RNase R treatment, actinomycin D treatment and fluorescence in situ hybridization (FISH). Gain- and loss-of-function assays were performed to evaluate the biological function of hsa_circ_0067842 in BC progression and immune escape. Mechanistically, the interaction between hsa_circ_0067842 and HuR was explored by RNA pull down, mass spectrometry (MS), subcellular component protein extraction and immunofluorescence (IF). The regulatory mechanisms of hsa_circ_0067842/HuR/CMTM6/PD-L1 axis were investigated by qRT-PCR, western blot, FISH, immunoprecipitation and rescue assays. RESULTS The expression of hsa_circ_0067842 was upregulated in BC tissues and cells, which was found to be significantly associated with poor prognosis, regardless of other clinical covariates. Function assays showed that hsa_circ_0067842 promoted the migration and invasion capacities of BC cells. Moreover, co-culture experiment with peripheral blood mononuclear cells (PBMCs) showed that hsa_circ_0067842 played a role in the immune escape of BC cells. Mechanistically, our study showed that hsa_circ_0067842 interacted with HuR, affecting its nuclear translocation, thus enhancing the stability of CMTM6. CMTM6 not only enhances the migration and invasion ability of BC cells, but also affects the ubiquitination of PD-L1 and inhibits its degradation. CONCLUSION Collectively, our results demonstrated that hsa_circ_0067842 promoted BC progression through the HuR/CMTM6/PD-L1 axis, providing new insight and a potential target for BC prognosis and therapy.
Collapse
Affiliation(s)
- Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xiangjun Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xue Kong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Yafen Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Yao Tong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Weili Duan
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
| | - Yanqun Wang
- Department of Clinical Laboratory, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, 250031, Shandong, China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
| |
Collapse
|
19
|
Merat R. The human antigen R as an actionable super-hub within the network of cancer cell persistency and plasticity. Transl Oncol 2023; 35:101722. [PMID: 37352624 DOI: 10.1016/j.tranon.2023.101722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is derived, including an experimental quantitative assessment of cell plasticity and an information theory-based detection of in vivo dependencies, for the discovery of post-transcriptional druggable mechanisms capable of preventing at multiple levels the emergence of plastic dedifferentiated slow-proliferating cells. The approach is illustrated by the author's own work in the example case of the adaptive response of BRAFV600-melanoma to BRAF inhibition. A bench-to-bedside and back to bench effort leads to a therapeutic strategy in which the inhibition of the baseline activity of the interferon-γ-activated inhibitor of translation (GAIT) complex, incriminated in the expression insufficiency of the RNA-binding protein HuR in a minority of cells, results in the suppression of the plastic, intermittently slow-proliferating cells involved in the adaptive response. A similar approach is recommended for the validation of other classes of mechanisms that we seek to modulate to overcome this complex challenge of modern cancer therapy.
Collapse
Affiliation(s)
- Rastine Merat
- Dermato-Oncology Unit, Division of Dermatology, Geneva University Hospitals, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Switzerland.
| |
Collapse
|
20
|
Vujovic A, de Rooij L, Chahi AK, Chen HT, Yee BA, Loganathan SK, Liu L, Chan DC, Tajik A, Tsao E, Moreira S, Joshi P, Xu J, Wong N, Balde Z, Jahangiri S, Zandi S, Aigner S, Dick JE, Minden MD, Schramek D, Yeo GW, Hope KJ. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. Blood Cancer Discov 2023; 4:180-207. [PMID: 36763002 PMCID: PMC10150294 DOI: 10.1158/2643-3230.bcd-22-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) selectively enriched in human AML LSCs. Using an in vivo two-step CRISPR-Cas9 screen to assay stem cell functionality, we found 32 RBPs essential for LSCs in MLL-AF9;NrasG12D AML. Loss-of-function approaches targeting key hit RBP ELAVL1 compromised LSC-driven in vivo leukemic reconstitution, and selectively depleted primitive malignant versus healthy cells. Integrative multiomics revealed differentiation, splicing, and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with mitochondrial import protein, TOMM34, being a direct ELAVL1-stabilized target whose repression impairs AML propagation. Altogether, using a stem cell-adapted in vivo CRISPR screen, this work demonstrates pervasive reliance on RBPs as regulators of LSCs and highlights their potential as therapeutic targets in AML. SIGNIFICANCE LSC-targeted therapies remain a significant unmet need in AML. We developed a stem-cell-adapted in vivo CRISPR screen to identify key LSC drivers. We uncover widespread RNA-binding protein dependencies in LSCs, including ELAVL1, which we identify as a novel therapeutic vulnerability through its regulation of mitochondrial metabolism. This article is highlighted in the In This Issue feature, p. 171.
Collapse
Affiliation(s)
- Ana Vujovic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Laura de Rooij
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ava Keyvani Chahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - He Tian Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Lina Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Derek C.H. Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Amanda Tajik
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Emily Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Steven Moreira
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Pratik Joshi
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Nicholas Wong
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Soheil Jahangiri
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sasan Zandi
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - John E. Dick
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D. Minden
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Kristin J. Hope
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| |
Collapse
|
21
|
Hilgers V. Regulation of neuronal RNA signatures by ELAV/Hu proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1733. [PMID: 35429136 DOI: 10.1002/wrna.1733] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 12/30/2022]
Abstract
The RNA-binding proteins encoded by the highly conserved elav/Hu gene family, found in all metazoans, regulate the expression of a wide range of genes, at both the co-transcriptional and posttranscriptional level. Nervous-system-specific ELAV/Hu proteins are prominent for their essential role in neuron differentiation, and mutations have been associated with human neurodevelopmental and neurodegenerative diseases. Drosophila ELAV, the founding member of the protein family, mediates the synthesis of neuronal RNA signatures by promoting alternative splicing and alternative polyadenylation of hundreds of genes. The recent identification of ELAV's direct RNA targets revealed the protein's central role in shaping the neuronal transcriptome, and highlighted the importance of neuronal transcript signatures for neuron maintenance and organism survival. Animals have evolved multiple cellular mechanisms to ensure robustness of ELAV/Hu function. In Drosophila, elav autoregulates in a 3'UTR-dependent manner to maintain optimal protein levels. A complete absence of ELAV causes the activation and nuclear localization of the normally cytoplasmic paralogue FNE, in a process termed EXon-Activated functional Rescue (EXAR). Other species, including mammals, seem to utilize different strategies, such as protein redundancy, to maintain ELAV protein function and effectively safeguard the identity of the neuronal transcriptome. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Development RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| |
Collapse
|
22
|
LncGMDS-AS1 promotes the tumorigenesis of colorectal cancer through HuR-STAT3/Wnt axis. Cell Death Dis 2023; 14:165. [PMID: 36849492 PMCID: PMC9970971 DOI: 10.1038/s41419-023-05700-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/01/2023]
Abstract
Chronic inflammation promotes the tumorigenesis and cell stemness maintenance of colorectal cancer (CRC). However, the bridge role of long noncoding RNA (lncRNA) in linking chronic inflammation to CRC development and progression needs better understanding. Here, we elucidated a novel function of lncRNA GMDS-AS1 in persistently activated signal transducer and transcription activator 3 (STAT3) and Wnt signaling and CRC tumorigenesis. Interleukin-6 (IL-6) and Wnt3a induced lncRNA GMDS-AS1 expression, which was highly expressed in the CRC tissues and plasma of CRC patients. GMDS-AS1 knockdown impaired the survival, proliferation and stem cell-like phenotype acquisition of CRC cells in vitro and in vivo. We performed RNA sequencing (RNA-seq) and mass spectrometry (MS) to probe target proteins and identify their contributions to the downstream signaling pathways of GMDS-AS1. In CRC cells, GMDS-AS1 physically interacted with the RNA-stabilizing protein HuR, thereby protecting the HuR protein from polyubiquitination- and proteasome-dependent degradation. HuR stabilized STAT3 mRNA and upregulated the levels of basal and phosphorylated STAT3 protein, persistently activating STAT3 signaling. Our research revealed that the lncRNA GMDS-AS1 and its direct target HuR constitutively activate STAT3/Wnt signaling and promote CRC tumorigenesis, the GMDS-AS1-HuR-STAT3/Wnt axis is a therapeutic, diagnostic and prognostic target in CRC.
Collapse
|
23
|
Chen Y, Zhang R, Yang L, Zhang P, Wang F, Lin G, Zhang J, Zhu Y. Eltrombopag Inhibits Metastasis in Breast Carcinoma by Targeting HuR Protein. Int J Mol Sci 2023; 24:ijms24043164. [PMID: 36834574 PMCID: PMC9963984 DOI: 10.3390/ijms24043164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Eltrombopag is a small molecule TPO-R agonist that has been shown in our previous studies to inhibit tumor growth by targeting Human antigen R (HuR) protein. HuR protein not only regulates the mRNA stability of tumor growth-related genes, but it also regulates the mRNA stability of a variety of cancer metastasis-related genes, such as Snail, Cox-2, and Vegf-c. However, the role and mechanisms of eltrombopag in breast cancer metastasis have not been fully investigated. The purpose of this study was to investigate whether eltrombopag can inhibit breast cancer metastasis by targeting HuR. Our study first found that eltrombopag can destroy HuR-AU-rich element (ARE) complexes at the molecular level. Secondly, eltrombopag was found to suppress 4T1 cell migration and invasion and inhibit macrophage-mediated lymphangiogenesis at the cellular level. In addition, eltrombopag exerted inhibitory effects on lung and lymph node metastasis in animal tumor metastasis models. Finally, it was verified that eltrombopag inhibited the expressions of Snail, Cox-2, and Vegf-c in 4T1 cells and Vegf-c in RAW264.7 cells by targeting HuR. In conclusion, eltrombopag displayed antimetastatic activity in breast cancer in an HuR dependent manner, which may provide a novel application for eltrombopag, hinting at the multiple effects of HuR inhibitors in cancer therapy.
Collapse
Affiliation(s)
- Yao Chen
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rui Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Liuqing Yang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Pei Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Feiyun Wang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoqiang Lin
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiange Zhang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (J.Z.); (Y.Z.); Tel./Fax: +86-21-51323104 (J.Z. & Y.Z.)
| | - Yuying Zhu
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Institute of Traditional Chinese Medicine, Shanghai 201203, China
- Correspondence: (J.Z.); (Y.Z.); Tel./Fax: +86-21-51323104 (J.Z. & Y.Z.)
| |
Collapse
|
24
|
Nishisaka H, Tomohiro T, Fukao A, Funakami Y, Fujiwara T. Neuronal RNA-Binding Protein HuD Interacts with Translation Initiation Factor eIF3. Biol Pharm Bull 2023; 46:158-162. [PMID: 36724943 DOI: 10.1248/bpb.b22-00478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Translation initiation is the rate-limiting step of protein synthesis and is the main target of translation regulation. RNA-binding proteins (RBPs) are key mediators of the spatiotemporal control of translation and are critical for cell proliferation, development, and differentiation. We have previously shown that HuD, one of the neuronal RBPs, enhances cap-dependent translation through the direct interaction with eukaryotic initiation factor 4A (eIF4A) and poly(A) tail using a HeLa-derived in vitro translation system. We have also found that translation stimulation of HuD is essential for HuD-induced neurite outgrowth in PC12 cells. However, it remains unclear how HuD is involved in the regulation of translation initiation. Here, we report that HuD binds to eukaryotic initiation factor 3 (eIF3) via the eIF3b subunit, which belongs to the functional core of mammalian eIF3. eIF3 plays an essential role in recruiting the 40S ribosomal subunit onto mRNA in translation initiation. We hypothesize that the interaction between HuD and eIF3 stabilizes the translation initiation complex and increases translation efficiency. We also showed that the linker region of HuD is required for the interaction with eIF3b. Moreover, we found that eIF3b-binding region of HuD is conserved in all Hu proteins (HuB, HuC, HuD, and HuR). These data might also help to explain how Hu proteins stimulate translation in a cap- and poly(A)-dependent way.
Collapse
|
25
|
Yu PL, Wu R, Cao SJ, Wen YP, Huang XB, Zhao S, Lang YF, Zhao Q, Lin JC, Du SY, Yu SM, Yan QG. Pseudorabies virus exploits N 6-methyladenosine modification to promote viral replication. Front Microbiol 2023; 14:1087484. [PMID: 36819040 PMCID: PMC9936159 DOI: 10.3389/fmicb.2023.1087484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Pseudorabies virus (PRV) is the pathogenic virus of porcine pseudorabies (PR), belonging to the Herpesviridae family. PRV has a wide range of hosts and in recent years has also been reported to infect humans. N6-methyladenosine (m6A) modification is the major pathway of RNA post-transcriptional modification. Whether m6A modification participates in the regulation of PRV replication is unknown. Methods Here, we investigated that the m6A modification was abundant in the PRV transcripts and PRV infection affected the epitranscriptome of host cells. Knockdown of cellular m6A methyltransferases METTL3 and METTL14 and the specific binding proteins YTHDF2 and YTHDF3 inhibited PRV replication, while silencing of demethylase ALKBH5 promoted PRV output. The overexpression of METTL14 induced more efficient virus proliferation in PRV-infected PK15 cells. Inhibition of m6A modification by 3-deazaadenosine (3-DAA), a m6A modification inhibitor, could significantly reduce viral replication. Results and Discussion Taken together, m6A modification played a positive role in the regulation of PRV replication and gene expression. Our research revealed m6A modification sites in PRV transcripts and determined that m6A modification dynamically mediated the interaction between PRV and host.
Collapse
Affiliation(s)
- Pei-Lun Yu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - San-Jie Cao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Ping Wen
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Bo Huang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shan Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yi-Fei Lang
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ju-Chun Lin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sen-Yan Du
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shu-Min Yu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qi-Gui Yan
- Department of Preventive Veterinary Medicine, Swine Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,*Correspondence: Qi-Gui Yan, ✉
| |
Collapse
|
26
|
RBP-RNA interactions in the control of autoimmunity and autoinflammation. Cell Res 2023; 33:97-115. [PMID: 36599968 PMCID: PMC9892603 DOI: 10.1038/s41422-022-00752-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/07/2022] [Indexed: 01/06/2023] Open
Abstract
Autoimmunity and autoinflammation arise from aberrant immunological and inflammatory responses toward self-components, contributing to various autoimmune diseases and autoinflammatory diseases. RNA-binding proteins (RBPs) are essential for immune cell development and function, mainly via exerting post-transcriptional regulation of RNA metabolism and function. Functional dysregulation of RBPs and abnormities in RNA metabolism are closely associated with multiple autoimmune or autoinflammatory disorders. Distinct RBPs play critical roles in aberrant autoreactive inflammatory responses via orchestrating a complex regulatory network consisting of DNAs, RNAs and proteins within immune cells. In-depth characterizations of RBP-RNA interactomes during autoimmunity and autoinflammation will lead to a better understanding of autoimmune pathogenesis and facilitate the development of effective therapeutic strategies. In this review, we summarize and discuss the functions of RBP-RNA interactions in controlling aberrant autoimmune inflammation and their potential as biomarkers and therapeutic targets.
Collapse
|
27
|
Fontemaggi G. Non-coding RNA regulatory networks in post-transcriptional regulation of VEGFA in cancer. IUBMB Life 2023; 75:30-39. [PMID: 35467790 PMCID: PMC10084289 DOI: 10.1002/iub.2620] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/10/2022] [Indexed: 12/29/2022]
Abstract
The switch from the normal quiescent vasculature to angiogenesis in tumors is induced by a variety of growth factors, released from cancer and stromal cells upon oxygen and nutrients deprivation. Vascular endothelial growth factor A (VEGF-A) is a potent-secreted mitogen and the only growth factor specific to endothelial cells that is observed almost ubiquitously at sites of angiogenesis. Expression of VEGF-A in cancer cells is controlled through transcriptional and post-transcriptional mechanisms. Post-transcriptional regulation of VEGF-A occurs at multiple levels, through the control of splicing, mRNA stability and translation rate, enabling a fine-tuned expression and release of VEGF-A. Mounting evidence is highlighting the important role played by microRNAs (miRNAs) in the control of VEGF-A mRNA stability and translation in cancer. Moreover, non-coding RNAs, as long non-coding RNAs and circular RNAs, are emerging as crucial modulators of VEGF-A-targeting miRNAs, with consequent ability to modulate VEGF-A expression. This review discusses the recent progress on the ncRNA-related networks controlling VEGF-A expression in cancer cells and provides insights into the complexity of VEGF-A post-transcriptional regulation.
Collapse
Affiliation(s)
- Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| |
Collapse
|
28
|
Smith MR, Costa G. RNA-binding proteins and translation control in angiogenesis. FEBS J 2022; 289:7788-7809. [PMID: 34796614 DOI: 10.1111/febs.16286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023]
Abstract
Tissue vascularization through the process of angiogenesis ensures adequate oxygen and nutrient supply during development and regeneration. The complex morphogenetic events involved in new blood vessel formation are orchestrated by a tightly regulated crosstalk between extra and intracellular factors. In this context, RNA-binding protein (RBP) activity and protein translation play fundamental roles during the cellular responses triggered by particular environmental cues. A solid body of work has demonstrated that key RBPs (such as HuR, TIS11 proteins, hnRNPs, NF90, QKIs and YB1) are implicated in both physiological and pathological angiogenesis. These RBPs are critical for the metabolism of messenger (m)RNAs encoding angiogenic modulators and, importantly, strong evidence suggests that RBP-mRNA interactions can be altered in disease. Lesser known, but not less important, the mechanistic aspects of protein synthesis can also regulate the generation of new vessels. In this review, we outline the key findings demonstrating the implications of RBP-mediated RNA regulation and translation control in angiogenesis. Furthermore, we highlight how these mechanisms of post-transcriptional control of gene expression have led to promising therapeutic strategies aimed at targeting undesired blood vessel formation.
Collapse
Affiliation(s)
- Madeleine R Smith
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| | - Guilherme Costa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| |
Collapse
|
29
|
Du Y, Xu X, Lv S, Liu H, Sun H, Wu J. SOCS7/HuR/FOXM1 signaling axis inhibited high-grade serous ovarian carcinoma progression. J Exp Clin Cancer Res 2022; 41:185. [PMID: 35624501 PMCID: PMC9137060 DOI: 10.1186/s13046-022-02395-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/12/2022] [Indexed: 12/01/2022] Open
Abstract
Background High-grade serous ovarian carcinoma (HGSOC) is clinically dominant and accounts for ~ 80% deaths in all types of ovarian cancer. The delayed diagnosis, rapid development, and wide dissemination of HGSOC collectively contribute to its high mortality rate and poor prognosis in the patients. Suppressors of cytokine signaling 7 (SOCS7) can regulate cytokine signaling and participate in cell cycle arrest and regulation of cell proliferation, which might also be involved in carcinogenesis. Here, we designated to investigate the functions and mechanisms of SOCS7 in HGSOC. Methods The clinical correlation between SOCS7 and HGSOC was examined by both bioinformatics and analysis of tissue samples in patients. Gain/Loss-of-function examinations were carried out to assess the effectiveness of SOCS7 in cell viability, cell cycle, and tumor growth of HGSOC. Furthermore, the underlying mechanisms were explored by identifying the downstream proteins and their interactions via proteomics analysis and immunoprecipitation. Results The expression of SOCS7, which was decreased in HGSOC tissues, was correlated with the clinical pathologic characteristics and overall survival of HGSOC patients. SOCS7 acted as a HGSOC suppressor by inhibiting cancer cell viability and tumor growth in vivo. The anti-HGSOC mechanism involves SOCS7’s regulatory effect on HuR by mediating its ubiquitination, the regulation of FOXM1 mRNA by HuR, as well as the interplays among these three clinically relevant factors. Conclusions The SOCS7 correlates with HGSOC and suppresses its tumorigenesis through regulating HuR and FOXM1, which also suggests that SOCS7 is a prospective biomarker for the clinical management of ovarian cancer, especially HGSOC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02395-1.
Collapse
|
30
|
The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation. Nat Commun 2022; 13:5892. [PMID: 36202814 PMCID: PMC9537309 DOI: 10.1038/s41467-022-33552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/22/2022] [Indexed: 11/08/2022] Open
Abstract
Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1's tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unusual mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1's double-stranded RNA binding domain (dsRBD), which is dispensable for binding of a subset of targets in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation.
Collapse
|
31
|
Post-Transcriptional Control of mRNA Metabolism and Protein Secretion: The Third Level of Regulation within the NF-κB System. Biomedicines 2022; 10:biomedicines10092108. [PMID: 36140209 PMCID: PMC9495616 DOI: 10.3390/biomedicines10092108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
The NF-κB system is a key transcriptional pathway that regulates innate and adaptive immunity because it triggers the activation and differentiation processes of lymphocytes and myeloid cells during immune responses. In most instances, binding to cytoplasmic inhibitory IκB proteins sequesters NF-κB into an inactive state, while a plethora of external triggers activate three complex signaling cascades that mediate the release and nuclear translocation of the NF-κB DNA-binding subunits. In addition to these cytosolic steps (level 1 of NF-κB regulation), NF-κB activity is also controlled in the nucleus by signaling events, cofactors and the chromatin environment to precisely determine chromatin recruitment and the specificity and timing of target gene transcription (level 2 of NF-κB regulation). Here, we discuss an additional layer of the NF-κB system that manifests in various steps of post-transcriptional gene expression and protein secretion. This less-studied regulatory level allows reduction of (transcriptional) noise and signal integration and endows time-shifted control of the secretion of inflammatory mediators. Detailed knowledge of these steps is important, as dysregulated post-transcriptional NF-κB signaling circuits are likely to foster chronic inflammation and contribute to the formation and maintenance of a tumor-promoting microenvironment.
Collapse
|
32
|
Hao X, Shiromoto Y, Sakurai M, Towers M, Zhang Q, Wu S, Havas A, Wang L, Berger S, Adams PD, Tian B, Nishikura K, Kossenkov AV, Liu P, Zhang R. ADAR1 downregulation by autophagy drives senescence independently of RNA editing by enhancing p16 INK4a levels. Nat Cell Biol 2022; 24:1202-1210. [PMID: 35851616 PMCID: PMC9757154 DOI: 10.1038/s41556-022-00959-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/07/2022] [Indexed: 02/03/2023]
Abstract
Cellular senescence plays a causal role in ageing and, in mice, depletion of p16INK4a-expressing senescent cells delays ageing-associated disorders1,2. Adenosine deaminases acting on RNA (ADARs) are RNA-editing enzymes that are also implicated as important regulators of human ageing, and ADAR inactivation causes age-associated pathologies such as neurodegeneration in model organisms3,4. However, the role, if any, of ADARs in cellular senescence is unknown. Here we show that ADAR1 is post-transcriptionally downregulated by autophagic degradation to promote senescence through p16INK4a upregulation. The ADAR1 downregulation is sufficient to drive senescence in both in vitro and in vivo models. Senescence induced by ADAR1 downregulation is p16INK4a-dependent and independent of its RNA-editing function. Mechanistically, ADAR1 promotes SIRT1 expression by affecting its RNA stability through HuR, an RNA-binding protein that increases the half-life and steady-state levels of its target mRNAs. SIRT1 in turn antagonizes translation of mRNA encoding p16INK4a. Hence, downregulation of ADAR1 and SIRT1 mediates p16INK4a upregulation by enhancing its mRNA translation. Finally, Adar1 is downregulated during ageing of mouse tissues such as brain, ovary and intestine, and Adar1 expression correlates with Sirt1 expression in these tissues in mice. Together, our study reveals an RNA-editing-independent role for ADAR1 in the regulation of senescence by post-transcriptionally controlling p16INK4a expression.
Collapse
Affiliation(s)
- Xue Hao
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Yusuke Shiromoto
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Department of Molecular Genetics, Graduate School of Medicine Kyoto University, Kyoto, Japan
| | - Masayuki Sakurai
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Martina Towers
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Qiang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Shuai Wu
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Aaron Havas
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Lu Wang
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley Berger
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Kazuko Nishikura
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Andrew V Kossenkov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Pingyu Liu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA, USA.
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.
| | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA, USA.
| |
Collapse
|
33
|
Li L, Xu N, Liu J, Chen Z, Liu X, Wang J. m6A Methylation in Cardiovascular Diseases: From Mechanisms to Therapeutic Potential. Front Genet 2022; 13:908976. [PMID: 35836571 PMCID: PMC9274458 DOI: 10.3389/fgene.2022.908976] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide. Recent studies have shown that n6-methyladenosine (m6A) plays a major role in cardiovascular homeostasis and pathophysiology. These studies have confirmed that m6A methylation affects the pathophysiology of cardiovascular diseases by regulating cellular processes such as differentiation, proliferation, inflammation, autophagy, and apoptosis. Moreover, plenty of research has confirmed that m6A modification can delay the progression of CVD via the post-transcriptional regulation of RNA. However, there are few available summaries of m6A modification regarding CVD. In this review, we highlight advances in CVD-specific research concerning m6A modification, summarize the mechanisms underlying the involvement of m6A modification during the development of CVD, and discuss the potential of m6A modification as a therapeutic target of CVD.
Collapse
Affiliation(s)
| | | | | | | | | | - Junnan Wang
- Department of Cardiology, Second Hospital of Jilin University, Changchun, China
| |
Collapse
|
34
|
Youn YH, Hou S, Wu CC, Kawauchi D, Orr BA, Robinson GW, Finkelstein D, Taketo MM, Gilbertson RJ, Roussel MF, Han YG. Primary cilia control translation and the cell cycle in medulloblastoma. Genes Dev 2022; 36:737-751. [PMID: 35798383 PMCID: PMC9296008 DOI: 10.1101/gad.349596.122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/17/2022] [Indexed: 11/24/2022]
Abstract
The primary cilium, a signaling organelle projecting from the surface of a cell, controls cellular physiology and behavior. The presence or absence of primary cilia is a distinctive feature of a given tumor type; however, whether and how the primary cilium contributes to tumorigenesis are unknown for most tumors. Medulloblastoma (MB) is a common pediatric brain cancer comprising four groups: SHH, WNT, group 3 (G3), and group 4 (G4). From 111 cases of MB, we show that primary cilia are abundant in SHH and WNT MBs but rare in G3 and G4 MBs. Using WNT and G3 MB mouse models, we show that primary cilia promote WNT MB by facilitating translation of mRNA encoding β-catenin, a major oncoprotein driving WNT MB, whereas cilium loss promotes G3 MB by disrupting cell cycle control and destabilizing the genome. Our findings reveal tumor type-specific ciliary functions and underlying molecular mechanisms. Moreover, we expand the function of primary cilia to translation control and reveal a molecular mechanism by which cilia regulate cell cycle progression, thereby providing new frameworks for studying cilium function in normal and pathologic conditions.
Collapse
Affiliation(s)
- Yong Ha Youn
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Shirui Hou
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Chang-Chih Wu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Giles W Robinson
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Makoto M Taketo
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Richard J Gilbertson
- Department of Oncology, Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, England
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Young-Goo Han
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| |
Collapse
|
35
|
Hu Antigen R (HuR) Protein Structure, Function and Regulation in Hepatobiliary Tumors. Cancers (Basel) 2022; 14:cancers14112666. [PMID: 35681645 PMCID: PMC9179498 DOI: 10.3390/cancers14112666] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Hepatobiliary tumors are a group of primary malignancies encompassing the liver, the intra- and extra-hepatic biliary tracts, and the gall bladder. Within the liver, hepatocellular carcinoma (HCC) is the most common type of primary cancer, which is, also, representing the third-most recurrent cause of cancer-associated death and the sixth-most prevalent type of tumor worldwide, nowadays. Although less frequent, cholangiocarcinoma (CCA) is, currently, a fatal cancer with limited therapeutic options. Here, we review the regulatory role of Hu antigen R (HuR), a ubiquitous member of the ELAV/Hu family of RNA-binding proteins (RBPs), in the pathogenesis, progression, and treatment of HCC and CCA. Overall, HuR is proposed as a valuable diagnostic and prognostic marker, as well as a therapeutic target in hepatobiliary cancers. Therefore, novel therapeutic approaches that can selectively modulate HuR function appear to be highly attractive for the clinical management of these types of tumors. Abstract Hu antigen R (HuR) is a 36-kDa ubiquitous member of the ELAV/Hu family of RNA-binding proteins (RBPs), which plays an important role as a post-transcriptional regulator of specific RNAs under physiological and pathological conditions, including cancer. Herein, we review HuR protein structure, function, and its regulation, as well as its implications in the pathogenesis, progression, and treatment of hepatobiliary cancers. In particular, we focus on hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), tumors where the increased cytoplasmic localization of HuR and activity are proposed, as valuable diagnostic and prognostic markers. An overview of the main regulatory axes involving HuR, which are associated with cell proliferation, invasion, metastasis, apoptosis, and autophagy in HCC, is provided. These include the transcriptional, post-transcriptional, and post-translational modulators of HuR function, in addition to HuR target transcripts. Finally, whereas studies addressing the relevance of targeting HuR in CCA are limited, in the past few years, HuR has emerged as a potential therapeutic target in HCC. In fact, the therapeutic efficacy of some pharmacological inhibitors of HuR has been evaluated, in early experimental models of HCC. We, further, discuss the major findings and future perspectives of therapeutic approaches that specifically block HuR interactions, either with post-translational modifiers or cognate transcripts in hepatobiliary cancers.
Collapse
|
36
|
Agarwal A, Alagar S, Kant S, Bahadur RP. Molecular insights into binding dynamics of tandem RNA recognition motifs (tRRMs) of human antigen R (HuR) with mRNA and the effect of point mutations in impaired HuR-mRNA recognition. J Biomol Struct Dyn 2022:1-17. [PMID: 35538713 DOI: 10.1080/07391102.2022.2073270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human antigen R (HuR) is a key regulatory protein with prominent roles in RNA metabolism and post-transcriptional gene regulation. Many studies have shown the involvement of HuR in plethora of human diseases, which are often manifestations of impaired HuR-RNA interactions. However, the inherent complexities of highly flexible protein-RNA interactions have limited our understanding of the structural basis of HuR-RNA recognition. In this study, we dissect the underlying molecular mechanism of interaction between N-terminal tandem RNA-recognition motifs (tRRMs) of HuR and mRNA using molecular dynamics simulation. We have also explored the effect of point mutations (T90A, R97A and R136A) of three reported critical residues in HuR-mRNA binding specificity. Our findings show that N-terminal tRRMs exhibit conformational stability upon RNA binding. We further show that R136A and R97A mutants significantly lose their binding affinity owing to the loss of critical interactions with mRNA. This may be attributed to the larger domain rearrangements in the mutant complexes, especially the β2β3 loops in both the tRRMs, leading to unfavourable conformations and loss of binding affinity. We have identified critical binding residues in tRRMs of HuR, contributing favourable binding energy in mRNA recognition. This study contributes significantly to understand the molecular mechanism of RNA recognition by tandem RRMs and provides a platform to modulate binding affinities through mutations. This may further guide in future structure-based drug-therapies targeting impaired HuR-RNA interactions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ankita Agarwal
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, India.,Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Suresh Alagar
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shri Kant
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| |
Collapse
|
37
|
Cai H, Zheng D, Yao Y, Yang L, Huang X, Wang L. Roles of Embryonic Lethal Abnormal Vision-Like RNA Binding Proteins in Cancer and Beyond. Front Cell Dev Biol 2022; 10:847761. [PMID: 35465324 PMCID: PMC9019298 DOI: 10.3389/fcell.2022.847761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/04/2022] [Indexed: 12/31/2022] Open
Abstract
Embryonic lethal abnormal vision-like (ELAVL) proteins are RNA binding proteins that were originally discovered as indispensable regulators of the development and functioning of the nervous system. Subsequent studies have shown that ELAVL proteins not only exist in the nervous system, but also have regulatory effects in other tissues. ELAVL proteins have attracted attention as potential therapeutic targets because they stabilize multiple mRNAs by binding within the 3′-untranslated region and thus promote the development of tumors, including hepatocellular carcinoma, pancreatic cancer, ovarian cancer, breast cancer, colorectal carcinoma and lung cancer. Previous studies have focused on these important relationships with downstream mRNAs, but emerging studies suggest that ELAVL proteins also interact with non-coding RNAs. In this review, we will summarize the relationship of the ELAVL protein family with mRNA and non-coding RNA and the roles of ELAVL protein family members in a variety of physiological and pathological processes.
Collapse
Affiliation(s)
| | | | | | - Lehe Yang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Xiaoying Huang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Liangxing Wang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| |
Collapse
|
38
|
Metz JB, Hornstein NJ, Sharma SD, Worley J, Gonzalez C, Sims PA. High-throughput translational profiling with riboPLATE-seq. Sci Rep 2022; 12:5718. [PMID: 35383235 PMCID: PMC8983706 DOI: 10.1038/s41598-022-09638-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages anti-rRNA ribosome immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases.
Collapse
Affiliation(s)
- Jordan B Metz
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas J Hornstein
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sohani Das Sharma
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Christian Gonzalez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| |
Collapse
|
39
|
Eitan C, Siany A, Barkan E, Olender T, van Eijk KR, Moisse M, Farhan SMK, Danino YM, Yanowski E, Marmor-Kollet H, Rivkin N, Yacovzada NS, Hung ST, Cooper-Knock J, Yu CH, Louis C, Masters SL, Kenna KP, van der Spek RAA, Sproviero W, Al Khleifat A, Iacoangeli A, Shatunov A, Jones AR, Elbaz-Alon Y, Cohen Y, Chapnik E, Rothschild D, Weissbrod O, Beck G, Ainbinder E, Ben-Dor S, Werneburg S, Schafer DP, Brown RH, Shaw PJ, Van Damme P, van den Berg LH, Phatnani H, Segal E, Ichida JK, Al-Chalabi A, Veldink JH, Hornstein E. Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3'UTR protect against ALS. Nat Neurosci 2022; 25:433-445. [PMID: 35361972 PMCID: PMC7614916 DOI: 10.1038/s41593-022-01040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 02/16/2022] [Indexed: 12/26/2022]
Abstract
The noncoding genome is substantially larger than the protein-coding genome but has been largely unexplored by genetic association studies. Here, we performed region-based rare variant association analysis of >25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole genomes and the whole genomes of 70,403 non-ALS controls. We identified interleukin-18 receptor accessory protein (IL18RAP) 3' untranslated region (3'UTR) variants as significantly enriched in non-ALS genomes and associated with a fivefold reduced risk of developing ALS, and this was replicated in an independent cohort. These variants in the IL18RAP 3'UTR reduce mRNA stability and the binding of double-stranded RNA (dsRNA)-binding proteins. Finally, the variants of the IL18RAP 3'UTR confer a survival advantage for motor neurons because they dampen neurotoxicity of human induced pluripotent stem cell (iPSC)-derived microglia bearing an ALS-associated expansion in C9orf72, and this depends on NF-κB signaling. This study reveals genetic variants that protect against ALS by reducing neuroinflammation and emphasizes the importance of noncoding genetic association studies.
Collapse
Affiliation(s)
- Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Aviad Siany
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Barkan
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kristel R van Eijk
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Yanowski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Sarah Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Shu-Ting Hung
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Chien-Hsiung Yu
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Cynthia Louis
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Seth L Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Kevin P Kenna
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Rick A A van der Spek
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - William Sproviero
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Ahmad Al Khleifat
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Alfredo Iacoangeli
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Aleksey Shatunov
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Ashley R Jones
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Yael Elbaz-Alon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Elik Chapnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Daphna Rothschild
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Omer Weissbrod
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Beck
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sebastian Werneburg
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, USA
| | - Eran Segal
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Ammar Al-Chalabi
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
- King's College Hospital, Denmark Hill, London, United Kingdom
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
40
|
Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
Collapse
Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
| |
Collapse
|
41
|
Uppala JK, Ghosh C, Sabat G, Dey M. Pull-down of Biotinylated RNA and Associated Proteins. Bio Protoc 2022; 12:e4331. [PMID: 35340298 PMCID: PMC8899547 DOI: 10.21769/bioprotoc.4331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/28/2021] [Accepted: 01/05/2022] [Indexed: 09/23/2023] Open
Abstract
Mapping networks of RNA-protein interactions in cells is essential for understanding the inner workings of many biological processes, including RNA processing, trafficking, and translation. Current in vivo methods for studying protein-RNA interactions rely mostly on purification of poly(A) transcripts, which represent only ~2-3% of total RNAs (Figure 1). Alternate robust methods for tagging RNA molecules with an RNA aptamer (e.g., MS2-, U1A- and biotin-RNA aptamer) and capturing the RNA-protein complex by the respective aptamer-specific partner are not extensively studied. Here, we describe a protocol (Figure 2) in which a biotin-RNA aptamer, referred to as the RNA mimic of biotin (RMB), was conjugated separately to two small RNA secondary structures that contribute to trafficking and translating HAC1 mRNA in the budding yeast Saccharomyces cerevisiae. The RMB-tagged RNA was expressed in yeast cells from a constitutive promoter. The biotinylated RNA bound to proteins was pulled down from the cell lysate by streptavidin agarose beads. RNA was detected by RT-PCR (Figure 3) and associated proteins by mass spectrometry (Figure 4). Our findings show that an RNA aptamer tag to RNA molecule is an effective method to explore the functional roles of RNA-protein networks in vivo.
Collapse
Affiliation(s)
- Jagadeesh K. Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| |
Collapse
|
42
|
Zhang W, Liu L, Zhao S, Chen L, Wei Y, Chen W, Ge F. Research progress on RNA‑binding proteins in breast cancer (Review). Oncol Lett 2022; 23:121. [PMID: 35261635 PMCID: PMC8867207 DOI: 10.3892/ol.2022.13241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
Breast cancer is the most common malignancy among women, and the abnormal regulation of gene expression serves an important role in its occurrence and development. However, the molecular mechanisms underlying gene expression are highly complex and heterogeneous, and RNA-binding proteins (RBPs) are among the key regulatory factors. RBPs bind targets in an environment-dependent or environment-independent manner to influence mRNA stability and the translation of genes involved in the formation, progression, metastasis and treatment of breast cancer. Due to the growing interest in these regulators, the present review summarizes the most influential studies concerning RBPs associated with breast cancer to elucidate the role of RBPs in breast cancer and to assess how they interact with other key pathways to provide new molecular targets for the diagnosis and treatment of breast cancer.
Collapse
Affiliation(s)
- Wenzhu Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Shengdi Zhao
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Liang Chen
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yuxian Wei
- Department of Endocrine Breast Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| |
Collapse
|
43
|
Rossi F, Beltran M, Damizia M, Grelloni C, Colantoni A, Setti A, Di Timoteo G, Dattilo D, Centrón-Broco A, Nicoletti C, Fanciulli M, Lavia P, Bozzoni I. Circular RNA ZNF609/CKAP5 mRNA interaction regulates microtubule dynamics and tumorigenicity. Mol Cell 2022; 82:75-89.e9. [PMID: 34942120 PMCID: PMC8751636 DOI: 10.1016/j.molcel.2021.11.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/07/2021] [Accepted: 11/23/2021] [Indexed: 12/31/2022]
Abstract
Circular RNAs (circRNAs) are widely expressed in eukaryotes and are regulated in many biological processes. Although several studies indicate their activity as microRNA (miRNA) and protein sponges, little is known about their ability to directly control mRNA homeostasis. We show that the widely expressed circZNF609 directly interacts with several mRNAs and increases their stability and/or translation by favoring the recruitment of the RNA-binding protein ELAVL1. Particularly, the interaction with CKAP5 mRNA, which interestingly overlaps the back-splicing junction, enhances CKAP5 translation, regulating microtubule function in cancer cells and sustaining cell-cycle progression. Finally, we show that circZNF609 downregulation increases the sensitivity of several cancer cell lines to different microtubule-targeting chemotherapeutic drugs and that locked nucleic acid (LNA) protectors against the pairing region on circZNF609 phenocopy such effects. These data set an example of how the small effects tuned by circZNF609/CKAP5 mRNA interaction might have a potent output in tumor growth and drug response.
Collapse
Affiliation(s)
- Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Manuel Beltran
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Michela Damizia
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy; Institute of Molecular Biology and Pathology CNR, Rome 00185, Italy
| | - Chiara Grelloni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Alvaro Centrón-Broco
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Carmine Nicoletti
- DAHFMO - Section of Histology and Medical Embryology, Sapienza University of Rome, Rome 00185, Italy
| | - Maurizio Fanciulli
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Patrizia Lavia
- Institute of Molecular Biology and Pathology CNR, Rome 00185, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy; Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy.
| |
Collapse
|
44
|
Chen X, Mayr C. A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly. RNA (NEW YORK, N.Y.) 2022; 28:76-87. [PMID: 34706978 PMCID: PMC8675283 DOI: 10.1261/rna.078995.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.
Collapse
Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
45
|
Raguraman R, Shanmugarama S, Mehta M, Elle Peterson J, Zhao YD, Munshi A, Ramesh R. Drug delivery approaches for HuR-targeted therapy for lung cancer. Adv Drug Deliv Rev 2022; 180:114068. [PMID: 34822926 PMCID: PMC8724414 DOI: 10.1016/j.addr.2021.114068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer (LC) is often diagnosed at an advanced stage and conventional treatments for disease management have limitations associated with them. Novel therapeutic targets are thus avidly sought for the effective management of LC. RNA binding proteins (RBPs) have been convincingly established as key players in tumorigenesis, and their dysregulation is linked to multiple cancers, including LC. In this context, we review the role of Human antigen R (HuR), an RBP that is overexpressed in LC, and further associated with various aspects of LC tumor growth and response to therapy. Herein, we describe the role of HuR in LC progression and outline the evidences supporting various pharmacologic and biologic approaches for inhibiting HuR expression and function. These approaches, including use of small molecule inhibitors, siRNAs and shRNAs, have demonstrated favorable results in reducing tumor cell growth, invasion and migration, angiogenesis and metastasis. Hence, HuR has significant potential as a key therapeutic target in LC. Use of siRNA-based approaches, however, have certain limitations that prevent their maximal exploitation as cancer therapies. To address this, in the conclusion of this review, we provide a list of nanomedicine-based HuR targeting approaches currently being employed for siRNA and shRNA delivery, and provide a rationale for the immense potential therapeutic benefits offered by nanocarrier-based HuR targeting and its promise for treating patients with LC.
Collapse
Affiliation(s)
- Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Santny Shanmugarama
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Meghna Mehta
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jo Elle Peterson
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yan D Zhao
- Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Anupama Munshi
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
46
|
Sidibé H, Khalfallah Y, Xiao S, Gómez NB, Fakim H, Tank EMH, Di Tomasso G, Bareke E, Aulas A, McKeever PM, Melamed Z, Destroimaisons L, Deshaies JE, Zinman L, Parker JA, Legault P, Tétreault M, Barmada SJ, Robertson J, Vande Velde C. TDP-43 stabilizes G3BP1 mRNA: relevance to amyotrophic lateral sclerosis/frontotemporal dementia. Brain 2021; 144:3461-3476. [PMID: 34115105 PMCID: PMC8677511 DOI: 10.1093/brain/awab217] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/26/2021] [Accepted: 05/27/2021] [Indexed: 12/04/2022] Open
Abstract
TDP-43 nuclear depletion and concurrent cytoplasmic accumulation in vulnerable neurons is a hallmark feature of progressive neurodegenerative proteinopathies such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cellular stress signalling and stress granule dynamics are now recognized to play a role in ALS/FTD pathogenesis. Defective stress granule assembly is associated with increased cellular vulnerability and death. Ras-GAP SH3-domain-binding protein 1 (G3BP1) is a critical stress granule assembly factor. Here, we define that TDP-43 stabilizes G3BP1 transcripts via direct binding of a highly conserved cis regulatory element within the 3' untranslated region. Moreover, we show in vitro and in vivo that nuclear TDP-43 depletion is sufficient to reduce G3BP1 protein levels. Finally, we establish that G3BP1 transcripts are reduced in ALS/FTD patient neurons bearing TDP-43 cytoplasmic inclusions/nuclear depletion. Thus, our data indicate that, in ALS/FTD, there is a compromised stress granule response in disease-affected neurons due to impaired G3BP1 mRNA stability caused by TDP-43 nuclear depletion. These data implicate TDP-43 and G3BP1 loss of function as contributors to disease.
Collapse
Affiliation(s)
- Hadjara Sidibé
- Department of Neurosciences, Université de Montréal, Montréal, QC H3A 0E8, Canada
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| | - Yousra Khalfallah
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
- Department of Biochemistry, Université de Montréal, Montréal, QC H3A 0E8, Canada
| | - Shangxi Xiao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Nicolás B Gómez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hana Fakim
- Department of Neurosciences, Université de Montréal, Montréal, QC H3A 0E8, Canada
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Geneviève Di Tomasso
- Department of Biochemistry, Université de Montréal, Montréal, QC H3A 0E8, Canada
| | - Eric Bareke
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| | - Anaïs Aulas
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
- Department of Biochemistry, Université de Montréal, Montréal, QC H3A 0E8, Canada
| | - Paul M McKeever
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Ze’ev Melamed
- University of California, San Diego/Ludwig Institute for Cancer Research, San Diego, CA 92093, USA
| | | | | | - Lorne Zinman
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - J Alex Parker
- Department of Neurosciences, Université de Montréal, Montréal, QC H3A 0E8, Canada
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| | - Pascale Legault
- Department of Biochemistry, Université de Montréal, Montréal, QC H3A 0E8, Canada
| | - Martine Tétreault
- Department of Neurosciences, Université de Montréal, Montréal, QC H3A 0E8, Canada
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, Montréal, QC H3A 0E8, Canada
- CHUM Research Center, Montréal, QC H2X 0A9, Canada
| |
Collapse
|
47
|
Natarajan K, Sundaramoorthy A, Shanmugam N. HnRNPK and lysine specific histone demethylase-1 regulates IP-10 mRNA stability in monocytes. Eur J Pharmacol 2021; 920:174683. [PMID: 34914972 DOI: 10.1016/j.ejphar.2021.174683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022]
Abstract
Altered mRNA metabolism is a feature of many inflammatory diseases. Post transcriptional regulation of interferon-γ-inducible protein (IP)-10 has been uncharacterized in diabetes conditions. RNA-affinity capture method and RNA immuno-precipitation revealed S100b treatment increased the binding of heterogeneous nuclear ribonucleoprotein (hnRNP)K to the IP-10 3'UTR and increased IP-10 mRNA accumulation. Luciferase activity assay using reporter plasmids showed involvement of IP-10 3'UTR. Knocking down of hnRNPK destabilized S100b induced IP-10 mRNA accumulation. S100b promoted the translocation of hnRNPK from nucleus to the cytoplasm and this was confirmed by phosphomimetic S284/353D mutant and non-phosphatable S284/353A hnRNPK mutant. S100b treatment demethylates hnRNPK at Lys219 by Lysine Specific Demethylase (LSD)-1. HnRNPKK219I, a demethylation defective mutant increased IP-10 mRNA stability. Apparently, triple mutant hnRNPKK219I/S284D/353D promoted IP-10 mRNA stability. Interestingly, knocking down LSD-1 abolished S100b induced IP-10 mRNA accumulation. These observations show for the first time that IP-10 mRNA stability is dynamically regulated by Lysine demethylation of hnRNPK by LSD-1. These results indicate that hnRNPK plays an important role in IP-10 mRNA stability induced by S100b which could exacerbate monocyte activation, relevant to the pathogenesis of diabetic complications like atherosclerosis.
Collapse
Affiliation(s)
- Kartiga Natarajan
- Diabetes and Cardiovascular Research Laboratory, Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India
| | - Arun Sundaramoorthy
- Diabetes and Cardiovascular Research Laboratory, Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India.
| | - Narkunaraja Shanmugam
- Diabetes and Cardiovascular Research Laboratory, Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India.
| |
Collapse
|
48
|
Ustaoglu P, Gill JK, Doubovetzky N, Haussmann IU, Dix TC, Arnold R, Devaud JM, Soller M. Dynamically expressed single ELAV/Hu orthologue elavl2 of bees is required for learning and memory. Commun Biol 2021; 4:1234. [PMID: 34711922 PMCID: PMC8553928 DOI: 10.1038/s42003-021-02763-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/09/2021] [Indexed: 12/16/2022] Open
Abstract
Changes in gene expression are a hallmark of learning and memory consolidation. Little is known about how alternative mRNA processing, particularly abundant in neuron-specific genes, contributes to these processes. Prototype RNA binding proteins of the neuronally expressed ELAV/Hu family are candidates for roles in learning and memory, but their capacity to cross-regulate and take over each other's functions complicate substantiation of such links. Honey bees Apis mellifera have only one elav/Hu family gene elavl2, that has functionally diversified by increasing alternative splicing including an evolutionary conserved microexon. RNAi knockdown demonstrates that ELAVL2 is required for learning and memory in bees. ELAVL2 is dynamically expressed with altered alternative splicing and subcellular localization in mushroom bodies, but not in other brain regions. Expression and alternative splicing of elavl2 change during memory consolidation illustrating an alternative mRNA processing program as part of a local gene expression response underlying memory consolidation.
Collapse
Affiliation(s)
- Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jatinder Kaur Gill
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicolas Doubovetzky
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, France
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, Birmingham, B15 3TN, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Roland Arnold
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jean-Marc Devaud
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, France
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
49
|
Seeking a Role for Translational Control by Alternative Polyadenylation in Saccharomyces cerevisiae. Microorganisms 2021; 9:microorganisms9091885. [PMID: 34576779 PMCID: PMC8464734 DOI: 10.3390/microorganisms9091885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Alternative polyadenylation (APA) represents an important mechanism for regulating isoform-specific translation efficiency, stability, and localisation. Though some progress has been made in understanding its consequences in metazoans, the role of APA in the model organism Saccharomyces cerevisiae remains a relative mystery because, despite abundant studies on the translational state of mRNA, none differentiate mRNA isoforms’ alternative 3′-end. This review discusses the implications of alternative polyadenylation in S. cerevisiae using other organisms to draw inferences. Given the foundational role that research in this yeast has played in the discovery of the mechanisms of cleavage and polyadenylation and in the drivers of APA, it is surprising that such an inference is required. However, because advances in ribosome profiling are insensitive to APA, how it impacts translation is still unclear. To bridge the gap between widespread observed APA and the discovery of any functional consequence, we also provide a review of the experimental techniques used to uncover the functional importance of 3′ UTR isoforms on translation.
Collapse
|
50
|
Gokhale NS, Smith JR, Van Gelder RD, Savan R. RNA regulatory mechanisms that control antiviral innate immunity. Immunol Rev 2021; 304:77-96. [PMID: 34405416 DOI: 10.1111/imr.13019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022]
Abstract
From the initial sensing of viral nucleotides by pattern recognition receptors, through the induction of type I and III interferons (IFN), upregulation of antiviral effector proteins, and resolution of the inflammatory response, each step of innate immune signaling is under tight control. Though innate immunity is often associated with broad regulation at the level of gene transcription, RNA-centric post-transcriptional processes have emerged as critical mechanisms for ensuring a proper antiviral response. Here, we explore the diverse RNA regulatory mechanisms that modulate the innate antiviral immune response, with a focus on RNA sensing by RIG-I-like receptors (RLR), interferon (IFN) and IFN signaling pathways, viral pathogenesis, and host genetic variation that contributes to these processes. We address the post-transcriptional interactions with RNA-binding proteins, non-coding RNAs, transcript elements, and modifications that control mRNA stability, as well as alternative splicing events that modulate the innate immune antiviral response.
Collapse
Affiliation(s)
- Nandan S Gokhale
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Julian R Smith
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Rachel D Van Gelder
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| |
Collapse
|