51
|
Shang R, Kretov DA, Adamson SI, Treiber T, Treiber N, Vedanayagam J, Chuang J, Meister G, Cifuentes D, Lai E. Regulated dicing of pre-mir-144 via reshaping of its terminal loop. Nucleic Acids Res 2022; 50:7637-7654. [PMID: 35801921 PMCID: PMC9303283 DOI: 10.1093/nar/gkac568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs.
Collapse
Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott I Adamson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Thomas Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Eric C Lai
- To whom correspondence should be addressed. Tel: +1 212 639 5578; Fax: +1 212 717 3604;
| |
Collapse
|
52
|
Zhang Y, Lei L, Zhou H, Lu X, Cai F, Li T. Roles of Micro Ribonucleic Acids in Astrocytes After Cerebral Stroke. Front Cell Neurosci 2022; 16:890762. [PMID: 35755778 PMCID: PMC9218061 DOI: 10.3389/fncel.2022.890762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cerebral stroke is one of the highest-ranking causes of death and the leading cause of disability globally, particularly with an increasing incidence and prevalence in developing countries. Steadily more evidence has indicated that micro ribonucleic acids (miRNAs) have important regulatory functions in gene transcription and translation in the course of cerebral stroke. It is beyond arduous to understand the pathophysiology of cerebral stroke, due in part to the perplexity of influencing the network of the inflammatory response, brain edema, autophagy and neuronal apoptosis. The recent research shows miRNA plays a key role in regulating aquaporin 4 (AQP4), and many essential pathological processes after cerebral stroke. This article reviews the recent knowledge on how miRNA influences the inflammatory response, brain edema, infarction size, and neuronal injury after cerebral stroke. In addition, some miRNAs may serve as potential biomarkers in stroke diagnosis and therapy since the expression of some miRNAs in the blood is stable after cerebral stroke.
Collapse
Affiliation(s)
- Yuansheng Zhang
- Department of Neurosurgery, The Affiliated Hospital of Medical College, Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Li Lei
- Department of Neurosurgery, The Affiliated Hospital of Medical College, Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Hu Zhou
- Department of Neurosurgery, The Affiliated Hospital of Medical College, Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Xiaoyang Lu
- Translational Neurosurgery and Neurobiology, University Hospital Aachen, RWTH Aachen, Aachen, Germany
| | - Feifei Cai
- Department of Radiology, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Tao Li
- Department of Neurosurgery, The Affiliated Hospital of Medical College, Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, Kunming, China
| |
Collapse
|
53
|
Conformational effects of a cancer-linked mutation in pri-miR-30c RNA. J Mol Biol 2022; 434:167705. [PMID: 35760371 DOI: 10.1016/j.jmb.2022.167705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that mediate post-transcriptional downregulation of specific target genes. These transcripts are the products of a two-step processing pathway; primary miRNAs (pri-miRNAs) are processed by Drosha into individual precursor miRNA (pre-miRNA) hairpins, which are subsequently processed by Dicer into mature miRNAs. Single nucleotide polymorphisms (SNPs) that occur in pri-miRNAs, pre-miRNAs and mature miRNAs have been shown to affect the processing of specific target genes by modulating Drosha and Dicer processing or interactions with RNA binding proteins (RBPs). Using NMR and single-molecule optical tweezer experiments, we have investigated the conformational effects of a cancer-linked G/A mutation in the terminal loop of pri-miR-30c RNA, and how this influences binding by the SRSF3 and hnRNP A1 RBPs, which are implicated in its processing. Our results reveal that the wildtype and G/A variant pri-miR-30c RNAs adopt very similar elongated stem-loop structures, both of which are bound by SRSF3. However, while both wildtype and G/A pri-miR-30c RNAs can form dimeric kissing hairpin structures, the G to A mutation results in partial destabilization of the dimer in the variant transcript. This promotes recognition and binding by hnRNP A1, an RBP that enhances pri-miR-30c processing. Our data provide structural insight into the conformational effects of a G/A mutation in pri-miR-30c RNA and how this could affect processing and promote cancer.
Collapse
|
54
|
Pandey M, Luhur A, Sokol NS, Chawla G. Molecular Dissection of a Conserved Cluster of miRNAs Identifies Critical Structural Determinants That Mediate Differential Processing. Front Cell Dev Biol 2022; 10:909212. [PMID: 35784477 PMCID: PMC9247461 DOI: 10.3389/fcell.2022.909212] [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: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Differential processing is a hallmark of clustered microRNAs (miRNAs) and the role of position and order of miRNAs in a cluster together with the contribution of stem-base and terminal loops has not been explored extensively within the context of a polycistronic transcript. To elucidate the structural attributes of a polycistronic transcript that contribute towards the differences in efficiencies of processing of the co-transcribed miRNAs, we constructed a series of chimeric variants of Drosophila let-7-Complex that encodes three evolutionary conserved and differentially expressed miRNAs (miR-100, let-7 and miR-125) and examined the expression and biological activity of the encoded miRNAs. The kinetic effects of Drosha and Dicer processing on the chimeric precursors were examined by in vitro processing assays. Our results highlight the importance of stem-base and terminal loop sequences in differential expression of polycistronic miRNAs and provide evidence that processing of a particular miRNA in a polycistronic transcript is in part determined by the kinetics of processing of adjacent miRNAs in the same cluster. Overall, this analysis provides specific guidelines for achieving differential expression of a particular miRNA in a cluster by structurally induced changes in primary miRNA (pri-miRNA) sequences.
Collapse
Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, India
| | - Arthur Luhur
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Nicholas S. Sokol
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, India
- *Correspondence: Geetanjali Chawla,
| |
Collapse
|
55
|
Fu Q, Yu W, Fu S, Xu Z, Zhang S. MicroRNA-449c-5p alleviates lipopolysaccharide-induced HUVECs injury via inhibiting the activation NF-κb signaling pathway by TAK1. Mol Immunol 2022; 146:18-26. [DOI: 10.1016/j.molimm.2022.03.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/23/2021] [Accepted: 03/27/2022] [Indexed: 12/01/2022]
|
56
|
Kremer V, Stanicek L, van Ingen E, Bink DI, Hilderink S, Tijsen AJ, Wittig I, Mägdefessel L, Nossent AY, Boon RA. Long non-coding RNA MEG8 induces endothelial barrier through regulation of microRNA-370 and -494 processing. J Cell Sci 2022; 135:275515. [PMID: 35611612 PMCID: PMC9270956 DOI: 10.1242/jcs.259671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/15/2022] [Indexed: 11/20/2022] Open
Abstract
The 14q32 locus is an imprinted region in the human genome which contains multiple non-coding RNAs. We investigated the role of Maternally Expressed Gene 8 (MEG8) in endothelial function and the underlying mechanism. A 5-fold increase in MEG8 was observed with increased passage number in Human Umbilical Vein Endothelial Cells, suggesting MEG8 is induced during aging. MEG8 knockdown resulted in a 1.8-fold increase in senescence, suggesting MEG8 might be protective during aging. Endothelial barrier was impaired after MEG8 silencing. MEG8 knockdown resulted in reduced expression of miRNA-370 and -494 but not -127, -487b and -410. Overexpression of miRNA-370/-494 partially rescued MEG8-silencing-induced barrier loss. Mechanistically, MEG8 regulates expression of miRNA-370 and -494 at the mature miRNA level through interaction with RNA binding proteins Cold Inducible RNA Binding Protein (CIRBP) and Hydroxyacyl-CoA Dehydrogenase Trifunctional Multi-enzyme Complex Subunit Beta (HADHB). Precursor and mature miRNA-370/-494 were shown to interact with HADHB and CIRBP respectively. CIRBP/HADHB silencing resulted in downregulation of miRNA-370 and induction of miRNA-494. These results suggest MEG8 interacts with CIRBP and HADHB and contributes to miRNA processing at the post-transcriptional level.
Collapse
Affiliation(s)
- Veerle Kremer
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Chemistry, Meibergdreef 9, Amsterdam, the Netherlands
| | - Laura Stanicek
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Eva van Ingen
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands
| | - Diewertje I Bink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Sarah Hilderink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Anke J Tijsen
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Experimental Cardiology, Meibergdreef 9, Amsterdam, the Netherlands
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| | - Lars Mägdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University of Munich, Germany.,Department of Medicine, Molecular Vascular Medicine Unit, Karolinska Institute, Stockholm, Sweden.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Anne Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands.,Departments of Laboratory Medicine and Internal Medicine II, Medical University of Vienna, Austria
| | - Reinier A Boon
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| |
Collapse
|
57
|
Selective inhibition of miRNA processing by a herpesvirus-encoded miRNA. Nature 2022; 605:539-544. [PMID: 35508655 DOI: 10.1038/s41586-022-04667-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and reactivation1,2. A long appreciated, yet undefined relationship exists between the lytic-latent switch and viral non-coding RNAs3,4. Here we identify viral microRNA (miRNA)-mediated inhibition of host miRNA processing as a cellular mechanism that human herpesvirus 6A (HHV-6A) exploits to disrupt mitochondrial architecture, evade intrinsic host defences and drive the switch from latent to lytic virus infection. We demonstrate that virus-encoded miR-aU14 selectively inhibits the processing of multiple miR-30 family members by direct interaction with the respective primary (pri)-miRNA hairpin loops. Subsequent loss of miR-30 and activation of the miR-30-p53-DRP1 axis triggers a profound disruption of mitochondrial architecture. This impairs induction of type I interferons and is necessary for both productive infection and virus reactivation. Ectopic expression of miR-aU14 triggered virus reactivation from latency, identifying viral miR-aU14 as a readily druggable master regulator of the herpesvirus lytic-latent switch. Our results show that miRNA-mediated inhibition of miRNA processing represents a generalized cellular mechanism that can be exploited to selectively target individual members of miRNA families. We anticipate that targeting miR-aU14 will provide new therapeutic options for preventing herpesvirus reactivations in HHV-6-associated disorders.
Collapse
|
58
|
Jiang Y, Xu X, Xiao L, Wang L, Qiang S. The Role of microRNA in the Inflammatory Response of Wound Healing. Front Immunol 2022; 13:852419. [PMID: 35386721 PMCID: PMC8977525 DOI: 10.3389/fimmu.2022.852419] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
Wound healing, a highly complex pathophysiological response to injury, includes four overlapping phases of hemostasis, inflammation, proliferation, and remodeling. Initiation and resolution of the inflammatory response are the primary requirements for wound healing, and are also key events that determines wound quality and healing time. Currently, the number of patients with persistent chronic wounds has generally increased, which imposes health and economic burden on patients and society. Recent studies have found that microRNA(miRNA) plays an essential role in the inflammation involved in wound healing and may provide a new therapeutic direction for wound treatment. Therefore, this review focused on the role and significance of miRNA in the inflammation phase of wound healing.
Collapse
Affiliation(s)
- Yuanyuan Jiang
- Center Laboratory, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Xiang Xu
- Center Laboratory, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Long Xiao
- Center Laboratory, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Lihong Wang
- Center Laboratory, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Sheng Qiang
- Center Laboratory, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| |
Collapse
|
59
|
Sacco A, Martelli F, Pal A, Saraceno C, Benussi L, Ghidoni R, Rongioletti M, Squitti R. Regulatory miRNAs in Cardiovascular and Alzheimer's Disease: A Focus on Copper. Int J Mol Sci 2022; 23:3327. [PMID: 35328747 PMCID: PMC8948703 DOI: 10.3390/ijms23063327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), are key regulators of differentiation and development. In the cell, transcription factors regulate the production of miRNA in response to different external stimuli. Copper (Cu) is a heavy metal and an essential micronutrient with widespread industrial applications. It is involved in a number of vital biological processes encompassing respiration, blood cell line maturation, and immune responses. In recent years, the link between deregulation of miRNAs' functionality and the development of various pathologies as well as cardiovascular diseases (CVDs) has been extensively studied. Alzheimer's disease (AD) is the most common cause of dementia in the elderly with a complex disease etiology, and its link with Cu abnormalities is being increasingly studied. A direct interaction between COMMD1, a regulator of the Cu pathway, and hypoxia-inducible factor (HIF) HIF-1a does exist in ischemic injury, but little information has been collected on the role of Cu in hypoxia associated with AD thus far. The current review deals with this matter in an attempt to structurally discuss the link between miRNA expression and Cu dysregulation in AD and CVDs.
Collapse
Affiliation(s)
- Anna Sacco
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy;
| | - Amit Pal
- Department of Biochemistry, AIIMS, Kalyani 741245, India;
| | - Claudia Saraceno
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (C.S.); (L.B.); (R.G.)
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (C.S.); (L.B.); (R.G.)
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (C.S.); (L.B.); (R.G.)
| | - Mauro Rongioletti
- Department of Laboratory Medicine, Research and Development Division, San Giovanni Calibita Fatebenefratelli Hospital, Isola Tiberina, 00186 Rome, Italy;
| | - Rosanna Squitti
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (C.S.); (L.B.); (R.G.)
| |
Collapse
|
60
|
Paithankar H, Tarang GS, Parvez F, Marathe A, Joshi M, Chugh J. Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. Biophys J 2022; 121:1038-1055. [PMID: 35134335 PMCID: PMC8943759 DOI: 10.1016/j.bpj.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/25/2021] [Accepted: 02/03/2022] [Indexed: 11/02/2022] Open
Abstract
Many double-stranded RNA-binding domains (dsRBDs) interact with topologically distinct dsRNAs in biological pathways pivotal to viral replication, cancer causation, neurodegeneration, and so on. We hypothesized that the adaptability of dsRBDs is essential to target different dsRNA substrates. A model dsRBD and a few dsRNAs, slightly different in shape from each other, were used to test the systematic shape dependence of RNA on the dsRBD-binding using nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. NMR-based titrations showed a distinct binding pattern for the dsRBD with the topologically distinct dsRNAs. The line broadening upon RNA binding was observed to cluster in the residues lying in close proximity, thereby suggesting an RNA-induced conformational exchange in the dsRBD. Further, while the intrinsic microsecond dynamics observed in the apo-dsRBD were found to quench upon binding with the dsRNA, the microsecond dynamics got induced at residues spatially proximal to quench sites upon binding with the dsRNA. This apparent relay of conformational exchange suggests the significance of intrinsic dynamics to help adapt the dsRBD to target various dsRNA-shapes. The conformational pool visualized in MD simulations for the apo-dsRBD reported here has also been observed to sample the conformations seen previously for various dsRBDs in apo- and in dsRNA-bound state structures, further suggesting the conformational adaptability of the dsRBDs. These investigations provide a dynamic basis for the substrate promiscuity for dsRBD proteins.
Collapse
Affiliation(s)
- Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Guneet Singh Tarang
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Firdousi Parvez
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Aniket Marathe
- Bioinformatics Center, Savitrabai Phule Pune University, Pune, Maharashtra, India
| | - Manali Joshi
- Bioinformatics Center, Savitrabai Phule Pune University, Pune, Maharashtra, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India; Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India.
| |
Collapse
|
61
|
Teoh SL, Das S. MicroRNAs in Various Body Fluids and its importance in Forensic Medicine. Mini Rev Med Chem 2022; 22:2332-2343. [PMID: 35240957 DOI: 10.2174/1389557522666220303141558] [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: 10/21/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs which regulate gene expression. miRNAs have tissue-specific expression and are also present in various extracellular body fluids, including blood, tears, semen, vaginal fluid and urine. Additionally, expression of miRNAs in body fluids is linked to various pathological diseases, including cancer and neurodegenerative diseases. Examination of body fluids is important in forensic medicine as they serve as a valuable form of evidence. Due to its stability, miRNA offers an advantage for body fluid identification, which can be detected even after several months or from compromised samples. Identification of unique miRNA profiles for different body fluids enable the identification of these body fluid. Furthermore, miRNAs profiling can be used to estimate post-mortem interval. Various biochemical and molecular methods have been used for identification of miRNAs have shown promising results. We discuss different miRNAs as specific biomarkers and their clinical importance regarding different pathological conditions, as well as their medico-legal importance.
Collapse
Affiliation(s)
- Seong Lin Teoh
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, 56000, Kuala Lumpur, Malaysia
| | - Srijit Das
- Department of Human & Clinical Anatomy, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat 123, Sultanate of Oman
| |
Collapse
|
62
|
Bofill-De Ros X, Hong Z, Birkenfeld B, Alamo-Ortiz S, Yang A, Dai L, Gu S. Flexible pri-miRNA structures enable tunable production of 5’ isomiRs. RNA Biol 2022; 19:279-289. [PMID: 35188062 PMCID: PMC8865264 DOI: 10.1080/15476286.2022.2025680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Drosha cleavage of a pri-miRNA defines mature microRNA sequence. Drosha cleavage at alternative positions generates 5’ isoforms (isomiRs) which have distinctive functions. To understand how pri-miRNA structures influence Drosha cleavage, we performed a systematic analysis of the maturation of endogenous pri-miRNAs and their variants both in vitro and in vivo. We show that in addition to previously known features, the overall structural flexibility of pri-miRNA impact Drosha cleavage fidelity. Internal loops and nearby G · U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5’ isomiR production. By analysing patient data deposited in the Cancer Genome Atlas, we provide evidence that alternative Drosha cleavage of pri-miRNAs is a tunable process that responds to the level of pri-miRNA-associated RNA-binding proteins. Together, our findings reveal that Drosha cleavage fidelity can be modulated by altering pri-miRNA structure, a potential mechanism underlying 5’ isomiR biogenesis in tumours. ![]()
Collapse
Affiliation(s)
- Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zhenyi Hong
- Neural Development Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ben Birkenfeld
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Sarangelica Alamo-Ortiz
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| |
Collapse
|
63
|
Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
Collapse
|
64
|
Yang Y, Su X, Shen K, Zhang C, Dai H, Ma H, Jiang Y, Shuai L, Liu Z, You J, Min K, Chen Z. PUM1 is upregulated by DNA methylation to suppress antitumor immunity and results in poor prognosis in pancreatic cancer. Transl Cancer Res 2022; 10:2153-2168. [PMID: 35116535 PMCID: PMC8798770 DOI: 10.21037/tcr-20-3295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/26/2021] [Indexed: 12/24/2022]
Abstract
Background Pancreatic carcinoma (PAAD) is a highly malignant cancer with a poor prognosis and high mortality rate. Pumilio homologous protein 1 (PUM1) promotes cell growth, invasion, and metastasis and suppresses apoptosis in many different kinds of cancers, such as non-small-cell lung carcinoma (NSCLC), ovarian cancer and lymphocyte leukemia. However, the underlying mechanism and potential role of PUM1 in PAAD have not been investigated. Methods Bioinformatics analysis was performed using multiple databases [The Cancer Genome Atlas (TCGA), Gene Expression Profiling Interactive Analysis (GEPIA), BBCancer, Human Protein Atlas (HPA), MethSurv, cBioPortal, The Cancer Imaging Archive (TCIA), xCell, Gene Expression Omnibus (GEO)] to explore the diagnostic and prognostic role of PUM1, and the relationship between expression of PUM1 and prognosis of patients with PAAD. The analysis was further validated using the Kaplan-Meier plotter. Results PUM1 plays a role in both diagnostic and prognostic prediction. The PUM1 mRNA expression level correlates with both the prognosis and incidence of pancreatic cancer. PUM1 can serve as a potential diagnostic indicator for pancreatic cancer. Furthermore, the DNA methylation levels of PUM1 affects its oncogene function in pancreatic cancer. PUM1 can also inhibit the immune microenvironment by altering immune cell infiltration, which affects immunotherapy response in pancreatic cancer. Conclusions PUM1 takes a crucial part in the immune microenvironment and immunotherapy response of PAAD and is potentially useful for the development of novel diagnostic and treatment strategies.
Collapse
Affiliation(s)
- Yishi Yang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Xingxing Su
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Kaicheng Shen
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Chengcheng Zhang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Haisu Dai
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Hongbo Ma
- Department of Oncology, The Fuling Central Hospital of Chongqing City, Chongqing, China
| | - Yan Jiang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Ling Shuai
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Zhipeng Liu
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Jinshan You
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Ke Min
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Zhiyu Chen
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| |
Collapse
|
65
|
Rosenblum SL, Garner AL. RiPCA: An Assay for the Detection of RNA-Protein Interactions in Live Cells. Curr Protoc 2022; 2:e358. [PMID: 35113480 PMCID: PMC8852372 DOI: 10.1002/cpz1.358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Increasing interest in studying and modulating the interactions between RNAs and their RNA-binding proteins has indicated the need for enabling technologies. Existing means of detecting RNA-protein interactions (RPIs) are often limited to biochemical or post-lysis methods or cell-based methods that require the addition of an RNA-based affinity tag, such as the MS2 hairpin, precluding them from use in detecting small or highly processed RNAs. Taking advantage of bioorthogonal chemistry- and split-luciferase-based technologies, we developed an assay for the detection of RPIs in live cells. This article details the protocol and design considerations for RiPCA, or RNA interaction with Protein-mediated Complementation Assay. © 2022 Wiley Periodicals LLC.
Collapse
Affiliation(s)
| | - Amanda L. Garner
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI,Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI
| |
Collapse
|
66
|
Pérez-García A, Torrecilla-Parra M, Fernández-de Frutos M, Martín-Martín Y, Pardo-Marqués V, Ramírez CM. Posttranscriptional Regulation of Insulin Resistance: Implications for Metabolic Diseases. Biomolecules 2022; 12:biom12020208. [PMID: 35204710 PMCID: PMC8961590 DOI: 10.3390/biom12020208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Insulin resistance defines an impairment in the biologic response to insulin action in target tissues, primarily the liver, muscle, adipose tissue, and brain. Insulin resistance affects physiology in many ways, causing hyperglycemia, hypertension, dyslipidemia, visceral adiposity, hyperinsulinemia, elevated inflammatory markers, and endothelial dysfunction, and its persistence leads to the development metabolic disease, including diabetes, obesity, cardiovascular disease, or nonalcoholic fatty liver disease (NAFLD), as well as neurological disorders such as Alzheimer’s disease. In addition to classical transcriptional factors, posttranscriptional control of gene expression exerted by microRNAs and RNA-binding proteins constitutes a new level of regulation with important implications in metabolic homeostasis. In this review, we describe miRNAs and RBPs that control key genes involved in the insulin signaling pathway and related regulatory networks, and their impact on human metabolic diseases at the molecular level, as well as their potential use for diagnosis and future therapeutics.
Collapse
|
67
|
Liu Y, Ao X, Ji G, Zhang Y, Yu W, Wang J. Mechanisms of Action And Clinical Implications of MicroRNAs in the Drug Resistance of Gastric Cancer. Front Oncol 2021; 11:768918. [PMID: 34912714 PMCID: PMC8667691 DOI: 10.3389/fonc.2021.768918] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors of digestive systems worldwide, with high recurrence and mortality. Chemotherapy is still the standard treatment option for GC and can effectively improve the survival and life quality of GC patients. However, with the emergence of drug resistance, the clinical application of chemotherapeutic agents has been seriously restricted in GC patients. Although the mechanisms of drug resistance have been broadly investigated, they are still largely unknown. MicroRNAs (miRNAs) are a large group of small non-coding RNAs (ncRNAs) widely involved in the occurrence and progression of many cancer types, including GC. An increasing amount of evidence suggests that miRNAs may play crucial roles in the development of drug resistance by regulating some drug resistance-related proteins as well as gene expression. Some also exhibit great potential as novel biomarkers for predicting drug response to chemotherapy and therapeutic targets for GC patients. In this review, we systematically summarize recent advances in miRNAs and focus on their molecular mechanisms in the development of drug resistance in GC progression. We also highlight the potential of drug resistance-related miRNAs as biomarkers and therapeutic targets for GC patients.
Collapse
Affiliation(s)
- Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China.,School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiang Ao
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Guoqiang Ji
- Clinical Laboratory, Linqu People's Hospital, Linqu, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wanpeng Yu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| |
Collapse
|
68
|
Zhao C, Li Y, Qiu C, Chen J, Wu H, Wang Q, Ma X, Song K, Kong B. Splicing Factor DDX23, Transcriptionally Activated by E2F1, Promotes Ovarian Cancer Progression by Regulating FOXM1. Front Oncol 2021; 11:749144. [PMID: 34966670 PMCID: PMC8710544 DOI: 10.3389/fonc.2021.749144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/23/2021] [Indexed: 12/19/2022] Open
Abstract
Ovarian carcinoma remains the most lethal gynecological carcinoma. Abnormal expression of splicing factors is closely related to the occurrence and development of tumors. The DEAD-box RNA helicases are important members of the splicing factor family. However, their role in the occurrence and progression of ovarian cancer is still unclear. In this study, we identified DEAD-box helicase 23 (DDX23) as a key DEAD-box RNA helicase in ovarian cancer using bioinformatics methods. We determined that DDX23 was upregulated in ovarian cancer and its high expression predicted poor prognosis. Functional assays indicated that DDX23 silencing significantly impeded cell proliferation/invasion in vitro and tumor growth in vivo. Mechanistically, transcriptomic analysis showed that DDX23 was involved in mRNA processing in ovarian cancer cells. Specifically, DDX23 regulated the mRNA processing of FOXM1. DDX23 silencing reduced the production of FOXM1C, the major oncogenic transcript of FOXM1 in ovarian cancer, thereby decreasing the FOXM1 protein expression and attenuating the malignant progression of ovarian cancer. Rescue assays indicated that FOXM1 was a key executor in DDX23-induced malignant phenotype of ovarian cancer. Furthermore, we confirmed that DDX23 was transcriptionally activated by the transcription factor (TF) E2F1 in ovarian cancer using luciferase reporter assays and chromatin immunoprecipitation (ChIP) assays. In conclusion, our study demonstrates that high DDX23 expression is involved in malignant behavior of ovarian cancer and DDX23 may become a potential target for precision therapy of ovarian cancer.
Collapse
Affiliation(s)
- Chen Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Chunping Qiu
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Jingying Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Huan Wu
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Qiuman Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xinyue Ma
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| |
Collapse
|
69
|
Lannom MC, Nielsen J, Nawaz A, Shilikbay T, Ceman S. FMRP and MOV10 regulate Dicer1 expression and dendrite development. PLoS One 2021; 16:e0260005. [PMID: 34847178 PMCID: PMC8631628 DOI: 10.1371/journal.pone.0260005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Fragile X syndrome results from the loss of expression of the Fragile X Mental Retardation Protein (FMRP). FMRP and RNA helicase Moloney Leukemia virus 10 (MOV10) are important Argonaute (AGO) cofactors for miRNA-mediated translation regulation. We previously showed that MOV10 functionally associates with FMRP. Here we quantify the effect of reduced MOV10 and FMRP expression on dendritic morphology. Murine neurons with reduced MOV10 and FMRP phenocopied Dicer1 KO neurons which exhibit impaired dendritic maturation Hong J (2013), leading us to hypothesize that MOV10 and FMRP regulate DICER expression. In cells and tissues expressing reduced MOV10 or no FMRP, DICER expression was significantly reduced. Moreover, the Dicer1 mRNA is a Cross-Linking Immunoprecipitation (CLIP) target of FMRP Darnell JC (2011), MOV10 Skariah G (2017) and AGO2 Kenny PJ (2020). MOV10 and FMRP modulate expression of DICER1 mRNA through its 3’untranslated region (UTR) and introduction of a DICER1 transgene restores normal neurite outgrowth in the Mov10 KO neuroblastoma Neuro2A cell line and branching in MOV10 heterozygote neurons. Moreover, we observe a global reduction in AGO2-associated microRNAs isolated from Fmr1 KO brain. We conclude that the MOV10-FMRP-AGO2 complex regulates DICER expression, revealing a novel mechanism for regulation of miRNA production required for normal neuronal morphology.
Collapse
Affiliation(s)
- Monica C. Lannom
- Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Joshua Nielsen
- Integrative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Aatiqa Nawaz
- Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Temirlan Shilikbay
- Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Stephanie Ceman
- Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
| |
Collapse
|
70
|
Chand S, Gowen A, Savine M, Moore D, Clark A, Huynh W, Wu N, Odegaard K, Weyrich L, Bevins RA, Fox HS, Pendyala G, Yelamanchili SV. A comprehensive study to delineate the role of an extracellular vesicle-associated microRNA-29a in chronic methamphetamine use disorder. J Extracell Vesicles 2021; 10:e12177. [PMID: 34913274 PMCID: PMC8674191 DOI: 10.1002/jev2.12177] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/27/2021] [Accepted: 11/25/2021] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs), which express a repertoire of cargo molecules (cf. proteins, microRNA, lipids, etc.), have been garnering a prominent role in the modulation of several cellular processes. Here, using both non-human primate and rodent model systems, we provide evidence that brain-derived EV (BDE) miRNA, miR-29a-3p (mir-29a), is significantly increased during chronic methamphetamine (MA) exposure. Further, miR-29a levels show significant increase both with drug-seeking and reinstatement in a rat MA self-administration model. We also show that EV-associated miR-29a is enriched in EV pool comprising of small EVs and exomeres and further plays a critical role in MA-induced inflammation and synaptodendritic damage. Furthermore, treatment with the anti-inflammatory drug ibudilast (AV411), which is known to reduce MA relapse, decreased the expression of miR-29a and subsequently attenuated inflammation and rescued synaptodendritic injury. Finally, using plasma from MUD subjects, we provide translational evidence that EV-miR29a could potentially serve as a biomarker to detect neuronal damage in humans diagnosed with MA use disorder (MUD). In summary, our work suggests that EV-associated miR-29a-3p plays a crucial role in MUD and might be used as a potential blood-based biomarker for detecting chronic inflammation and synaptic damage.
Collapse
Affiliation(s)
- Subhash Chand
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Austin Gowen
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Mason Savine
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Dalia Moore
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Alexander Clark
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Wendy Huynh
- Department of PsychologyUniversity of Nebraska–Lincoln (UNL)LincolnNebraskaUSA
| | - Niming Wu
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Katherine Odegaard
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | | | - Rick A. Bevins
- Department of PsychologyUniversity of Nebraska–Lincoln (UNL)LincolnNebraskaUSA
| | - Howard S. Fox
- Department of Neurological SciencesUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Gurudutt Pendyala
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| | - Sowmya V. Yelamanchili
- Department of AnesthesiologyUniversity of Nebraska Medical Center (UNMC)OmahaNebraskaUSA
| |
Collapse
|
71
|
Xu W, Anwaier A, Liu W, Tian X, Zhu WK, Wang J, Qu Y, Zhang H, Ye D. Systematic Genome-Wide Profiles Reveal Alternative Splicing Landscape and Implications of Splicing Regulator DExD-Box Helicase 21 in Aggressive Progression of Adrenocortical Carcinoma. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:243-256. [PMID: 36939770 PMCID: PMC9590509 DOI: 10.1007/s43657-021-00026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing (AS) in the tumor biological process has provided a novel perspective on carcinogenesis. However, the clinical significance of individual AS patterns of adrenocortical carcinoma (ACC) has been underestimated, and in-depth investigations are lacking. We selected 76 ACC samples from the Cancer Genome Atlas (TCGA) SpliceSeq and SpliceAid2 databases, and 39 ACC samples from Fudan University Shanghai Cancer Center (FUSCC). Prognosis-related AS events (PASEs) and survival analysis were evaluated based on prediction models constructed by machine-learning algorithm. In total, 23,984 AS events and 3,614 PASEs were detected in the patients with ACC. The predicted risk score of each patient suggested that eight PASEs groups were significantly correlated with the clinical outcomes of these patients (p < 0.001). Prognostic models produced AUC values of 0.907 in all PASEs' groups. Eight splicing factors (SFs), including BAG2, CXorf56, DExD-Box Helicase 21 (DDX21), HSPB1, MBNL3, MSI1, RBMXL2, and SEC31B, were identified in regulatory networks of ACC. DDX21 was identified and validated as a novel clinical promoter and therapeutic target in 115 patients with ACC from TCGA and FUSCC cohorts. In conclusion, the strict standards used in this study ensured the systematic discovery of profiles of AS events using genome-wide cohorts. Our findings contribute to a comprehensive understanding of the landscape and underlying mechanism of AS, providing valuable insights into the potential usages of DDX21 for predicting prognosis for patients with ACC. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-021-00026-x.
Collapse
Affiliation(s)
- Wenhao Xu
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Aihetaimujiang Anwaier
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Wangrui Liu
- grid.412987.10000 0004 0630 1330Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 People’s Republic of China
| | - Xi Tian
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Wen-Kai Zhu
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Jian Wang
- grid.412987.10000 0004 0630 1330Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 People’s Republic of China
| | - Yuanyuan Qu
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Hailiang Zhang
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Dingwei Ye
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong’an Road, Shanghai, 200032 People’s Republic of China
- grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| |
Collapse
|
72
|
Kang W, Fromm B, Houben AJ, Høye E, Bezdan D, Arnan C, Thrane K, Asp M, Johnson R, Biryukova I, Friedländer MR. MapToCleave: High-throughput profiling of microRNA biogenesis in living cells. Cell Rep 2021; 37:110015. [PMID: 34788611 DOI: 10.1016/j.celrep.2021.110015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/17/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors with a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from 20 animal species. We systematically compare the importance of known and novel sequence and structural features and test biogenesis of miRNA precursors from 10 animal and plant species in human cells. Lastly, we provide evidence that the GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryogenic electron microscopy (cryo-EM) studies. In summary, we apply a screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.
Collapse
Affiliation(s)
- Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Anna J Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Eirik Høye
- Department of Tumor Biology, Oslo Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Daniela Bezdan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Kim Thrane
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Michaela Asp
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland; Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
73
|
Nasiri-Aghdam M, Garcia-Garduño TC, Jave-Suárez LF. CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. Int J Mol Sci 2021; 22:11056. [PMID: 34681716 PMCID: PMC8537729 DOI: 10.3390/ijms222011056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional modifications to coding and non-coding RNAs are unquestionably a pivotal way in which human mRNA and protein diversity can influence the different phases of a transcript's life cycle. CELF (CUGBP Elav-like family) proteins are RBPs (RNA-binding proteins) with pleiotropic capabilities in RNA processing. Their responsibilities extend from alternative splicing and transcript editing in the nucleus to mRNA stability, and translation into the cytoplasm. In this way, CELF family members have been connected to global alterations in cancer proliferation and invasion, leading to their identification as potential tumor suppressors or even oncogenes. Notably, genetic variants, alternative splicing, phosphorylation, acetylation, subcellular distribution, competition with other RBPs, and ultimately lncRNAs, miRNAs, and circRNAs all impact CELF regulation. Discoveries have emerged about the control of CELF functions, particularly via noncoding RNAs, and CELF proteins have been identified as competing, antagonizing, and regulating agents of noncoding RNA biogenesis. On the other hand, CELFs are an intriguing example through which to broaden our understanding of the RBP/noncoding RNA regulatory axis. Balancing these complex pathways in cancer is undeniably pivotal and deserves further research. This review outlines some mechanisms of CELF protein regulation and their functional consequences in cancer physiology.
Collapse
Affiliation(s)
- Maryam Nasiri-Aghdam
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Texali C. Garcia-Garduño
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
| |
Collapse
|
74
|
Pradhan UK, Sharma NK, Kumar P, Kumar A, Gupta S, Shankar R. miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles. PLoS One 2021; 16:e0258550. [PMID: 34637468 PMCID: PMC8509996 DOI: 10.1371/journal.pone.0258550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
Formation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in the processing of miRNAs. Deciphering of conditional networks for these RBP-miRNA interactions may help to reason the spatio-temporal nature of miRNAs which can also be used to predict miRNA profiles. In this direction, >25TB of data from different platforms were studied (CLIP-seq/RNA-seq/miRNA-seq) to develop Bayesian causal networks capable of reasoning miRNA biogenesis. The networks ably explained the miRNA formation when tested across a large number of conditions and experimentally validated data. The networks were modeled into an XGBoost machine learning system where expression information of the network components was found capable to quantitatively explain the miRNAs formation levels and their profiles. The models were developed for 1,204 human miRNAs whose accurate expression level could be detected directly from the RNA-seq data alone without any need of doing separate miRNA profiling experiments like miRNA-seq or arrays. A first of its kind, miRbiom performed consistently well with high average accuracy (91%) when tested across a large number of experimentally established data from several conditions. It has been implemented as an interactive open access web-server where besides finding the profiles of miRNAs, their downstream functional analysis can also be done. miRbiom will help to get an accurate prediction of human miRNAs profiles in the absence of profiling experiments and will be an asset for regulatory research areas. The study also shows the importance of having RBP interaction information in better understanding the miRNAs and their functional projectiles where it also lays the foundation of such studies and software in future.
Collapse
Affiliation(s)
- Upendra Kumar Pradhan
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, India
| | - Nitesh Kumar Sharma
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Prakash Kumar
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, India
| | - Ashwani Kumar
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
| | - Sagar Gupta
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India)CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- * E-mail:
| |
Collapse
|
75
|
Ok K, Filipovic MR, Michel SLJ. Targeting Zinc Finger Proteins with Exogenous Metals and Molecules: Lessons learned from Tristetraprolin, a CCCH type Zinc Finger. Eur J Inorg Chem 2021; 2021:3795-3805. [PMID: 34867080 PMCID: PMC8635303 DOI: 10.1002/ejic.202100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Indexed: 11/09/2022]
Abstract
ZF proteins are ubiquitous eukaryotic proteins that play important roles in gene regulation. ZFs contain small domains made up of a combination of four cysteine and histidine residues, and are classified based up on the identity of these residues and their spacing. One emerging class of ZFs are the Cys3His (or CCCH) class of ZFs. These ZFs play key roles in regulating RNA. In this minireview, an overview of the CCCH class of ZFs, with a focus on tristetraprolin (TTP) is provided. TTP regulates inflammation by controlling cytokine mRNAs, and there is an interest in modulating TTP activity to control inflammation. Two methods to control TTP activity are to target with exogenous metals (a 'metals in medicine' approach) or to target with endogenous signaling molecules. Work that has been done to target TTP with Fe, Cu, Cd and Au as well as with H2S is reviewed. This includes attention to new methods that have been developed to monitor metal exchange with the spectroscopically silent ZnII including native electro-spray ionization mass spectrometry (ESI-MS), spin-filter inductively coupled plasma mass spectrometry (ICP-MS) and cryo-electro-spray mass spectrometry (CSI-MS); along with fluorescence anisotropy (FA) to follow RNA binding.
Collapse
Affiliation(s)
- Kiwon Ok
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Milos R Filipovic
- Leibniz-Institut für Analytische, Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| |
Collapse
|
76
|
Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Am J Cancer Res 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
Collapse
|
77
|
Abstract
Herculean efforts by the Wellcome Sanger Institute, the National Cancer Institute, and the National Human Genome Research Institute to sequence thousands of tumors representing all major cancer types have yielded more than 700 genes that contribute to neoplastic growth when mutated, amplified, or deleted. While some of these genes (now included in the COSMIC Cancer Gene Census) encode proteins previously identified in hypothesis-driven experiments (oncogenic transcription factors, protein kinases, etc.), additional classes of cancer drivers have emerged, perhaps none more surprisingly than RNA-binding proteins (RBPs). Over 40 RBPs responsible for virtually all aspects of RNA metabolism, from synthesis to degradation, are recurrently mutated in cancer, and just over a dozen are considered major cancer drivers. This Review investigates whether and how their RNA-binding activities pertain to their oncogenic functions. Focusing on several well-characterized steps in RNA metabolism, we demonstrate that for virtually all cancer-driving RBPs, RNA processing activities are either abolished (the loss-of-function phenotype) or carried out with low fidelity (the LoFi phenotype). Conceptually, this suggests that in normal cells, RBPs act as gatekeepers maintaining proper RNA metabolism and the "balanced" proteome. From the practical standpoint, at least some LoFi phenotypes create therapeutic vulnerabilities, which are beginning to be exploited in the clinic.
Collapse
|
78
|
Jiang R, Su G, Chen X, Chen S, Li Q, Xie B, Zhao Y. Esculetin inhibits endometrial cancer proliferation and promotes apoptosis via hnRNPA1 to downregulate BCLXL and XIAP. Cancer Lett 2021; 521:308-321. [PMID: 34480971 DOI: 10.1016/j.canlet.2021.08.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/10/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
Endometrial cancer represents one of the most common gynecological tumors in the world. Advanced and relapsed patients rely on drug therapy. Therefore, it is extremely important to seek more effective targeted drugs. This study found that esculetin has an anti-tumor effect on endometrial cancer through cellular proliferation and apoptosis. At the same time, its anti-tumor effect has also been verified in human endometrial cancer xenograft models in nude mice. Western blot results showed that BCLXL, XIAP, and pAKT protein expression level were down-regulated. A pulldown experiment and LC-MS/MS analysis technology revealed that esculetin targets the hnRNPA1 protein. Cellular proliferation experiments following si-hnRNPA1 transfection verified the tumor-promoting effect of hnRNPA1 in endometrial cancer cells. Nuclear and cytoplasmic separation experiment demonstrated esculetin affecting the export of the hnRNPA1/mRNA complex from the nucleus into the cytoplasm. Thus, esculetin targets hnRNPA1, thereby downregulates BCLXL and XIAP mRNA transcription and translation, resulting in apoptosis and an arrest in proliferation.
Collapse
Affiliation(s)
- Ruqi Jiang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Guifeng Su
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Qianhui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| |
Collapse
|
79
|
Kim K, Baek SC, Lee YY, Bastiaanssen C, Kim J, Kim H, Kim VN. A quantitative map of human primary microRNA processing sites. Mol Cell 2021; 81:3422-3439.e11. [PMID: 34320405 DOI: 10.1016/j.molcel.2021.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/26/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022]
Abstract
Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as "nick" or "inverse" processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.
Collapse
Affiliation(s)
- Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - S Chan Baek
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Young-Yoon Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Carolien Bastiaanssen
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Haedong Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
80
|
Liu Y, Liu X, Gu Y, Lu H. A novel RNA binding protein-associated prognostic model to predict overall survival in hepatocellular carcinoma patients. Medicine (Baltimore) 2021; 100:e26491. [PMID: 34398005 PMCID: PMC8294901 DOI: 10.1097/md.0000000000026491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is 1 of the deadliest malignancies worldwide. Despite significant advances in diagnosis and treatment, the mortality rate from HCC persists at a substantial level. Construction of a prognostic model that can reliably predict HCC patients' overall survival is urgently needed.Two RNA-seq dataset (the Cancer Genome Atlas and International Cancer Genome Consortium) and 1 microarray dataset (GSE14520) were included in our study. RNA-binding proteins (RBPs) in HCC patients was examined by differentially expressed genes analysis, functional enrichment analysis and protein-protein interaction network analysis. Subsequently, the Cancer Genome Atlas dataset was randomly divided into training and testing cohort with a prognostic model developed in the training cohort. In order to evaluate the prognostic value of the model, a comprehensive survival assessment was conducted.Five RBPs (ribosomal protein L10-like, enhancer of zeste homolog 2 (EZH2), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A), zinc finger protein 239, interferon-induced protein with tetratricopeptide repeats 1) were used to construct the model. The model accurately predicted the prognosis of liver cancer patients in both the training cohort and validation cohort. HCC patients could be assigned into a high-risk group and a low-risk group by this model, and the overall survival of these 2 groups was significantly different (P < .05). Furthermore, the risk scores obtained by this model were highly correlated with immune cell infiltration.The prognostic model helps to identify HCC patients at high risk of mortality, which optimizes decision-making for individualized treatment.
Collapse
Affiliation(s)
- Ye Liu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xiaohong Liu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Yang Gu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Haofeng Lu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| |
Collapse
|
81
|
Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein. Curr Issues Mol Biol 2021; 43:767-781. [PMID: 34449532 PMCID: PMC8929021 DOI: 10.3390/cimb43020056] [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: 04/30/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein-protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.
Collapse
|
82
|
Zhiyanov A, Nersisyan S, Tonevitsky A. Hairpin sequence and structure is associated with features of isomiR biogenesis. RNA Biol 2021; 18:430-438. [PMID: 34286662 DOI: 10.1080/15476286.2021.1952759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5'-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. In this manuscript, we analysed the distribution of miRNA cleavage positions across 31 different cancers using miRNA sequencing data of TCGA project. As a result, we found that the processing positions are not tissue specific and that all miRNAs could be correctly classified as ones exhibiting homogeneous or heterogeneous cleavage at one of the four cleavage sites. In 42% of cases (42 out of 100 miRNAs), we observed imprecise 5'-end Dicer cleavage, while this fraction was only 14% for Drosha (14 out of 99). To the contrary, almost all cleavage sites of 3'-ends (either Drosha or Dicer) were heterogeneous. With the use of only four nucleotides surrounding a 5'-end Dicer cleavage position we built a model which allowed us to distinguish between homogeneous and heterogeneous cleavage with the reliable quality (ROC AUC = 0.68). Finally, we showed the possible applications of the study by the analysis of two 5'-end isoforms originating from the same exogeneous shRNA hairpin. It turned out that the less expressed shRNA variant was functionally active, which led to the increased off-targeting. Thus, the obtained results could be applied to the design of shRNAs whose processing will result in a single 5'-variant.
Collapse
Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | | |
Collapse
|
83
|
Liu X, Chen D, Chen H, Wang W, Liu Y, Wang Y, Duan C, Ning Z, Guo X, Otkur W, Liu J, Qi H, Liu X, Lin A, Xia T, Liu H, Piao H. YB1 regulates miR-205/200b-ZEB1 axis by inhibiting microRNA maturation in hepatocellular carcinoma. Cancer Commun (Lond) 2021; 41:576-595. [PMID: 34110104 PMCID: PMC8286141 DOI: 10.1002/cac2.12164] [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: 01/27/2021] [Revised: 04/15/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Y-box binding protein 1 (YB1 or YBX1) plays a critical role in tumorigenesis and cancer progression. However, whether YB1 affects malignant transformation by modulating non-coding RNAs remains largely unknown. This study aimed to investigate the relationship between YB1 and microRNAs and reveal the underlying mechanism by which YB1 impacts on tumor malignancy via miRNAs-mediated regulatory network. METHODS The biological functions of YB1 in hepatocellular carcinoma (HCC) cells were investigated by cell proliferation, wound healing, and transwell invasion assays. The miRNAs dysregulated by YB1 were screened by microarray analysis in HCC cell lines. The regulation of YB1 on miR-205 and miR-200b was determined by quantitative real-time PCR, dual-luciferase reporter assay, RNA immunoprecipitation, and pull-down assay. The relationships of YB1, DGCR8, Dicer, TUT4, and TUT1 were identified by pull-down and coimmunoprecipitation experiments. The cellular co-localization of YB1, DGCR8, and Dicer were detected by immunofluorescent staining. The in vivo effect of YB1 on tumor metastasis was determined by injecting MHCC97H cells transduced with YB1 shRNA or shControl via the tail vein in nude BALB/c mice. The expression levels of epithelial to mesenchymal transition markers were detected by immunoblotting and immunohistochemistry assays. RESULTS YB1 promoted HCC cell migration and tumor metastasis by regulating miR-205/200b-ZEB1 axis partially in a Snail-independent manner. YB1 suppressed miR-205 and miR-200b maturation by interacting with the microprocessors DGCR8 and Dicer as well as TUT4 and TUT1 via the conserved cold shock domain. Subsequently, the downregulation of miR-205 and miR-200b enhanced ZEB1 expression, thus leading to increased cell migration and invasion. Furthermore, statistical analyses on gene expression data from HCC and normal liver tissues showed that YB1 expression was positively associated with ZEB1 expression and remarkably correlated with clinical prognosis. CONCLUSION This study reveals a previously undescribed mechanism by which YB1 promotes cancer progression by regulating the miR-205/200b-ZEB1 axis in HCC cells. Furthermore, these results highlight that YB1 may play biological functions via miRNAs-mediated gene regulation, and it can serve as a potential therapeutic target in human cancers.
Collapse
Affiliation(s)
- Xiumei Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Di Chen
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Huan Chen
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Wen Wang
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Thoracic SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityShenyangLiaoning110042P. R. China
| | - Yawei Wang
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Thoracic SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityShenyangLiaoning110042P. R. China
| | - Chao Duan
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Thoracic SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityShenyangLiaoning110042P. R. China
| | - Zhen Ning
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of Dalian Medical UniversityDalian Medical UniversityDalianLiaoning116000P. R. China
| | - Xin Guo
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of Dalian Medical UniversityDalian Medical UniversityDalianLiaoning116000P. R. China
| | - Wuxiyar Otkur
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Jing Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Huan Qi
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Xiaolong Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Tian Xia
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
| | - Hong‐xu Liu
- Department of Thoracic SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityShenyangLiaoning110042P. R. China
| | - Hai‐long Piao
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianLiaoning116023P. R. China
- Department of Biochemistry & Molecular BiologySchool of Life SciencesChina Medical UniversityShenyangLiaoning110122P. R. China
| |
Collapse
|
84
|
PGC1s and Beyond: Disentangling the Complex Regulation of Mitochondrial and Cellular Metabolism. Int J Mol Sci 2021; 22:ijms22136913. [PMID: 34199142 PMCID: PMC8268830 DOI: 10.3390/ijms22136913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolism is the central engine of living organisms as it provides energy and building blocks for many essential components of each cell, which are required for specific functions in different tissues. Mitochondria are the main site for energy production in living organisms and they also provide intermediate metabolites required for the synthesis of other biologically relevant molecules. Such cellular processes are finely tuned at different levels, including allosteric regulation, posttranslational modifications, and transcription of genes encoding key proteins in metabolic pathways. Peroxisome proliferator activated receptor γ coactivator 1 (PGC1) proteins are transcriptional coactivators involved in the regulation of many cellular processes, mostly ascribable to metabolic pathways. Here, we will discuss some aspects of the cellular processes regulated by PGC1s, bringing up some examples of their role in mitochondrial and cellular metabolism, and how metabolic regulation in mitochondria by members of the PGC1 family affects the immune system. We will analyze how PGC1 proteins are regulated at the transcriptional and posttranslational level and will also examine other regulators of mitochondrial metabolism and the related cellular functions, considering approaches to identify novel mitochondrial regulators and their role in physiology and disease. Finally, we will analyze possible therapeutical perspectives currently under assessment that are applicable to different disease states.
Collapse
|
85
|
Sauer M, Was N, Ziegenhals T, Wang X, Hafner M, Becker M, Fischer U. The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST. J Cell Sci 2021; 134:jcs257535. [PMID: 34151974 DOI: 10.1242/jcs.257535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/11/2021] [Indexed: 01/13/2023] Open
Abstract
Repressor element 1-silencing transcription factor (REST) plays a crucial role in the differentiation of neural progenitor cells (NPCs). C-terminal domain small phosphatases (CTDSPs) are REST effector proteins that reduce RNA polymerase II activity on genes required for neurogenesis. miR-26b regulates neurogenesis in zebrafish by targeting ctdsp2 mRNA, but the molecular events triggered by this microRNA (miR) remain unknown. Here, we show in a murine embryonic stem cell differentiation paradigm that inactivation of miR-26 family members disrupts the formation of neurons and astroglia and arrests neurogenesis at the neural progenitor level. Furthermore, we show that miR-26 directly targets Rest, thereby inducing the expression of a large set of REST complex-repressed neuronal genes, including miRs required for induction of the neuronal gene expression program. Our data identify the miR-26 family as the trigger of a self-amplifying system required for neural differentiation that acts upstream of REST-controlled miRs.
Collapse
Affiliation(s)
- Mark Sauer
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Nina Was
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Thomas Ziegenhals
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| | - Xiantao Wang
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Markus Hafner
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Matthias Becker
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| |
Collapse
|
86
|
The expanding world of metabolic enzymes moonlighting as RNA binding proteins. Biochem Soc Trans 2021; 49:1099-1108. [PMID: 34110361 DOI: 10.1042/bst20200664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme-RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme-RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme-RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme-RNA interactions in connecting intermediary metabolism and gene expression.
Collapse
|
87
|
Souza VDGPD, Souza GTD, Lemos DRD, Guimarães JMDO, Quintão CCR, Munk M, Saraiva NZ, Camargo LSDA. Heat shock during in vitro maturation of bovine oocytes disturbs bta-miR-19b and DROSHA transcripts abundance after in vitro fertilization. Reprod Domest Anim 2021; 56:1128-1136. [PMID: 34021645 DOI: 10.1111/rda.13956] [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: 11/12/2020] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
While microRNAs (miRNAs) are a class of non-coding RNAs important for embryo development, the relationship between them and heat stress during oocyte maturation has not yet been established. This study investigated the effect of heat shock during in vitro maturation (IVM) on the abundance of bta-miR-20a, -27b, -103, -21-5p, -19b, -1246 miRNAs and DROSHA and DICER1 mRNAs, previously reported for being involved in oocyte maturation, response to heat stress and miRNA biogenesis. Oocytes were exposed for 12h to heat shock during IVM, fertilized in vitro and the presumptive zygotes cultured for eight days. The relative quantification of miRNAs and mRNAs was performed by real-time PCR in vitro-matured oocytes and 8-cell stage embryos. Progression of meiosis, embryonic development and apoptotic indices was also evaluated. Heat shock compromised (p < .05) oocyte nuclear maturation, cleavage and embryo development, with a higher (p < .05) embryonic apoptotic index than the control group. The abundance of bta-miR-19b increased (p < .05) whereas the abundance of DROSHA transcripts decreased (p < .05) in embryos derived from heat-shocked oocytes. In conclusion, heat shock during IVM influences the abundance of bta-miR-19b and DROSHA in pre-implantation embryos, indicating a persistent effect of heat shock that can be associated with impaired embryo development.
Collapse
Affiliation(s)
- Vanessa das Graças Pereira de Souza
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Gustavo Torres de Souza
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Diana Rangel de Lemos
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Federal University of Viçosa, UFV, Viçosa, Minas Gerais, Brazil
| | - Judith Maria de Oliveira Guimarães
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | - Michele Munk
- Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Naiara Zoccal Saraiva
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil
| | - Luiz Sérgio de Almeida Camargo
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil
| |
Collapse
|
88
|
Inoue A. RBM10: Structure, functions, and associated diseases. Gene 2021; 783:145463. [PMID: 33515724 PMCID: PMC10445532 DOI: 10.1016/j.gene.2021.145463] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
RBM10 is a nuclear RNA-binding protein (RBP) that regulates the alternative splicing of primary transcripts. Recently, research on RBM10 has become increasingly active owing to its clinical importance, as indicated by studies on RBM0 mutations that cause TARP syndrome, an X-linked congenital pleiotropic developmental anomaly, and various cancers such as lung adenocarcinoma in adults. Herein, the molecular biology of RBM10 and its significance in medicine are reviewed, focusing on the gene and protein structures of RBM10, its cell biology, molecular functions and regulation, relationship with the paralogous protein RBM5, and the mutations of RBM10 and their associated diseases. Finally, the challenges in future studies of RBM10 are discussed in the concluding remarks.
Collapse
Affiliation(s)
- Akira Inoue
- Department of Otolaryngology, Osaka City University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan.
| |
Collapse
|
89
|
Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 2021; 184:3022-3040.e28. [PMID: 33961781 PMCID: PMC8165030 DOI: 10.1016/j.cell.2021.04.011] [Citation(s) in RCA: 390] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/05/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022]
Abstract
Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins-half the proteome-in 293T cells and includes 118,162 interactions among 14,586 proteins. The second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome whose structure encodes protein function, localization, and complex membership. Comparison across cell lines validates thousands of interactions and reveals extensive customization. Whereas shared interactions reside in core complexes and involve essential proteins, cell-specific interactions link these complexes, "rewiring" subnetworks within each cell's interactome. Interactions covary among proteins of shared function as the proteome remodels to produce each cell's phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.
Collapse
Affiliation(s)
- Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Raphael J Bruckner
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Joe R Cannon
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kurt Baltier
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fana Gebreab
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Melanie P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Thornock
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriela Zarraga
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley Tam
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Panov
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Parzen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Arvene Golbazi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Eila Maenpaa
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Keegan Stricker
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ramin Rad
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua Pan
- Broad Institute, Cambridge, MA 02142, USA
| | - David P Nusinow
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
90
|
Drew K, Wallingford JB, Marcotte EM. hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. Mol Syst Biol 2021; 17:e10016. [PMID: 33973408 PMCID: PMC8111494 DOI: 10.15252/msb.202010016] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/30/2022] Open
Abstract
A general principle of biology is the self‐assembly of proteins into functional complexes. Characterizing their composition is, therefore, required for our understanding of cellular functions. Unfortunately, we lack knowledge of the comprehensive set of identities of protein complexes in human cells. To address this gap, we developed a machine learning framework to identify protein complexes in over 15,000 mass spectrometry experiments which resulted in the identification of nearly 7,000 physical assemblies. We show our resource, hu.MAP 2.0, is more accurate and comprehensive than previous state of the art high‐throughput protein complex resources and gives rise to many new hypotheses, including for 274 completely uncharacterized proteins. Further, we identify 253 promiscuous proteins that participate in multiple complexes pointing to possible moonlighting roles. We have made hu.MAP 2.0 easily searchable in a web interface (http://humap2.proteincomplexes.org/), which will be a valuable resource for researchers across a broad range of interests including systems biology, structural biology, and molecular explanations of disease.
Collapse
Affiliation(s)
- Kevin Drew
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, USA
| |
Collapse
|
91
|
Torres Fernández LA, Mitschka S, Ulas T, Weise S, Dahm K, Becker M, Händler K, Beyer M, Windhausen J, Schultze JL, Kolanus W. The stem cell-specific protein TRIM71 inhibits maturation and activity of the pro-differentiation miRNA let-7 via two independent molecular mechanisms. RNA (NEW YORK, N.Y.) 2021; 27:rna.078696.121. [PMID: 33975917 PMCID: PMC8208056 DOI: 10.1261/rna.078696.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/29/2021] [Indexed: 05/05/2023]
Abstract
The stem cell-specific RNA-binding protein TRIM71/LIN-41 was the first identified target of the pro-differentiation and tumor suppressor miRNA let-7. TRIM71 has essential functions in embryonic development and a proposed oncogenic role in several cancer types, such as hepatocellular carcinoma. Here, we show that TRIM71 regulates let-7 expression and activity via two independent mechanisms. On the one hand, TRIM71 enhances pre-let-7 degradation through its direct interaction with LIN28 and TUT4, thereby inhibiting let-7 maturation and indirectly promoting the stabilization of let-7 targets. On the other hand, TRIM71 represses the activity of mature let-7 via its RNA-dependent interaction with the RNA-Induced Silencing Complex (RISC) effector protein AGO2. We found that TRIM71 directly binds and stabilizes let-7 targets, suggesting that let-7 activity inhibition occurs on active RISCs. MiRNA enrichment analysis of several transcriptomic datasets from mouse embryonic stem cells and human hepatocellular carcinoma cells suggests that these let-7 regulatory mechanisms shape transcriptomic changes during developmental and oncogenic processes. Altogether, our work reveals a novel role for TRIM71 as a miRNA repressor and sheds light on a dual mechanism of let-7 regulation.
Collapse
Affiliation(s)
| | | | - Thomas Ulas
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Stefan Weise
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Kilian Dahm
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Marc Beyer
- Life and Medical Sciences Institute (LIMES)
| | | | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
| | | |
Collapse
|
92
|
Flynt AS. Insecticidal RNA interference, thinking beyond long dsRNA. PEST MANAGEMENT SCIENCE 2021; 77:2179-2187. [PMID: 33078549 PMCID: PMC8048086 DOI: 10.1002/ps.6147] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Over 20 years ago double-stranded RNA (dsRNA) was described as the trigger of RNAi interference (RNAi)-based gene silencing. This paradigm has held since, especially for insect biopesticide technologies where dsRNAs, similar to those described in 1998, are used to inhibit gene expression. In the intervening years, investigation of RNAi pathways has revealed the small RNA effectors of RNAi are diverse and rapidly evolving. The rich biology of insect small RNAs suggests potential to use multiple RNAi modes for manipulating gene expression. By exploiting different RNAi pathways, the menu of options for pest control can be expanded and could lead to better tailored solutions. Fortunately, basic delivery strategies used for dsRNA such as direct application or transgenic expression will translate well between RNAs transiting different RNAi pathways. Importantly, further engineering of RNAi-based biopesticides may provide an opportunity to address dsRNA insensitivity seen in some pests. Characterization of RNAi pathways unique to target species will be indispensable to this end and may require thinking beyond long dsRNA. © 2020 Society of Chemical Industry.
Collapse
Affiliation(s)
- Alex S Flynt
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, USA
| |
Collapse
|
93
|
Gaza A, Fritz V, Malek L, Wormser L, Treiber N, Danner J, Kremer AE, Thasler WE, Siebler J, Meister G, Neurath MF, Hellerbrand C, Bosserhoff AK, Dietrich P. Identification of novel targets of miR-622 in hepatocellular carcinoma reveals common regulation of cooperating genes and outlines the oncogenic role of zinc finger CCHC-type containing 11. Neoplasia 2021; 23:502-514. [PMID: 33901943 PMCID: PMC8099721 DOI: 10.1016/j.neo.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The poor prognosis of advanced hepatocellular carcinoma (HCC) is driven by diverse features including dysregulated microRNAs inducing drug resistance and stemness. Lin-28 homolog A (LIN28A) and its partner zinc finger CCHC-type containing 11 (ZCCHC11) cooperate in binding, oligouridylation and subsequent degradation of tumorsuppressive let-7 precursor microRNAs. Functionally, activation of LIN28A was recently shown to promote stemness and chemoresistance in HCC. However, the expression and regulation of LIN28A in HCC had been unclear. Moreover, the expression, regulation and function of ZCCHC11 in liver cancer remained elusive. In contrast to "one-microRNA-one-target" interactions, we identified common binding sites for miR-622 in both LIN28A and ZCCHC11, suggesting miR-622 to function as a superior pathway regulator. Applying comprehensive microRNA database screening, human hepatocytes and HCC cell lines, patient-derived tissue samples as well as "The Cancer Genome Atlas" (TCGA) patient cohorts, we demonstrated that loss of tumorsuppressive miR-622 mediates derepression and overexpression of LIN28A in HCC. Moreover, the cooperator of LIN28A, ZCCHC11, was newly identified as a prognostic and therapeutic target of miR-622 in liver cancer. Together, identification of novel miR-622 target genes revealed common regulation of cooperating genes and outlines the previously unknown oncogenic role of ZCCHC11 in liver cancer.
Collapse
Affiliation(s)
- Anne Gaza
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Valerie Fritz
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Lara Malek
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Laura Wormser
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Johannes Danner
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Andreas E Kremer
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang E Thasler
- Department of General and Visceral Surgery, Red Cross Hospital of Munich, Germany
| | - Jürgen Siebler
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Markus F Neurath
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Anja K Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany.
| |
Collapse
|
94
|
Freischmidt A, Goswami A, Limm K, Zimyanin VL, Demestre M, Glaß H, Holzmann K, Helferich AM, Brockmann SJ, Tripathi P, Yamoah A, Poser I, Oefner PJ, Böckers TM, Aronica E, Ludolph AC, Andersen PM, Hermann A, Weis J, Reinders J, Danzer KM, Weishaupt JH. A serum microRNA sequence reveals fragile X protein pathology in amyotrophic lateral sclerosis. Brain 2021; 144:1214-1229. [PMID: 33871026 PMCID: PMC8105042 DOI: 10.1093/brain/awab018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/19/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
Knowledge about converging disease mechanisms in the heterogeneous syndrome amyotrophic lateral sclerosis (ALS) is rare, but may lead to therapies effective in most ALS cases. Previously, we identified serum microRNAs downregulated in familial ALS, the majority of sporadic ALS patients, but also in presymptomatic mutation carriers. A 5-nucleotide sequence motif (GDCGG; D = G, A or U) was strongly enriched in these ALS-related microRNAs. We hypothesized that deregulation of protein(s) binding predominantly to this consensus motif was responsible for the ALS-linked microRNA fingerprint. Using microRNA pull-down assays combined with mass spectrometry followed by extensive biochemical validation, all members of the fragile X protein family, FMR1, FXR1 and FXR2, were identified to directly and predominantly interact with GDCGG microRNAs through their structurally disordered RGG/RG domains. Preferential association of this protein family with ALS-related microRNAs was confirmed by in vitro binding studies on a transcriptome-wide scale. Immunohistochemistry of lumbar spinal cord revealed aberrant expression level and aggregation of FXR1 and FXR2 in C9orf72- and FUS-linked familial ALS, but also patients with sporadic ALS. Further analysis of ALS autopsies and induced pluripotent stem cell-derived motor neurons with FUS mutations showed co-aggregation of FXR1 with FUS. Hence, our translational approach was able to take advantage of blood microRNAs to reveal CNS pathology, and suggests an involvement of the fragile X-related proteins in familial and sporadic ALS already at a presymptomatic stage. The findings may uncover disease mechanisms relevant to many patients with ALS. They furthermore underscore the systemic, extra-CNS aspect of ALS.
Collapse
Affiliation(s)
- Axel Freischmidt
- Department of Neurology, Ulm University, Ulm, Germany.,German Center For Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Anand Goswami
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Katharina Limm
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Vitaly L Zimyanin
- Department of Neurology, Technical University Dresden, Dresden, Germany.,Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Maria Demestre
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Hannes Glaß
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | | | | | | | - Priyanka Tripathi
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Alfred Yamoah
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Tobias M Böckers
- German Center For Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany.,Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Albert C Ludolph
- Department of Neurology, Ulm University, Ulm, Germany.,German Center For Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Andreas Hermann
- Department of Neurology, Technical University Dresden, Dresden, Germany.,Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany.,Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, Rostock, Germany.,German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, Rostock, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Jörg Reinders
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | | | - Jochen H Weishaupt
- Department of Neurology, Ulm University, Ulm, Germany.,Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, Mannheim, Germany
| |
Collapse
|
95
|
Robinson H, Ruelcke JE, Lewis A, Bond CS, Fox AH, Bharti V, Wani S, Cloonan N, Lai A, Margolin D, Li L, Salomon C, Richards RS, Farrell A, Gardiner RA, Parton RG, Cristino AS, Hill MM. Caveolin-1-driven membrane remodelling regulates hnRNPK-mediated exosomal microRNA sorting in cancer. Clin Transl Med 2021; 11:e381. [PMID: 33931969 PMCID: PMC8031663 DOI: 10.1002/ctm2.381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Caveolae proteins play diverse roles in cancer development and progression. In prostate cancer, non-caveolar caveolin-1 (CAV1) promotes metastasis, while CAVIN1 attenuates CAV1-induced metastasis. Here, we unveil a novel mechanism linking CAV1 to selective loading of exosomes with metastasis-promoting microRNAs. RESULTS We identify hnRNPK as a CAV1-regulated microRNA binding protein. In the absence of CAVIN1, non-caveolar CAV1 drives localisation of hnRPNK to multi-vesicular bodies (MVBs), recruiting AsUGnA motif-containing miRNAs and causing their release within exosomes. This process is dependent on the lipid environment of membranes as shown by cholesterol depletion using methyl-β-cyclodextrin or by treatment with n-3 polyunsaturated fatty acids. Consistent with a role in bone metastasis, knockdown of hnRNPK in prostate cancer PC3 cells abolished the ability of PC3 extracellular vesicles (EV) to induce osteoclastogenesis, and biofluid EV hnRNPK is elevated in metastatic prostate and colorectal cancer. CONCLUSIONS Taken together, these results support a novel pan-cancer mechanism for CAV1-driven exosomal release of hnRNPK and associated miRNA in metastasis, which is modulated by the membrane lipid environment.
Collapse
Affiliation(s)
- Harley Robinson
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Jayde E. Ruelcke
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Amanda Lewis
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S. Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H. Fox
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- The Harry Perkins Institute of Medical ResearchQEII Medical CentreNedlandsWAAustralia
| | - Vandhana Bharti
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Shivangi Wani
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Nicole Cloonan
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Andrew Lai
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - David Margolin
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Li Li
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Carlos Salomon
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
- Department of Clinical Biochemistry and Immunology, Faculty of PharmacyUniversity of ConcepciónConcepciónChile
| | - Renée S. Richards
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Aine Farrell
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert A. Gardiner
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert G. Parton
- Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Centre for Microscopy and MicroanalysisThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alexandre S. Cristino
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- Griffith Institute for Drug DiscoveryGriffith UniversityBrisbaneQueenslandAustralia
| | - Michelle M. Hill
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| |
Collapse
|
96
|
miR-122/SIRT1 axis regulates chondrocyte extracellular matrix degradation in osteoarthritis. Biosci Rep 2021; 40:224116. [PMID: 32395770 PMCID: PMC7308613 DOI: 10.1042/bsr20191908] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 12/16/2022] Open
Abstract
Background/Aims: MicroRNAs (miRNAs) are involved in the pathogenesis of osteoarthritis (OA). The present study aimed to investigate the potential function of miR-122 in the development of OA and its potential molecular mechanisms. Methods: The expression of miR-122, silent information regulator 1 (SIRT1), collagen II, aggrecan, matrix metalloproteinase (MMP) 13 (MMP13) and ADAMTS4 in OA cartilage was detected by RT-qPCR. Target gene prediction and screening, luciferase reporter assay were used to verify downstream target genes of miR-122. Results: Compared with osteonecrosis, the expression of miR-122 was significantly increased in OA cartilage, while the expression of SIRT1 was significantly decreased. Overexpression of miR-122 increased the expression of extracellular matrix (ECM) catabolic factors, for example disintegrins, MMPs and metalloproteinases with platelet reaction protein motifs, and inhibited the expression of synthetic metabolic genes such as collagen II and aggregating proteoglycan. Inhibition of miR-122 expression had the opposite effect. Furthermore, SIRT1 was identified as a direct target of miR-122. SIRT1 was significantly inhibited by miR-122 overexpression. Knockdown of SIRT1 reversed the degradation of chondrocyte ECM by miR-122 inhibitors. Conclusion: The miR-122/SIRT1 axis can regulate the degradation of ECM in OA, thus providing new insights into the treatment of OA.
Collapse
|
97
|
Moraghebi M, Maleki R, Ahmadi M, Negahi AA, Abbasi H, Mousavi P. In silico Analysis of Polymorphisms in microRNAs Deregulated in Alzheimer Disease. Front Neurosci 2021; 15:631852. [PMID: 33841080 PMCID: PMC8024493 DOI: 10.3389/fnins.2021.631852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a degenerative condition characterized by progressive cognitive impairment and dementia. Findings have revolutionized current knowledge of miRNA in the neurological conditions. Two regulatory mechanisms determine the level of mature miRNA expression; one is miRNA precursor processing, and the other is gene expression regulation by transcription factors. This study is allocated to the in-silico investigation of miRNA's SNPs and their effect on other cell mechanisms. METHODS We used databases which annotate the functional effect of SNPs on mRNA-miRNA and miRNA-RBP interaction. Also, we investigated SNPs which are located on the promoter or UTR region. RESULTS miRNA SNP3.0 database indicated several SNPs in miR-339 and miR-34a in the upstream and downstream of pre-miRNA and mature miRNAs. While, for some miRNAs miR-124, and miR-125, no polymorphism was observed, and also miR-101 with ΔG -3.1 and mir-328 with ΔG 5.8 had the highest and lowest potencies to produce mature microRNA. SNP2TFBS web-server presented several SNPs which altered the Transcription Factor Binding Sites (TFBS) or generated novel TFBS in the promoter regions of related miRNA. At last, RBP-Var database provided a list of SNPs which alter miRNA-RBP interaction pattern and can also influence other miRNAs' expression. DISCUSSION The results indicated that SNPs microRNA affects both miRNA function and miRNA expression. Our study expands molecular insight into how SNPs in different parts of miRNA, including the regulatory (promoter), the precursor (pre-miRNA), functional regions (seed region of mature miRNA), and RBP-binding motifs, which theoretically may be correlated to the Alzheimer's disease.
Collapse
Affiliation(s)
- Mahta Moraghebi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Reza Maleki
- Student Research Committee, Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Ahmadi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ahmad Agha Negahi
- Department of Internal Medicine, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hossein Abbasi
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| |
Collapse
|
98
|
Wu W, Chen Y, Ye S, Yang H, Yang J, Quan J. Transcription factor forkhead box K1 regulates miR-32 expression and enhances cell proliferation in colorectal cancer. Oncol Lett 2021; 21:407. [PMID: 33841568 PMCID: PMC8020380 DOI: 10.3892/ol.2021.12668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Increased microRNA (miR)-32 expression in colorectal cancer (CRC) tissues enhances CRC cell proliferation, migration, invasion and attenuates CRC cell apoptosis by repressing the expression of phosphatase and tensin homolog (PTEN). Forkhead box K1 (FOXK1) was identified as a potential interacting transcription factor using DNA pull-down assays and mass spectrometry. The present study aimed to elucidate the role of FOXK1 in regulating miR-32 expression in CRC. The expressions of FOXK1, miR-32, transmembrane protein 245 gene (TMEM245) and PTEN were compared between CRC and normal colonic tissues. Levels of miR-32, TMEM245, PTEN and the proliferation and apoptosis of CRC cells were studied using FOXK1-overexpression or knockdown, or by simultaneously interfering with FOXK1 and miR-32 expression. Direct FOXK1 binding to the miR-32 promoter was verified using chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays. The results showed elevated FOXK1, miR-32 and TMEM245 expression, and significantly decreased PTEN expression in CRC, compared with normal colonic tissues. Correlations between the expressions of TMEM245 and miR-32, FOXK1 and miR-32, and FOXK1 and TMEM245 were positive and significant. FOXK1-knockdown led to decreased miR-32 and TMEM245 expression and increased PTEN expression, whereas FOXK1-overexpression had the opposite effect. Overexpressed FOXK1 promoted the malignancy of CRC cells in vitro by stimulating proliferation and reducing apoptosis; whereas FOXK1-depletion suppressed such malignancy and a miR-32 inhibitor partially reversed the effects of FOXK1. The results of ChIP and dual-luciferase reporter assays indicated that FOXK1 directly binds to the promoter of TMEM245/miR-32. Thus, the FOXK1-miR-32-PTEN signaling axis may play a crucial role in the pathogenesis and development of CRC.
Collapse
Affiliation(s)
- Weiyun Wu
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Yongze Chen
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Shicai Ye
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Hui Yang
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Jianyun Yang
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Juanhua Quan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| |
Collapse
|
99
|
Yang C, Nan B, Ye H, Yan H, Wang M, Yuan Y. MiR-193b-5p protects BRL-3A cells from acrylamide-induced cell cycle arrest by targeting FoxO3. Food Chem Toxicol 2021; 150:112059. [PMID: 33582169 DOI: 10.1016/j.fct.2021.112059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/16/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
Acrylamide (AA), an important by-product of the Maillard reaction, has been reported to be genotoxic and carcinogenic. The present study employed miRNAs to investigate the toxic mechanism of AA and their role against AA toxicity. Deep sequencing of small RNA libraries was performed and miR-193b-5p was applied for further study. AA significantly reduced the level of miR-193b-5p and its ectopic expression promoted cell cycle G1/S transition and cell proliferation by upregulating the cyclin-dependent kinase regulator Cyclin D1 and downregulating the cyclin-dependent kinase inhibitor p21, while miR-193b-5p inhibitor led to the opposite results. Dual luciferase assay demonstrated miR-193b-5p regulated the expression of FoxO3 by directly targeting the FoxO3 3'-untranslated region (3'-UTR). Knockdown of FoxO3 induced cell cycle G1/S transition and cell proliferation, which was suppressed by the inhibition of miR-193b-5p but promoted by miR-193b-5p mimics. MiR-193b-5p inhibitor strengthened the effect of FoxO3, contrary to the effect of miR-193b-5p mimics. In conclusion, miR-193b-5p acted as a regulator of cell cycle G1/S transition and cell proliferation by targeting FoxO3 to mediate the expression of p21 and Cyclin D1.
Collapse
Affiliation(s)
- Chaoyue Yang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Bo Nan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haiqing Ye
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haiyang Yan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Minghua Wang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yuan Yuan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
| |
Collapse
|
100
|
Wang F, Gao Y, Yuan Y, Du R, Li P, Liu F, Tian Y, Wang Y, Zhang R, Zhao B, Wang C. MicroRNA-31 Can Positively Regulate the Proliferation, Differentiation and Migration of Keratinocytes. Biomed Hub 2021; 5:93-104. [PMID: 33564659 DOI: 10.1159/000508612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
In the past decades, the key roles of most microRNA in dermatosis and skin development have been explored one after another. Among them, microRNA-31 (miR-31) has a prominent role in the regulation of keratinocytes. Numerous studies show that miR-31 can positively regulate the proliferation, differentiation and cell activity of keratinocytes via regulating the NF-κB, RAS/MAPK, Notch signaling pathways, and some cytokines. At present, the interaction between miR-31 and the NF-κB signaling pathway in keratinocytes is a hot research topic. The positive feedback loop formed by miR-31 and NF-κB signaling may bring new ideas for the prevention of psoriasis. The abnormal state of keratinocytes is usually the pathological basis of many skin and immune system diseases. Therefore, strengthening the ability to regulate keratinocytes may be a breakthrough for a variety of diseases. At the same time, miR-31's capacity to accelerate wound healing via positively regulating keratinocytes should be further investigated in the treatment of chronic ulcers and trauma.
Collapse
Affiliation(s)
- Fei Wang
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Yuantao Gao
- Nanchang University Queen Mary School, Nanchang, China
| | - Yitong Yuan
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Ruochen Du
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Pengfei Li
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Fang Liu
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Ye Tian
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Yali Wang
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Ruxin Zhang
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Bichun Zhao
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| | - Chunfang Wang
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, China
| |
Collapse
|