51
|
snoRNAs Offer Novel Insight and Promising Perspectives for Lung Cancer Understanding and Management. Cells 2020; 9:cells9030541. [PMID: 32111002 PMCID: PMC7140444 DOI: 10.3390/cells9030541] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs localized in the nucleolus, where they participate in the cleavage and chemical modification of ribosomal RNAs. Their biogenesis and molecular functions have been extensively studied since their identification in the 1960s. However, their role in cancer has only recently started to emerge. In lung cancer, efforts to profile snoRNA expression have enabled the definition of snoRNA-related signatures, not only in tissues but also in biological fluids, exposing these small RNAs as potential non-invasive biomarkers. Moreover, snoRNAs appear to be essential actors of lung cancer onset and dissemination. They affect diverse cellular functions, from regulation of the cell proliferation/death balance to promotion of cancer cell plasticity. snoRNAs display both oncogenic and tumor suppressive activities that are pivotal in lung cancer tumorigenesis and progression. Altogether, we review how further insight into snoRNAs may improve our understanding of basic lung cancer biology and the development of innovative diagnostic tools and therapies.
Collapse
|
52
|
Che Y, Siprashvili Z, Kovalski JR, Jiang T, Wozniak G, Elcavage L, Khavari PA. KRAS regulation by small non-coding RNAs and SNARE proteins. Nat Commun 2019; 10:5118. [PMID: 31712554 PMCID: PMC6848142 DOI: 10.1038/s41467-019-13106-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/13/2019] [Indexed: 12/30/2022] Open
Abstract
KRAS receives and relays signals at the plasma membrane (PM) where it transmits extracellular growth factor signals to downstream effectors. SNORD50A/B were recently found to bind KRAS and inhibit its tumorigenic action by unknown mechanisms. KRAS proximity protein labeling was therefore undertaken in SNORD50A/B wild-type and knockout cells, revealing that SNORD50A/B RNAs shape the composition of proteins proximal to KRAS, notably by inhibiting KRAS proximity to the SNARE vesicular transport proteins SNAP23, SNAP29, and VAMP3. To remain enriched on the PM, KRAS undergoes cycles of endocytosis, solubilization, and vesicular transport to the PM. Here we report that SNAREs are essential for the final step of this process, with KRAS localization to the PM facilitated by SNAREs but antagonized by SNORD50A/B. Antagonism between SNORD50A/B RNAs and specific SNARE proteins thus controls KRAS localization, signaling, and tumorigenesis, and disrupting SNARE-enabled KRAS function represents a potential therapeutic opportunity in KRAS-driven cancer.
Collapse
Affiliation(s)
- Yonglu Che
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Joanna R Kovalski
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tiffany Jiang
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Glenn Wozniak
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lara Elcavage
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA.
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA.
- VA Palo Alto Healthcare System, Palo Alto, CA, 94304, USA.
| |
Collapse
|
53
|
Liang J, Wen J, Huang Z, Chen XP, Zhang BX, Chu L. Small Nucleolar RNAs: Insight Into Their Function in Cancer. Front Oncol 2019; 9:587. [PMID: 31338327 PMCID: PMC6629867 DOI: 10.3389/fonc.2019.00587] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs divided into two classes: C/D box snoRNAs and H/ACA box snoRNAs. The canonical function of C/D box and H/ACA box snoRNAs are 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. Emerging evidence has demonstrated that snoRNAs are involved in various physiological and pathological cellular processes. Mutations and aberrant expression of snoRNAs have been reported in cell transformation, tumorigenesis, and metastasis, indicating that snoRNAs may serve as biomarkers and/or therapeutic targets of cancer. Hence, further study of the functions and underlying mechanism of snoRNAs is valuable. In this review, we summarize the biogenesis and functions of snoRNAs, as well as the association of snoRNAs in different types of cancers and their potential roles in cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
54
|
Shi J, Deng Y, Huang S, Huang C, Wang J, Xiang AP, Yao C. Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing. RNA Biol 2019; 16:1448-1460. [PMID: 31242075 DOI: 10.1080/15476286.2019.1636596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3' processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5' splicing site (5'-SS) is moderately enriched ~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.
Collapse
Affiliation(s)
- Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Jinkai Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou , China.,Center for Precision Medicine, Sun Yat-sen University , Guangzhou , China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou , China
| |
Collapse
|
55
|
Jang S, Cook NJ, Pye VE, Bedwell GJ, Dudek AM, Singh PK, Cherepanov P, Engelman AN. Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Nucleic Acids Res 2019; 47:4663-4683. [PMID: 30916345 PMCID: PMC6511849 DOI: 10.1093/nar/gkz206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 02/12/2019] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor 5 (CPSF5) and serine/arginine-like protein CPSF6, regulates alternative polyadenylation (APA). Loss of CFIm function results in proximal polyadenylation site usage, shortening mRNA 3' untranslated regions (UTRs). Although CPSF6 plays additional roles in human disease, its nuclear translocation mechanism remains unresolved. Two β-karyopherins, transportin (TNPO) 1 and TNPO3, can bind CPSF6 in vitro, and we demonstrate here that while the TNPO1 binding site is dispensable for CPSF6 nuclear import, the arginine/serine (RS)-like domain (RSLD) that mediates TNPO3 binding is critical. The crystal structure of the RSLD-TNPO3 complex revealed potential CPSF6 interaction residues, which were confirmed to mediate TNPO3 binding and CPSF6 nuclear import. Both binding and nuclear import were independent of RSLD phosphorylation, though a hyperphosphorylated mimetic mutant failed to bind TNPO3 and mislocalized to the cell cytoplasm. Although hypophosphorylated CPSF6 largely supported normal polyadenylation site usage, a significant number of mRNAs harbored unnaturally extended 3' UTRs, similar to what is observed when other APA regulators, such as CFIIm component proteins, are depleted. Our results clarify the mechanism of CPSF6 nuclear import and highlight differential roles for RSLD phosphorylation in nuclear translocation versus regulation of APA.
Collapse
Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda M Dudek
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
56
|
Abstract
While only a small part of the human genome encodes for proteins, biological functions for the so-called junk genome are increasingly being recognized through high-throughput technologies and mechanistic experimental studies. Indeed, novel mechanisms of gene regulation are being discovered that require coordinated interaction between DNA, RNA, and proteins. Therefore, interdisciplinary efforts are still needed to decipher these complex transcriptional networks. In this review, we discuss how non-coding RNAs (ncRNAs) are epigenetically regulated in cancer and metastases and consequently how ncRNAs participate in the sculpting of the epigenetic profile of a cancer cell, thus modulating the expression of other RNA molecules. In the latter case, ncRNAs not only affect the DNA methylation status of certain genomic loci but also interact with histone-modifying complexes, changing the structure of the chromatin itself. We present several examples of epigenetic changes causing aberrant expression of ncRNAs in the context of tumor progression. Interestingly, there are also important epigenetic changes and transcriptional regulatory effects derived from their aberrant expression. As ncRNAs can also be used as biomarkers for diagnosis and prognosis or explored as potential targets, we present insights into the use of ncRNAs for targeted cancer therapy.
Collapse
|
57
|
Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
58
|
Stamm S, Lodmell JS. C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks. Noncoding RNA Res 2019; 4:46-53. [PMID: 31193534 PMCID: PMC6533054 DOI: 10.1016/j.ncrna.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022] Open
Abstract
C/D box snoRNAs (SNORDs) are a highly expressed class of non-coding RNAs. Besides their well-established role in rRNA modification, C/D box snoRNAs form protein complexes devoid of fibrillarin and regulate pre-mRNA splicing and polyadenylation of numerous genes. There is an emerging body of evidence for functional interactions between RNA viruses and C/D box snoRNAs. The infectivity of some RNA viruses depends on enzymatically active fibrillarin, and many RNA viral proteins associate with nucleolin or nucleophosmin, suggesting that viruses benefit from their cytosolic accumulation. These interactions are likely reflected by morphological changes in the nucleolus, often leading to relocalization of nucleolar proteins and ncRNAs to the cytosol that are a characteristic feature of viral infections. Knock-down studies have also shown that RNA viruses need specific C/D box snoRNAs for optimal replication, suggesting that RNA viruses benefit from gene expression programs regulated by SNORDs, or that viruses have evolved “new” uses for these humble ncRNAs to advance their prospects during infection.
Collapse
Affiliation(s)
- Stefan Stamm
- University of Kentucky, Molecular and Cellular Biochemistry, 741 South Limestone, Lexington, KY 40536, USA
| | - J Stephen Lodmell
- Division of Biological Sciences and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, MT, USA
| |
Collapse
|
59
|
Yi Q, Zou WJ. A novel four‑snoRNA signature for predicting the survival of patients with uveal melanoma. Mol Med Rep 2018; 19:1294-1301. [PMID: 30569172 DOI: 10.3892/mmr.2018.9766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/14/2018] [Indexed: 11/06/2022] Open
Abstract
Uveal melanoma (UM), the predominant histological subtype of intraocular malignant tumors in adults, often results in high rates of mortality; effective prognostic signatures used to predict the survival of patients with UM are limited. Small nucleolar RNAs (snoRNAs) are emerging as important regulators in the processes of carcinogenesis and tumor progression, but knowledge of their application as prognostic markers in UM is limited. In the present study, the expression profiles of snoRNAs in UM were determined; a total of 60 snoRNAs were notably associated with the overall survival of patients with UM via univariate Cox survival analysis. Subsequently, a prognostic signature based on four snoRNAs was proposed, which retained their prognostic significance determined by a multivariate Cox survival analysis. The formula is as follows: ACA17 * (‑1.602) + ACA45 * 0.803 + HBII‑276 * 0.603 + SNORD12 * 1.348. Furthermore, the results of in silico analysis indicated that perturbation of the phototransduction, GABAergic synapse and amphetamine addiction pathways may be the potential molecular mechanisms underlying the poor prognosis of patients with UM. Collectively, the present study proposed a potential prognostic signature for patients with UM and the prospective mechanisms at the genome‑wide level were determined.
Collapse
Affiliation(s)
- Qiong Yi
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Wen-Jin Zou
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| |
Collapse
|
60
|
Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
Collapse
Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| |
Collapse
|
61
|
Kitagawa T, Taniuchi K, Tsuboi M, Sakaguchi M, Kohsaki T, Okabayashi T, Saibara T. Circulating pancreatic cancer exosomal RNAs for detection of pancreatic cancer. Mol Oncol 2018; 13:212-227. [PMID: 30358104 PMCID: PMC6360365 DOI: 10.1002/1878-0261.12398] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/09/2018] [Accepted: 10/14/2018] [Indexed: 12/13/2022] Open
Abstract
Diagnostic biomarkers for the early diagnosis of pancreatic cancer are needed to improve prognosis for this disease. The aim of this study was to investigate differences in the expression of four messenger RNAs (mRNAs: CCDC88A,ARF6, Vav3, and WASF2) and five small nucleolar RNAs (snoRNAs: SNORA14B,SNORA18,SNORA25,SNORA74A, and SNORD22) in serum of patients with pancreatic cancer and control participants for use in the diagnosis of pancreatic cancer. Results were compared with the expression of sialylated Lewis (a) blood group antigen CA19‐9, the standard clinical tumor biomarker. Reverse transcription quantitative real‐time PCR showed that all of the mRNAs and snoRNAs, except CCDC88A, were encapsulated in exosomes and secreted from cultured pancreatic cancer cells, and present in cell culture medium. In a discovery‐stage clinical study involving 27 pancreatic cancer patients and 13 controls, the area under the receiver operating characteristic curve (AUC) of two mRNAs (WASF2 and ARF6) and two snoRNAs (SNORA74A and SNORA25) was > 0.9 for distinguishing pancreatic cancer patients from controls; the AUC of CA19‐9 was 0.897. Comparing serum levels of WASF2,ARF6,SNORA74A,SNORA25, and CA19‐9 revealed that levels of WASF2 were the most highly correlated with the risk of pancreatic cancer. The AUCs of WASF2,ARF6,SNORA74A, and SNORA25 in serum from patients in the early stages of pancreatic cancer (stages 0, I, and IIA) were > 0.9, compared with an AUC of 0.93 for the level of CA19‐9. The results of this study suggest that WASF2,ARF6,SNORA74A, and SNORA25 may be useful tools for the early detection of pancreatic cancer. Monitoring serum levels of WASF2 mRNA may be particularly useful, as it was the most highly correlated with pancreatic cancer risk.
Collapse
Affiliation(s)
- Tatsuya Kitagawa
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Keisuke Taniuchi
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Japan.,Department of Endoscopic Diagnostics and Therapeutics, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Makiko Tsuboi
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Masahiko Sakaguchi
- Department of Integrated Center for Advanced Medical Technologies, Kochi Medical School, Kochi University, Nankoku, Japan.,Cancer Prevention and Control Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Takuhiro Kohsaki
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Japan
| | | | - Toshiji Saibara
- Department of Gastroenterology and Hepatology, Kochi Medical School, Kochi University, Nankoku, Japan.,Department of Endoscopic Diagnostics and Therapeutics, Kochi Medical School, Kochi University, Nankoku, Japan
| |
Collapse
|
62
|
Lykke-Andersen S, Ardal BK, Hollensen AK, Damgaard CK, Jensen TH. Box C/D snoRNP Autoregulation by a cis-Acting snoRNA in the NOP56 Pre-mRNA. Mol Cell 2018; 72:99-111.e5. [PMID: 30220559 DOI: 10.1016/j.molcel.2018.08.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/18/2018] [Accepted: 08/09/2018] [Indexed: 01/23/2023]
Abstract
Box C/D snoRNAs constitute a class of abundant noncoding RNAs that associate with common core proteins to form catalytic snoRNPs. Most of these operate in trans to assist the maturation of rRNAs by guiding and catalyzing the 2'-O-methylation of specific nucleotides. Here, we report that the human intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor and master switch controlling levels of the limiting snoRNP core protein NOP56, which is important for proper ribosome biogenesis. Our results support a model in which snoRD86 adopts different RNP conformations that dictate the usage of nearby alternative splice donors in the NOP56 pre-mRNA. Excess snoRNP core proteins prevent further production of NOP56 and instead trigger the generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway. Our findings reveal a feedback mechanism based on RNA structure that controls the precise coordination between box C/D snoRNP core proteins and global snoRNA levels.
Collapse
Affiliation(s)
- Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark.
| | - Britt Kidmose Ardal
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Anne Kruse Hollensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Christian Kroun Damgaard
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark.
| |
Collapse
|
63
|
Shi J, Huang C, Huang S, Yao C. snoRNAs associate with mRNA 3' processing complex: New wine in old bottles. RNA Biol 2017; 15:194-197. [PMID: 29283311 DOI: 10.1080/15476286.2017.1416278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
3' end processing is required for the maturation of all eukaryotic RNAs. Current model suggests that canonical mRNA 3' processing is carried out exclusively within a protein complex termed mRNA 3' processing complex. In a recent study, by using RNA-biotin based pull-down assay and high-throughput sequencing, we reported that a subset of small nucleolar RNAs (snoRNAs) were physically associated with this macromolecular machinery. Through detailed characterization of one of these snoRNAs, SNORD50A, we revealed that non-coding RNA, such as snoRNA, may play a regulatory role in mRNA 3' processing. Our results provided novel insight into both the regulatory mechanism of mRNA 3' processing and the non-canonical functions of snoRNAs.
Collapse
Affiliation(s)
- Junjie Shi
- a Center for Stem Cell Biology and Tissue Engineering , Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University , Guangzhou , China
| | - Chunliu Huang
- a Center for Stem Cell Biology and Tissue Engineering , Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University , Guangzhou , China
| | - Shanshan Huang
- a Center for Stem Cell Biology and Tissue Engineering , Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University , Guangzhou , China
| | - Chengguo Yao
- a Center for Stem Cell Biology and Tissue Engineering , Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University , Guangzhou , China.,b Department of Biology , Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , China
| |
Collapse
|