1
|
Almeida PP, Moraes JA, Barja-Fidalgo TC, Renovato-Martins M. Extracellular vesicles as modulators of monocyte and macrophage function in tumors. AN ACAD BRAS CIENC 2024; 96:e20231212. [PMID: 38922279 DOI: 10.1590/0001-3765202420231212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 06/27/2024] Open
Abstract
The tumor microenvironment (TME) harbors several cell types, such as tumor cells, immune cells, and non-immune cells. These cells communicate through several mechanisms, such as cell-cell contact, cytokines, chemokines, and extracellular vesicles (EVs). Tumor-derived vesicles are known to have the ability to modulate the immune response. Monocytes are a subset of circulating innate immune cells and play a crucial role in immune surveillance, being recruited to tissues where they differentiate into macrophages. In the context of tumors, it has been observed that tumor cells can attract monocytes to the TME and induce their differentiation into tumor-associated macrophages with a pro-tumor phenotype. Tumor-derived EVs have emerged as essential structures mediating this process. Through the transfer of specific molecules and signaling factors, tumor-derived EVs can shape the phenotype and function of monocytes, inducing the expression of cytokines and molecules by these cells, thus modulating the TME towards an immunosuppressive environment.
Collapse
Affiliation(s)
- Palloma P Almeida
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - João Alfredo Moraes
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Biologia Redox, Av. Carlos Chagas Filho, 373, Prédio do ICB - Anexo B1F3, Ilha do Fundão, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Thereza Christina Barja-Fidalgo
- Universidade do Estado do Rio de Janeiro, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes - IBRAG, Laboratório de Farmacologia Celular e Molecular, Av. 28 de setembro, 87, 20551-030 Rio de Janeiro, RJ, Brazil
| | - Mariana Renovato-Martins
- Universidade Federal Fluminense, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Laboratório de Inflamação e Metabolismo, Rua Professor Marcos Waldemar de Freitas Reis, s/n, 24020-140 Niterói, RJ, Brazil
| |
Collapse
|
2
|
Szakats S, McAtamney A, Wilson MJ. Identification of novel microRNAs in the embryonic mouse brain using deep sequencing. Mol Cell Biochem 2024; 479:297-311. [PMID: 37059894 PMCID: PMC10890980 DOI: 10.1007/s11010-023-04730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.
Collapse
Affiliation(s)
- Susanna Szakats
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Alice McAtamney
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| |
Collapse
|
3
|
Everaert C, Verwilt J, Verniers K, Vandamme N, Marcos Rubio A, Vandesompele J, Mestdagh P. Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation. Biol Proced Online 2023; 25:7. [PMID: 36890441 PMCID: PMC9996952 DOI: 10.1186/s12575-023-00193-3] [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: 01/05/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND RNA sequencing has become the gold standard for transcriptome analysis but has an inherent limitation of challenging quantification of low-abundant transcripts. In contrast to microarray technology, RNA sequencing reads are proportionally divided in function of transcript abundance. Therefore, low-abundant RNAs compete against highly abundant - and sometimes non-informative - RNA species. RESULTS We developed an easy-to-use strategy based on high-affinity RNA-binding oligonucleotides to block reverse transcription and PCR amplification of specific RNA transcripts, thereby substantially reducing their abundance in the final sequencing library. To demonstrate the broad application potential of our method, we applied it to different transcripts and library preparation strategies, including YRNAs in small RNA sequencing of human blood plasma, mitochondrial rRNAs in both 3' end sequencing and long-read sequencing, and MALAT1 in single-cell 3' end sequencing. We demonstrate that the blocking strategy is highly efficient, reproducible, specific, and generally results in better transcriptome coverage and complexity. CONCLUSION Our method does not require modifications of the library preparation procedure apart from simply adding blocking oligonucleotides to the RT reaction and can thus be easily integrated into virtually any RNA sequencing library preparation protocol.
Collapse
Affiliation(s)
- Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jasper Verwilt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Niels Vandamme
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- VIB Single Cell Core, Vlaams Instituut voor Biotechnologie, Ghent-Leuven, Belgium
| | - Alvaro Marcos Rubio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.
| |
Collapse
|
4
|
The Impact of YRNAs on HNSCC and HPV Infection. Biomedicines 2023; 11:biomedicines11030681. [PMID: 36979661 PMCID: PMC10045647 DOI: 10.3390/biomedicines11030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.
Collapse
|
5
|
Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. Expression profiles of small non-coding RNAs in breast cancer tumors characterize clinicopathological features and show prognostic and predictive potential. Sci Rep 2022; 12:22614. [PMID: 36585466 PMCID: PMC9803687 DOI: 10.1038/s41598-022-26954-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Precision medicine approaches are required for more effective therapies for cancer. As small non-coding RNAs (sncRNAs) have recently been suggested as intriguing candidates for cancer biomarkers and have shown potential also as novel therapeutic targets, we aimed at profiling the non-miRNA sncRNAs in a large sample set to evaluate their role in invasive breast cancer (BC). We used small RNA sequencing and 195 fresh-frozen invasive BC and 22 benign breast tissue samples to identify significant associations of small nucleolar RNAs, small nuclear RNAs, and miscellaneous RNAs with the clinicopathological features and patient outcome of BC. Ninety-six and five sncRNAs significantly distinguished (Padj < 0.01) invasive local BC from benign breast tissue and metastasized BC from invasive local BC, respectively. Furthermore, 69 sncRNAs significantly associated (Padj < 0.01) with the tumor grade, hormone receptor status, subtype, and/or tumor histology. Additionally, 42 sncRNAs were observed as candidates for prognostic markers and 29 for predictive markers for radiotherapy and/or tamoxifen response (P < 0.05). We discovered the clinical relevance of sncRNAs from each studied RNA type. By introducing new sncRNA biomarker candidates for invasive BC and validating the potential of previously described ones, we have guided the way for further research that is warranted for providing novel insights into BC biology.
Collapse
Affiliation(s)
- Emmi Kärkkäinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
| | - Sami Heikkinen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland ,grid.9668.10000 0001 0726 2490School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Tengström
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Oncology, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XCancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- grid.9668.10000 0001 0726 2490School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Yliopistonranta 1 C, 70210 Kuopio, Finland
| |
Collapse
|
6
|
Eliason S, Hong L, Sweat Y, Chalkley C, Cao H, Liu Q, Qi H, Xu H, Zhan F, Amendt BA. Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism. Clin Transl Med 2022; 12:e1037. [PMID: 36116139 PMCID: PMC9482803 DOI: 10.1002/ctm2.1037] [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: 04/28/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) has a high mortality rate, and therapeutic approaches to treat these cancers are varied and depend on the metabolic state of the tumour. Profiles of CRC tumours have identified several biomarkers, including microRNAs. microRNA-210 (miR-210) levels are directly correlated with CRC survival. miR-210 expression is higher in metastatic colon cancer cells versus non-metastatic and normal colon epithelium. Therefore, efficient methods to inhibit miR-210 expression in CRC may provide new advances in treatments. METHODS Expression of miRs was determined in several metastatic and non-metastatic cell lines. miR-210 expression was inhibited using PMIS-miR-210 in transduced cells, which were transplanted into xenograft mice. In separate experiments, CRC tumours were allowed to grow in xenograft mice and treated with therapeutic injections of PMIS-miR-210. Molecular and biochemical experiments identified several new pathways targeted by miR-210 inhibition. RESULTS miR-210 inhibition can significantly reduce tumour growth of implanted colon cancer cells in xenograft mouse models. The direct administration of PMIS-miR-210 to existing tumours can inhibit tumour growth in both NSG and Foxn1nu/j mouse models and is more efficacious than capecitabine treatments. Tumour cells further transfer the PMIS-miR-210 inhibitor to neighbouring cells by extracellular vesicles to inhibit miR-210 throughout the tumour. miR-210 inhibition activates the cleaved caspase 3 apoptotic pathway to reduce tumour formation. We demonstrate that the long non-coding transcript XIST is regulated by miR-210 correlating with decreased XIST expression in CRC tumours. XIST acts as a competing endogenous RNA for miR-210, which reduces XIST levels and miR-210 inhibition increases XIST transcripts in the nucleus and cytoplasm. The increased expression of NME1 is associated with H3K4me3 and H3K27ac modifications in the NME1 proximal promoter by XIST. CONCLUSION Direct application of the PMIS-miR-210 inhibitor to growing tumours may be an effective colorectal cancer therapeutic.
Collapse
Affiliation(s)
- Steven Eliason
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
- Craniofacial Anomalies Research CenterThe University of IowaIowa CityIowaUSA
| | - Liu Hong
- Craniofacial Anomalies Research CenterThe University of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchThe University of IowaIowa CityIowaUSA
| | - Yan Sweat
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
- Craniofacial Anomalies Research CenterThe University of IowaIowa CityIowaUSA
| | - Camille Chalkley
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
- Craniofacial Anomalies Research CenterThe University of IowaIowa CityIowaUSA
| | - Huojun Cao
- Iowa Institute for Oral Health ResearchThe University of IowaIowa CityIowaUSA
| | - Qi Liu
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
| | - Hank Qi
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
| | - Hongwei Xu
- Department of Internal MedicineUniversity of Arkansas for Medical ScienceLittle RockArkansasUSA
| | - Fenghuang Zhan
- Department of Internal MedicineUniversity of Arkansas for Medical ScienceLittle RockArkansasUSA
| | - Brad A. Amendt
- Department of Anatomy and Cell BiologyThe University of IowaIowa CityIowaUSA
- Craniofacial Anomalies Research CenterThe University of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchThe University of IowaIowa CityIowaUSA
| |
Collapse
|
7
|
Li C, Wang W, Sun Y, Ni Y, Qin F, Li X, Wang T, Guo M, Sun G. Selective sorting and secretion of hY4 RNA fragments into extracellular vesicles mediated by methylated YBX1 to promote lung cancer progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:136. [PMID: 35410432 PMCID: PMC8996536 DOI: 10.1186/s13046-022-02346-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 03/25/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Extracellular vesicles (EVs) are emerging mediators of intercellular communication that have been shown to play important roles in tumor progression. YRNA fragments, a type of small non-coding RNA, are dysregulated in non-small cell lung cancer (NSCLC) cell-derived EVs, suggesting that they may be an effective biomarker for cancer diagnosis and treatment strategies. METHODS Differentially expressed YRNA hY4 fragments (hY4F) in EVs from NSCLC cells and normal lung fibroblasts were isolated by differential ultra-centrifugation. RNA-binding proteins that interacted with hY4F were identified by screening with an RNA pulldown assay and mass spectrometry. The molecular mechanism of hY4F and the RNA-binding protein Y box binding protein 1 (YBX1) was demonstrated by qRT-PCR, western blot, RNA pulldown, and rescue experiments. Transcriptome sequencing, qRT-PCR validation, bioinformatics analysis and NF-κB pathway inhibitor assays elucidate the mechanism of YBX1 and hY4F inhibiting lung cancer. A peptide pulldown assay was performed to screen and identify a potential methyltransferase for YBX1. The roles of hY4F, YBX1, and SET domain containing 3 in biological functions, such as proliferation, migration, invasion, and apoptosis, in lung cancer cells were also examined by EdU incorporation assay, Transwell assay, flow cytometry, and other methods. Lastly, a mouse xenograft assay was used to assess the clinical relevance of YBX1 and hY4F in vivo. RESULTS Our data demonstrate that hY4 RNA fragments were upregulated in lung cancer- derived EVs, hY4F inhibits tumor progression through downregulating MAPK/NF-κB signaling, and then the selective sorting and secretion of hY4F into lung cancer EVs is regulated by the RNA-binding protein YBX1. Furthermore, we identified lysine K264 within the YBX1 C-terminal domain as the necessary site for its interaction with hY4Fs. K264 is modified by methylation, which affects its binding to hY4F and subsequent selective sorting into EVs in lung cancer cells. CONCLUSION Our findings demonstrate that hY4F acts as a tumor suppressor and is selectively sorted into lung cancer cell-derived EVs by interacting with methylated YBX1, which in turn promotes lung cancer progression. hY4F is a promising circulating biomarker for non-small cell lung cancer diagnosis and prognosis and an exceptional candidate for further therapeutic exploration.
Collapse
Affiliation(s)
- Chuang Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Wei Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Yuting Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Yifan Ni
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Fang Qin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Xiaolu Li
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Tao Wang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Mingxiong Guo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China.
| | - Guihong Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, P. R. China. .,Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, Hubei, P. R. China.
| |
Collapse
|
8
|
Billmeier M, Green D, Hall AE, Turnbull C, Singh A, Xu P, Moxon S, Dalmay T. Mechanistic insights into non-coding Y RNA processing. RNA Biol 2022; 19:468-480. [PMID: 35354369 PMCID: PMC8973356 DOI: 10.1080/15476286.2022.2057725] [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] [Indexed: 11/23/2022] Open
Abstract
Y RNAs (84–112 nt) are non-coding RNAs transcribed by RNA polymerase III and are characterized by a distinctive secondary structure. Human Y RNAs interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y RNAs also perform regulatory roles in DNA and RNA replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y RNAs are cleaved into 3’ and 5’ end fragments termed Y RNA-derived small RNAs (ysRNAs). Although some ysRNA functions in stress, apoptosis and cancer have been reported, their fundamental biogenesis has not been described. Here we report that 3’ end RNY5 cleavage is structure dependent. In high throughput mutagenesis experiments, cleavage occurred between the 2nd and 3rd nt above a double stranded stem comprising high GC content. We demonstrate that an internal loop above stem S3 is critical for producing 3’ end ysRNAs (31 nt) with mutants resulting in longer or no ysRNAs. We show a UGGGU sequence motif at position 22 of RNY5 is critical for producing 5’ end ysRNAs (22–25 nt). We show that intact RO60 is critical for ysRNA biogenesis. We conclude that ribonuclease L (RNASEL) contributes to Y RNA cleavage in mouse embryonic fibroblasts but is not the only endoribonuclease important in human cells.
Collapse
Affiliation(s)
- Martina Billmeier
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Adam E Hall
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,Horizon Discovery, Cambridge Research Park, Waterbeach, UK
| | - Carly Turnbull
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,Shanghai Engineering Research Center of Plant Germplasm Resource, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
9
|
Rojas AP, Vo DV, Mwangi L, Rehman S, Peiris AN. Oncologic manifestations of Klinefelter syndrome. Hormones (Athens) 2020; 19:497-504. [PMID: 33000452 DOI: 10.1007/s42000-020-00241-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 09/01/2020] [Indexed: 10/23/2022]
Abstract
Klinefelter syndrome (47,XXY) has a prevalence of approximately 1 in 500 males. It is a condition characterized by an extra X chromosome and is an underdiagnosed clinical entity. Inactivation of genes enables their escape from regulatory mechanisms, which can result in such classic physical manifestations as hypogonadism, gynecomastia, infertility, and various hormonal and physical abnormalities. While the endocrine manifestations of 47,XXY are well-known, the oncologic manifestations have received less attention. An association between cancer and 47,XXY has not as yet been clearly defined, with variability noted in the prevalence of different malignancies in 47,XXY patients. The mechanisms underlying these altered oncologic risks are still under debate. Some of the proposed explanations include hormone imbalance, developmental malfunctions, and failed DNA repair mechanisms. However, the recognition of the oncological associations linked to 47,XXY could be helpful. Screening measures in certain malignancies may enable an earlier diagnosis of 47,XXY and the implementation of more customized care in 47,XXY and the mosaic variants.. The data for this review was compiled from relevant PubMed articles published within the last three decades and organized based on cancer type.
Collapse
Affiliation(s)
- Alexsandra P Rojas
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
- , Lubbock, TX, USA.
| | - Diana V Vo
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Lance Mwangi
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Shabnam Rehman
- Oncology Division of Internal medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Alan N Peiris
- Clinical Research Institute and Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| |
Collapse
|
10
|
miR-1975 serves as an indicator of clinical severity upon influenza infection. Eur J Clin Microbiol Infect Dis 2020; 40:141-149. [PMID: 32814996 PMCID: PMC7437959 DOI: 10.1007/s10096-020-04008-1] [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: 03/12/2020] [Accepted: 08/11/2020] [Indexed: 10/29/2022]
Abstract
Emerging evidence highlights the role of non-coding small RNAs in host-influenza interaction. We have identified a Y RNA-derived small RNA, miR-1975, which is upregulated upon influenza A virus infection in A549 cells. The aim of this study is to investigate whether miR-1975 serves as an indicator of clinical severity upon influenza infection. We investigate the abundance of miR-1975 in sera from clinical patients and its correlation with hypoxemia status. We quantified its amounts in sera from influenza virus-infected patients and healthy volunteers by means of stem-loop RT-PCR. Median values of miR-1975 were significantly higher in influenza virus-infected patients, especially in hypoxemic patients. miR-1975 levels at the acute stage of the disease were highly correlated with the fraction of inspired oxygen used by the patients and total ventilator days. Receiver operator characteristic curve analysis revealed that miR-1975 levels in combination with days of fever before presenting to hospital had significant predictive value for hypoxemia and respiratory failure for patients infected with influenza virus. Our results reveal that circulating miR-1975 has great potential to serve as a biomarker for predicting prognosis in patients infected with influenza virus.
Collapse
|
11
|
Guglas K, Kołodziejczak I, Kolenda T, Kopczyńska M, Teresiak A, Sobocińska J, Bliźniak R, Lamperska K. YRNAs and YRNA-Derived Fragments as New Players in Cancer Research and Their Potential Role in Diagnostics. Int J Mol Sci 2020; 21:ijms21165682. [PMID: 32784396 PMCID: PMC7460810 DOI: 10.3390/ijms21165682] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-loop structure and each part of that structure carries a different function. YRNAs are transcribed in the nucleus by RNA polymerase III. Then, the YRNA molecule is bound to the polyuridine tail of the La protein responsible for both its nuclear retention and protection from degradation. They also bind to the Ro60 protein, making the molecule more stable. In turn, YRNA-derived small RNAs (YsRNAs) are a class of YRNAs produced in apoptotic cells as a result of YRNA degradation. This process is performed by caspase-3-dependent pathways that form two groups of YsRNAs, with lengths of either approximately 24 or 31 nucleotides. From all four YRNA transcripts, 75 well-described pseudogenes are generated as a result of the mutation. However, available data indicates the formation of up to 1000 pseudogenes. YRNAs and YRNA-derived small RNAs may play a role in carcinogenesis due to their altered expression in cancers and influence on cell proliferation and inflammation. Nevertheless, our knowledge is still limited, and more research is required. The main aim of this review is to describe the current state of knowledge about YRNAs, their function and contribution to carcinogenesis, as well as their potential role in cancer diagnostics. To confirm the promising potential of YRNAs and YRNA-derived fragments as biomarkers, their significant role in several tumor types was taken into consideration.
Collapse
Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Iga Kołodziejczak
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
- International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| |
Collapse
|
12
|
Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
Collapse
Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
| |
Collapse
|
13
|
Y RNA: An Overview of Their Role as Potential Biomarkers and Molecular Targets in Human Cancers. Cancers (Basel) 2020; 12:cancers12051238. [PMID: 32423154 PMCID: PMC7281143 DOI: 10.3390/cancers12051238] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Y RNA are a class of small non-coding RNA that are largely conserved. Although their discovery was almost 40 years ago, their function is still under investigation. This is evident in cancer biology, where their role was first studied just a dozen years ago. Since then, only a few contributions were published, mostly scattered across different tumor types and, in some cases, also suffering from methodological limitations. Nonetheless, these sparse data may be used to make some estimations and suggest routes to better understand the role of Y RNA in cancer formation and characterization. Here we summarize the current knowledge about Y RNA in multiple types of cancer, also including a paragraph about tumors that might be included in this list in the future, if more evidence becomes available. The picture arising indicates that Y RNA might be useful in tumor characterization, also relying on non-invasive methods, such as the analysis of the content of extracellular vesicles (EV) that are retrieved from blood plasma and other bodily fluids. Due to the established role of Y RNA in DNA replication, it is possible to hypothesize their therapeutic targeting to inhibit cell proliferation in oncological patients.
Collapse
|
14
|
Branco GP, Valieris R, Povoa LV, Araújo LFD, Fernandes GR, Souza JESD, Amorim MGD, Ferreira ENE, Silva ITD, Nunes DN, Dias-Neto E. A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines. Genet Mol Biol 2020; 43:e20180351. [PMID: 32352476 PMCID: PMC7201575 DOI: 10.1590/1678-4685-gmb-2018-0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/06/2019] [Indexed: 11/22/2022] Open
Abstract
Next-generation sequencing (NGS) platforms allow the analysis of hundreds of
millions of molecules in a single sequencing run, revolutionizing many research
areas. NGS-based microRNA studies enable expression quantification in
unprecedented scale without the limitations of closed-platforms. Yet, whereas a
massive amount of data produced by these platforms is available, comparisons of
quantification/discovery capabilities between platforms are still lacking. Here
we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA
identification/quantification capabilities using two breast-derived cell-lines.
A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of
the miRNAs, and the few discrepancies in miRNA counts were attributable to
molecules that have very low expression. Quantification divergences indicative
of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads)
and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed
an increased and statistically significant count of uracyls and uracyl-stretches
for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel,
adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We
conclude that, whereas both platforms are overall consistent and can be used
interchangeably for microRNA expression studies, particular sequence features
appear to be indicative of specific platform bias, and their presence in
microRNAs should be considered for database-analyses.
Collapse
Affiliation(s)
| | - Renan Valieris
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Lucas Venezian Povoa
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil.,Instituto Tecnológico de Aeronáutica, Divisão de Ciências Computacionais, Grupo de Inteligência Artificial e Robótica, São José dos Campos, SP, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Caraguatatuba, SP, Brazil
| | | | | | | | - Maria Galli de Amorim
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Elisa Napolitano E Ferreira
- A.C.Camargo Cancer Center, Laboratório de Genômica e Biologia, CIPE, São Paulo, SP, Brazil.,Grupo Fleury Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Israel Tojal da Silva
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Diana Noronha Nunes
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento & Instituto de Psiquiatria, Laboratório de Neurociências Alzira Denise Hertzog Silva (LIM-27), São Paulo, SP, Brazil
| |
Collapse
|
15
|
Valkov N, Das S. Y RNAs: Biogenesis, Function and Implications for the Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:327-342. [PMID: 32285422 DOI: 10.1007/978-981-15-1671-9_20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, progress in the field of high-throughput sequencing technology and its application to a wide variety of biological specimens has greatly advanced the discovery and cataloging of a diverse set of non-coding RNAs (ncRNAs) that have been found to have unexpected biological functions. Y RNAs are an emerging class of highly conserved, small ncRNAs. There is a growing number of reports in the literature demonstrating that Y RNAs and their fragments are not just random degradation products but are themselves bioactive molecules. This review will outline what is currently known about Y RNA including biogenesis, structure and functional roles. In addition, we will provide an overview of studies reporting the presence and functions attributed to Y RNAs in the cardiovascular system.
Collapse
Affiliation(s)
- Nedyalka Valkov
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saumya Das
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
16
|
Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 2020; 17:1196-1213. [PMID: 32186461 DOI: 10.1080/15476286.2020.1737442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
Collapse
Affiliation(s)
- Domenico Rosace
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Judith López
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Sandra Blanco
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| |
Collapse
|
17
|
Gaffo E, Bortolomeazzi M, Bisognin A, Di Battista P, Lovisa F, Mussolin L, Bortoluzzi S. MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. Int J Mol Sci 2020; 21:ijms21051754. [PMID: 32143373 PMCID: PMC7084216 DOI: 10.3390/ijms21051754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.
Collapse
Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
- Correspondence: (E.G.); (S.B.); Tel.: +39-049-827-6502 (S.B.)
| | - Michele Bortolomeazzi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
| | - Andrea Bisognin
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
| | - Piero Di Battista
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Federica Lovisa
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Lara Mussolin
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
- Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35131 Padova, Italy
- Correspondence: (E.G.); (S.B.); Tel.: +39-049-827-6502 (S.B.)
| |
Collapse
|
18
|
Guzzi N, Bellodi C. Novel insights into the emerging roles of tRNA-derived fragments in mammalian development. RNA Biol 2020; 17:1214-1222. [PMID: 32116113 PMCID: PMC7549657 DOI: 10.1080/15476286.2020.1732694] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
tRNA-derived fragments or tRFs were long considered merely degradation intermediates of full-length tRNAs; however, emerging research is highlighting unanticipated new and highly distinct functions in epigenetic control, metabolism, immune activity and stem cell fate commitment. Importantly, recent studies suggest that RNA epitranscriptomic modifications may provide an additional regulatory layer that dynamically directs tRF activity in stem and cancer cells. In this review, we explore current work illustrating unanticipated roles of tRFs in mammalian stem cells with a focus on the impact of post-transcriptional RNA modifications for the biogenesis and function of this growing class of small noncoding RNAs.
Collapse
Affiliation(s)
- Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
| |
Collapse
|
19
|
Dhahbi J, Nunez Lopez YO, Schneider A, Victoria B, Saccon T, Bharat K, McClatchey T, Atamna H, Scierski W, Golusinski P, Golusinski W, Masternak MM. Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half. Front Oncol 2019; 9:959. [PMID: 31616639 PMCID: PMC6775249 DOI: 10.3389/fonc.2019.00959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.
Collapse
Affiliation(s)
- Joseph Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Tatiana Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Krish Bharat
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Thaddeus McClatchey
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Hani Atamna
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Wojciech Scierski
- Department of Otorhinolaryngology and Laryngological Oncology in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Zielona Gora, Poland
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| |
Collapse
|
20
|
Exosome-delivered and Y RNA-derived small RNA suppresses influenza virus replication. J Biomed Sci 2019; 26:58. [PMID: 31416454 PMCID: PMC6694579 DOI: 10.1186/s12929-019-0553-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background Multiple interplays between viral and host factors are involved in influenza virus replication and pathogenesis. Several small RNAs have recently emerged as important regulators of host response to viral infections. The aim of this study was to characterize the functional role of hsa-miR-1975, a Y5 RNA-derived small RNA, in defending influenza virus and delineate the mechanisms. Methods We performed high throughput sequencing of small RNAs in influenza virus-infected cells to identify up- or down- regulated small RNA species. The expression of the most abundant RNA species (hsa-miR-1975) was validated by stem-loop reverse transcription-polymerase chain reaction (RT-PCR). Antiviral effects of hsa-miR-1975 were confirmed by Western Blot, RT-PCR and plaque assay. In vitro perturbation of hsa-miR-1975 combined with exosomes isolation was used to elucidate the role and mechanism of hsa-miR-1975 in the context of antiviral immunity. Results Small RNA sequencing revealed that hsa-miR-1975 was the most up-regulated small RNA in influenza virus-infected cells. The amount of intracellular hsa-miR-1975 increased in the late stage of the influenza virus replication cycle. The increased hsa-miR-1975 was at least partially derived from degradation of Y5RNA as a result of cellular apoptosis. Unexpectedly, hsa-miR-1975 mimics inhibited influenza virus replication while hsa-miR-1975 sponges enhanced the virus replication. Moreover, hsa-miR-1975 was secreted in exosomes and taken up by the neighboring cells to induce interferon expression. Conclusions Our findings unravel a critical role of Y-class small RNA in host’s defense against influenza virus infection and reveal its antiviral mechanism through exosome delivery. This may provide a new candidate for targeting influenza virus. Electronic supplementary material The online version of this article (10.1186/s12929-019-0553-6) contains supplementary material, which is available to authorized users.
Collapse
|
21
|
Clues to Non-Invasive Implantation Window Monitoring: Isolation and Characterisation of Endometrial Exosomes. Cells 2019; 8:cells8080811. [PMID: 31375021 PMCID: PMC6721457 DOI: 10.3390/cells8080811] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
Despite the significant advances in the last decades, low implantation rate per transferred embryo still remains a major concern in assisted reproductive techniques, highlighting a need to better characterize endometrial receptivity also by mean of specific biomarkers. Based on physiology and on the intimate contact with endometrium as the tissue of interest, in this study we developed and validated an optimized protocol that uses extracellular vesicles (EVs) recovered from uterine flushings and from a cervical brush, the latter never used until now as an EVs source, as surrogates for endometrial biopsies. This method combines the safety of sampling with the ability to study the expression profile across the uterine cycle. We have compared the yield and composition of EVs recovered from different biofluids samples and fractions thereof, opting for chemical precipitation as the EV isolation procedure, assuring the highest yield without introducing any bias in specific EV recovery. Moreover, collected EVs, in particular exosome-like vesicles, express putative endometrial markers, such as glycodelin A and receptors for estrogen and progesterone, thus confirming their endometrial origin. We also identified uterine flushing EVs, in particular those recovered from its mucous fraction, as the richest source of endometrial transcripts, likely correlated to cellular (epithelial) origin of these vesicles. Finally, our pilot quantitative assessment of three endometrial gene profiles, in samples collected at different time points along the luteal phase, revealed the fluctuations apparently recapitulating gene expression variability prior reported during the menstrual cycle. Unlike tissue biopsy that is subjected to inter- and intra-sample differences, our data suggest that EVs from liquid biopsies (from uterine flushings and a cervical brush) obtained through less-invasive procedures, can be substrate to detect and track the tissue representative expression profiles, better depicting the total endometrium complexity.
Collapse
|
22
|
Kesharwani RK, Chiesa M, Bellazzi R, Colombo GI. CBS-miRSeq: A comprehensive tool for accurate and extensive analyses of microRNA-sequencing data. Comput Biol Med 2019; 110:234-243. [DOI: 10.1016/j.compbiomed.2019.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
|
23
|
Sadik N, Cruz L, Gurtner A, Rodosthenous RS, Dusoswa SA, Ziegler O, Van Solinge TS, Wei Z, Salvador-Garicano AM, Gyorgy B, Broekman M, Balaj L. Extracellular RNAs: A New Awareness of Old Perspectives. Methods Mol Biol 2019; 1740:1-15. [PMID: 29388131 DOI: 10.1007/978-1-4939-7652-2_1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Extracellular RNA (exRNA) has recently expanded as a highly important area of study in biomarker discovery and cancer therapeutics. exRNA consists of diverse RNA subpopulations that are normally protected from degradation by incorporation into membranous vesicles or by lipid/protein association. They are found circulating in biofluids, and have proven highly promising for minimally invasive diagnostic and prognostic purposes, particularly in oncology. Recent work has made progress in our understanding of exRNAs-from their biogenesis, compartmentalization, and vesicle packaging to their various applications as biomarkers and therapeutics, as well as the new challenges that arise in isolation and purification for accurate and reproducible analysis. Here we review the most recent advancements in exRNA research.
Collapse
Affiliation(s)
- Noah Sadik
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lilian Cruz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alessandra Gurtner
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Rodosthenis S Rodosthenous
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sophie A Dusoswa
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands.,Amsterdam Infection & Immunity Institute, VU University Medical Center, Amsterdam, The Netherlands.,Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Olivia Ziegler
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas Sebastiaan Van Solinge
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Bence Gyorgy
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marike Broekman
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, Brain Center Rudolf Magnus University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
24
|
Driedonks TAP, van der Grein SG, Ariyurek Y, Buermans HPJ, Jekel H, Chow FWN, Wauben MHM, Buck AH, 't Hoen PAC, Nolte-'t Hoen ENM. Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells. Cell Mol Life Sci 2018; 75:3857-3875. [PMID: 29808415 PMCID: PMC6154026 DOI: 10.1007/s00018-018-2842-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023]
Abstract
The release and uptake of nano-sized extracellular vesicles (EV) is a highly conserved means of intercellular communication. The molecular composition of EV, and thereby their signaling function to target cells, is regulated by cellular activation and differentiation stimuli. EV are regarded as snapshots of cells and are, therefore, in the limelight as biomarkers for disease. Although research on EV-associated RNA has predominantly focused on microRNAs, the transcriptome of EV consists of multiple classes of small non-coding RNAs with potential gene-regulatory functions. It is not known whether environmental cues imposed on cells induce specific changes in a broad range of EV-associated RNA classes. Here, we investigated whether immune-activating or -suppressing stimuli imposed on primary dendritic cells affected the release of various small non-coding RNAs via EV. The small RNA transcriptomes of highly pure EV populations free from ribonucleoprotein particles were analyzed by RNA sequencing and RT-qPCR. Immune stimulus-specific changes were found in the miRNA, snoRNA, and Y-RNA content of EV from dendritic cells, whereas tRNA and snRNA levels were much less affected. Only part of the changes in EV-RNA content reflected changes in cellular RNA, which urges caution in interpreting EV as snapshots of cells. By comprehensive analysis of RNA obtained from highly purified EV, we demonstrate that multiple RNA classes contribute to genetic messages conveyed via EV. The identification of multiple RNA classes that display cell stimulation-dependent association with EV is the prelude to unraveling the function and biomarker potential of these EV-RNAs.
Collapse
Affiliation(s)
- Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Susanne G van der Grein
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk P J Buermans
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrike Jekel
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Franklin W N Chow
- School of Biological Sciences, Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Marca H M Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Amy H Buck
- School of Biological Sciences, Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Centre for Biomolecular and Molecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
25
|
Yang J, Elbaz-Younes I, Primo C, Murungi D, Hirschi KD. Intestinal permeability, digestive stability and oral bioavailability of dietary small RNAs. Sci Rep 2018; 8:10253. [PMID: 29980707 PMCID: PMC6035168 DOI: 10.1038/s41598-018-28207-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Impactful dietary RNA delivery requires improving uptake and enhancing digestive stability. In mouse feeding regimes, we have demonstrated that a plant-based ribosomal RNA (rRNA), MIR2911, is more bioavailable than synthetic MIR2911 or canonical microRNAs (miRNAs). Here mutagenesis was used to discern if MIR2911 has a distinctive sequence that aids stability and uptake. Various mutations had modest impacts while one scrambled sequence displayed significantly enhanced digestive stability, serum stability, and bioavailability. To assess if small RNA (sRNA) bioavailability in mice could be improved by increasing gut permeability, various diets, genetic backgrounds and pharmacological methods were surveyed. An intraperitoneal injection of anti-CD3 antibody enhanced gut permeability which correlated with improved uptake of the digestively stable scrambled MIR2911 variant. However, the bioavailability of canonical miRNAs was not enhanced. Similarly, interleukin-10 (IL-10)-deficient mice and mice treated with aspirin displayed enhanced gut permeability that did not enhance uptake of most plant-based sRNAs. This work supports a model where dietary RNAs are vulnerable to digestion and altering gut permeability alone will not impact apparent bioavailability. We suggest that some dietary sRNA may be more digestively stable and methods to broadly increase sRNA uptake requires delivery vehicles to optimize gut and serum stability in the consumer.
Collapse
Affiliation(s)
- Jian Yang
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Ismail Elbaz-Younes
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Cecilia Primo
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Danna Murungi
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Kendal D Hirschi
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA.
- Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX, 77845, USA.
| |
Collapse
|
26
|
Clark PM, Chitnis N, Shieh M, Kamoun M, Johnson FB, Monos D. Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex. Sci Rep 2018; 8:3832. [PMID: 29497078 PMCID: PMC5832780 DOI: 10.1038/s41598-018-19427-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/23/2017] [Indexed: 02/06/2023] Open
Abstract
The MHC is recognized for its importance in human health and disease. However, many disease-associated variants throughout the region remain of unknown significance, residing predominantly within non-coding regions of the MHC. The characterization of non-coding RNA transcripts throughout the MHC is thus central to understanding the genetic contribution of these variants. Therefore, we characterize novel miRNA transcripts throughout the MHC by performing deep RNA sequencing of two B lymphoblastoid cell lines with completely characterized MHC haplotypes. Our analysis identifies 89 novel miRNA transcripts, 48 of which undergo Dicer-dependent biogenesis and are loaded onto the Argonaute silencing complex. Several of the identified mature miRNA and pre-miRNA transcripts are unique to specific MHC haplotypes and overlap common SNPs. Furthermore, 43 of the 89 identified novel miRNA transcripts lie within linkage disequilibrium blocks that contain a disease-associated SNP. These disease associated SNPs are associated with 65 unique disease phenotypes, suggesting that these transcripts may play a role in the etiology of numerous diseases associated with the MHC. Additional in silico analysis reveals the potential for thousands of putative pre-miRNA encoding loci within the MHC that may be expressed by different cell types and at different developmental stages.
Collapse
Affiliation(s)
- P M Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - N Chitnis
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Shieh
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - F B Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D Monos
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
27
|
Saberi Anvar M, Minuchehr Z, Shahlaei M, Kheitan S. Gastric cancer biomarkers; A systems biology approach. Biochem Biophys Rep 2018; 13:141-146. [PMID: 29556568 PMCID: PMC5857180 DOI: 10.1016/j.bbrep.2018.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/12/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
Gastric cancer is one of the most fatal cancers in the world. Many efforts in recent years have attempted to find effective proteins in gastric cancer. By using a comprehensive list of proteins involved in gastric cancer, scientists were able to retrieve interaction information. The study of protein-protein interaction networks through systems biology based analysis provides appropriate strategies to discover candidate proteins and key biological pathways. In this study, we investigated dominant functional themes and centrality parameters including betweenness as well as the degree of each topological clusters and expressionally active sub-networks in the resulted network. The results of functional analysis on gene sets showed that neurotrophin signaling pathway, cell cycle and nucleotide excision possess the strongest enrichment signals. According to the computed centrality parameters, HNF4A, TAF1 and TP53 manifested as the most significant nodes in the interaction network of the engaged proteins in gastric cancer. This study also demonstrates pathways and proteins that are applicable as diagnostic markers and therapeutic targets for future attempts to overcome gastric cancer. A systematic study of protein-protein interaction networks through comprehensive extracted list of proteins involved in gastric cancer. Dominant functional theme and pathways of each topological clusters and expressionally active subnetworks were reported. The most effective proteins in gastric cancer formation were proposed according to the computed centrality parameters. HNF4A, TAF1and TP53 were mentioned as the key proteins in gastric cancer.
Collapse
Affiliation(s)
- Mohammad Saberi Anvar
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Samira Kheitan
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| |
Collapse
|
28
|
Babatunde KA, Mbagwu S, Hernández-Castañeda MA, Adapa SR, Walch M, Filgueira L, Falquet L, Jiang RHY, Ghiran I, Mantel PY. Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles. Sci Rep 2018; 8:884. [PMID: 29343745 PMCID: PMC5772623 DOI: 10.1038/s41598-018-19149-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown. We isolated EVs from cultured iRBCs to determine their small RNA content. We identified several types of human and plasmodial regulatory RNAs. While the miRNAs and tRNA-derived fragments were the most abundant human RNAs, we also found Y-RNAs, vault RNAs, snoRNAs and piRNAs. Interestingly, we found about 120 plasmodial RNAs, including mRNAs coding for exported proteins and proteins involved in drug resistance, as well as non-coding RNAs, such as rRNAs, small nuclear (snRNAs) and tRNAs. These data show, that iRBC-EVs carry small regulatory RNAs. A role in cellular communication is possible since the RNAs were transferred to endothelial cells. Furthermore, the presence of Plasmodium RNAs, in EVs suggests that they may be used as biomarker to track and detect disease.
Collapse
Affiliation(s)
| | - Smart Mbagwu
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | | | - Swamy R Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Michael Walch
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Luis Filgueira
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Ionita Ghiran
- Division of Allergy and Infection, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Pierre-Yves Mantel
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland.
| |
Collapse
|
29
|
Guo H, Zhang X, Chen Q, Bao Y, Dong C, Wang X. miR-132 suppresses the migration and invasion of lung cancer cells by blocking USP9X-induced epithelial-mesenchymal transition. Am J Transl Res 2018; 10:224-234. [PMID: 29423007 PMCID: PMC5801360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/19/2017] [Indexed: 06/08/2023]
Abstract
miR-132, a microRNA, has been reported to be down-regulated in several human cancers and is related with tumor progression; however, its function in non-small cell lung cancer (NSCLC) progression remains unclear. This study aimed to investigate the putative role of miR-132 in the metastasis of NSCLC. We determined the function of miR-132 in the migration and invasion of a NSCLC cell line in vitro using a miR-132 inhibitor and mimic. Our results showed overexpression of miR-132 significantly inhibited the migration and invasion of NSCLC cells in vitro. We then identified USP9X as a potential target of miR-132, and demonstrated miR-132 could regulate the expression of USP9X at both the mRNA and protein level. miR-132 could directly bind to the 3' untranslated region (3'-UTR) of USP9X. Inhibition of USP9X by its inhibitor WP1130 reduced the migration and invasion of NSCLC cells. Furthermore, USP9X inhibition also reversed the increased migration and invasion mediated by miR-132 inhibition. We found USP9X inhibition up-regulated expression of the epithelial-mesenchymal transition (EMT) marker E-cadherin, but down-regulated vimentin expression. A similar effect was seen with miR-132 overexpression, while the opposite effect occurred with miR-132 knockdown. USP9X inhibition reversed the miR-132 inhibitor-induced vimentin up-regulation and E-cadherin down-regulation. Taken together, these results indicate miR-132 prohibits the migration and invasion of NSCLC cells via targeting USP9X-induced EMT. Our data provides further evidence for the critical role of miR-132 and USP9X in regulating cell invasion and migration of NSCLC.
Collapse
Affiliation(s)
- Huihui Guo
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| | - Xilin Zhang
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| | - Qiuqiang Chen
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| | - Ying Bao
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| | - Chaohui Dong
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| | - Xiang Wang
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou UniversityHuzhou 313000, Zhejiang, China
| |
Collapse
|
30
|
Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI. Nonprotein-Coding RNAs as Regulators of Development in Tunicates. Results Probl Cell Differ 2018; 65:197-225. [PMID: 30083922 DOI: 10.1007/978-3-319-92486-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.
Collapse
Affiliation(s)
- Cristian A Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.
- Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Adriaan Gittenberger
- Institute of Biology, Leiden University, Leiden, Netherlands
- GiMaRIS, BioScience Park Leiden, Leiden, Netherlands
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | | |
Collapse
|
31
|
Cimino L, Salemi M, Cannarella R, Condorelli RA, Giurato G, Marchese G, La Vignera S, Calogero AE. Decreased miRNA expression in Klinefelter syndrome. Sci Rep 2017; 7:16672. [PMID: 29192217 PMCID: PMC5709391 DOI: 10.1038/s41598-017-16892-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 01/18/2023] Open
Abstract
The widelyvariable phenotypic spectrum and the different severity of symptoms in men with Klinefelter syndrome (KS) suggest a role for epigenetic mediators. Therefore, the aim of this study is to evaluate the possible involvement of miRNAs in the clinical manifestations of KS. To accomplish this, we performed a transcriptome analysis in peripheral blood mononuclear cells (PBMCs) of 10 non-mosaic KS patients, 10 aged-matched healthy men and 10 aged-matched healthy female controls with normal karyotype. After RNA extraction from PBMC and the preparation of RNA libraries, the samples were sequenced using next generation high-throughput sequencing technology. Expression profiling analysis revealed a significant differential expression of 2 miRNAs in KS compared to male controls. In particular, MIR3648 resulted significantly (q-value < 0.0001) down-regulated by -19.084- fold, while MIR3687was strongly down-regulated (q-value < 0.0001) considering KS patients. These results were confirmed by qRT-PCR. The functional analysis of the two transcripts showed that they seem to play a role in breast cancer, hemopoietic abnormalities, immune defects and adipocyte differentiation and fat cell maturation. Therefore, we speculate that both miRNAs may play a role in the immune and metabolic disorders and in the risk of breast cancer development in men with KS.
Collapse
Affiliation(s)
- Laura Cimino
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy
| | - Michele Salemi
- Oasi Institute for Research on Mental Retardation and Brain Aging (IRCCS), Troina, 94018, Italy
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy
| | - Rosita A Condorelli
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, 84081, Italy
- Genomix4Life Srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi (SA), 84081, Italy
| | - Giovanna Marchese
- Genomix4Life Srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi (SA), 84081, Italy
| | - Sandro La Vignera
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy
| | - Aldo E Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy.
| |
Collapse
|
32
|
Wei Z, Batagov AO, Schinelli S, Wang J, Wang Y, El Fatimy R, Rabinovsky R, Balaj L, Chen CC, Hochberg F, Carter B, Breakefield XO, Krichevsky AM. Coding and noncoding landscape of extracellular RNA released by human glioma stem cells. Nat Commun 2017; 8:1145. [PMID: 29074968 PMCID: PMC5658400 DOI: 10.1038/s41467-017-01196-x] [Citation(s) in RCA: 354] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023] Open
Abstract
Tumor-released RNA may mediate intercellular communication and serve as biomarkers. Here we develop a protocol enabling quantitative, minimally biased analysis of extracellular RNAs (exRNAs) associated with microvesicles, exosomes (collectively called EVs), and ribonucleoproteins (RNPs). The exRNA complexes isolated from patient-derived glioma stem-like cultures exhibit distinct compositions, with microvesicles most closely reflecting cellular transcriptome. exRNA is enriched in small ncRNAs, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in EVs and exRNPs. EV-enclosed mRNAs are mostly fragmented, and UTRs enriched; nevertheless, some full-length mRNAs are present. Overall, there is less than one copy of non-rRNA per EV. Our results suggest that massive EV/exRNA uptake would be required to ensure functional impact of transferred RNA on brain recipient cells and predict the most impactful miRNAs in such conditions. This study also provides a catalog of diverse exRNAs useful for biomarker discovery and validates its feasibility on cerebrospinal fluid. While circulating DNA has been extensively explored as a potential cancer biomarker, RNA potential has been overlooked so far. Here the authors present a comprehensive analysis of extracellular RNA secreted by glioblastoma cells that could prove a valuable resource for biomarker discovery and a means of intercellular communication.
Collapse
Affiliation(s)
- Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Arsen O Batagov
- Vishuo Biomedical, #3-33 Teletech Park, 20 Science Park Road, Singapore, 117674, Singapore
| | - Sergio Schinelli
- Department of Drug Sciences, University of Pavia, Pavia, 27100, Italy
| | - Jintu Wang
- Beijing Genomics Institute, Shenzhen, 518083, China
| | - Yang Wang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Leonora Balaj
- Department of Neurology and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Clark C Chen
- Neurosurgery Department, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fred Hochberg
- Department of Neurosurgery, University of California, La Jolla, San Diego, CA, 92093, USA.,Scintillon Institute, San Diego, CA, 92121, USA
| | - Bob Carter
- Department of Neurosurgery, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Xandra O Breakefield
- Department of Neurology and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA.
| |
Collapse
|
33
|
Cambier L, de Couto G, Ibrahim A, Echavez AK, Valle J, Liu W, Kreke M, Smith RR, Marbán L, Marbán E. Y RNA fragment in extracellular vesicles confers cardioprotection via modulation of IL-10 expression and secretion. EMBO Mol Med 2017; 9:337-352. [PMID: 28167565 PMCID: PMC5331234 DOI: 10.15252/emmm.201606924] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cardiosphere‐derived cells (CDCs) reduce myocardial infarct size via secreted extracellular vesicles (CDC‐EVs), including exosomes, which alter macrophage polarization. We questioned whether short non‐coding RNA species of unknown function within CDC‐EVs contribute to cardioprotection. The most abundant RNA species in CDC‐EVs is a Y RNA fragment (EV‐YF1); its relative abundance in CDC‐EVs correlates with CDC potency in vivo. Fluorescently labeled EV‐YF1 is actively transferred from CDCs to target macrophages via CDC‐EVs. Direct transfection of macrophages with EV‐YF1 induced transcription and secretion of IL‐10. When cocultured with rat cardiomyocytes, EV‐YF1‐primed macrophages were potently cytoprotective toward oxidatively stressed cardiomyocytes through induction of IL‐10. In vivo, intracoronary injection of EV‐YF1 following ischemia/reperfusion reduced infarct size. A fragment of Y RNA, highly enriched in CDC‐EVs, alters Il10 gene expression and enhances IL‐10 protein secretion. The demonstration that EV‐YF1 confers cardioprotection highlights the potential importance of diverse exosomal contents of unknown function, above and beyond the usual suspects (e.g., microRNAs and proteins).
Collapse
Affiliation(s)
- Linda Cambier
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Geoffrey de Couto
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Antonio K Echavez
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jackelyn Valle
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Weixin Liu
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - Eduardo Marbán
- Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| |
Collapse
|
34
|
Overexpression of MicroRNA-145 Ameliorates Astrocyte Injury by Targeting Aquaporin 4 in Cerebral Ischemic Stroke. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9530951. [PMID: 29057271 PMCID: PMC5615955 DOI: 10.1155/2017/9530951] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/03/2017] [Accepted: 06/18/2017] [Indexed: 12/30/2022]
Abstract
Cerebral ischemic stroke, which affects the global population, is a major disease with high incidence, mortality, and disability. Accumulating evidence has indicated that abnormal microRNA (miRNA) expression plays essential roles in the pathologies of ischemic stroke. Yet, the underlying regulatory mechanism of miRNAs in cerebral ischemic stroke remains unclear. We investigated the role of miR-145 in cerebral ischemic stroke and its potential mechanism in a model using primary cultured astrocytes. We detected the expression levels of miR-145 and its target gene AQP4 and assessed the role of miR-145 in cell death and apoptosis caused by oxygen-glucose deprivation (OGD). Bioinformatics analysis was used to explore the targets of miR-145. miR-145 expression levels were significantly decreased in primary astrocytes subjected to OGD. miR-145 overexpression promoted astrocyte health and inhibited OGD-induced apoptosis. AQP4 was a direct target of miR-145, and miR-145 suppressed AQP4 expression. Moreover, AQP4 enhanced astrocyte injury in ischemic stroke, and AQP4 knockdown diminished the miR-145-mediated protective effect on ischemic injury. Taken together, our results show that miR-145 plays an important role in protecting astrocytes from ischemic injury by downregulating AQP4 expression. These findings may highlight a novel therapeutic target in cerebral ischemic stroke.
Collapse
|
35
|
Circulating miR-122 and miR-200a as biomarkers for fatal liver disease in ART-treated, HIV-1-infected individuals. Sci Rep 2017; 7:10934. [PMID: 28883647 PMCID: PMC5589757 DOI: 10.1038/s41598-017-11405-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 06/23/2017] [Indexed: 02/07/2023] Open
Abstract
Liver disease is one of the main contributors to the increased levels of morbidity and mortality seen in the HIV-1-infected, ART-treated population. Circulating miRNAs, particularly those located inside extracellular vesicles, are seen as promising biomarkers for a number of human disease conditions, including liver-related diseases. Here, we show that serum levels of miR-122 and miR-200a are greater in HIV/HCV co-infected individuals compared to HIV-1 mono-infected individuals. We also show that miR-122 and miR-200a are elevated in ART-treated, HIV-1-infected individuals prior to the development of fatal liver disease, suggesting that these miRNA may have some potential clinical utility as biomarkers. While this study is hypothesis generating, it shows clearly that both miR-122 and miR-200a are promising novel biomarkers for liver disease in the ART-treated, HIV-1-infected population.
Collapse
|
36
|
Gao L, Li SH, Tian YX, Zhu QQ, Chen G, Pang YY, Hu XH. Role of downregulated miR-133a-3p expression in bladder cancer: a bioinformatics study. Onco Targets Ther 2017; 10:3667-3683. [PMID: 28790856 PMCID: PMC5530854 DOI: 10.2147/ott.s137433] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It has been discovered that miR-133a-3p acts as a tumor suppressor in bladder cancer (BC). Nevertheless, the function of miR-133a-3p in BC remains unclarified. Thus, we carried out this study to validate the expression of miR-133a-3p in BC and provide insights into the molecular mechanism underlying it. To assess the expression of miR-133a-3p in BC, we searched eligible studies from literature and Gene expression Omnibus (GEO) to perform a meta-analysis. We also plotted the summary receiver operating characteristic (SROC) curve to evaluate the diagnostic ability of miR-133a-3p in BC. Additionally, the potential target genes of miR-133a-3p were acquired from 14 online software programs and GEO database. Protein-protein interaction (PPI) network was created to identify the hub genes. Then, Gene Ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out to investigate the regulatory network of the target genes. From the meta-analysis, miR-133a-3p was remarkably downregulated in BC tissues compared with that in non-cancer tissues (standard mean difference =−3.84, 95% confidence interval =−6.99–0.29). Moreover, results from SROC suggested that miR-133a-3p exhibited the ability to diagnose BC (area under curve =0.8418). As for the bioinformatics study, 488 genes were chosen as the potential targets of miR-133a-3p in BC, among which 10 genes were defined as hub genes (all degrees >5). Further GO and KEGG pathway analysis indicated that the target genes of miR-133a-3p aggregated in specific biological process and pathways. In conclusion, miR-133a-3p possessed great diagnostic potential with its downregulation in BC, and miR-133a-3p might serve as a novel biomarker for BC.
Collapse
Affiliation(s)
- Li Gao
- Department of Medical Oncology
| | | | | | | | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yu-Yan Pang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | | |
Collapse
|
37
|
Yeri A, Courtright A, Reiman R, Carlson E, Beecroft T, Janss A, Siniard A, Richholt R, Balak C, Rozowsky J, Kitchen R, Hutchins E, Winarta J, McCoy R, Anastasi M, Kim S, Huentelman M, Van Keuren-Jensen K. Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects. Sci Rep 2017; 7:44061. [PMID: 28303895 PMCID: PMC5356006 DOI: 10.1038/srep44061] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/01/2017] [Indexed: 02/08/2023] Open
Abstract
Interest in circulating RNAs for monitoring and diagnosing human health has grown significantly. There are few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. In this study, total extracellular RNA (exRNA) was isolated and sequenced from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 male college athletes ages 18–25 years. Many participants provided more than one sample, allowing us to investigate variability in an individual’s exRNA expression levels over time. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. The small RNA profile of each biofluid is distinct. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid, and profiles of miRNA are different for each biofluid. Not unexpectedly, saliva samples have high levels of exogenous sequence that can be traced to bacteria. These data significantly contribute to the current number of sequenced exRNA samples from normal healthy individuals.
Collapse
Affiliation(s)
- Ashish Yeri
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Amanda Courtright
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Rebecca Reiman
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Elizabeth Carlson
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Taylor Beecroft
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Alex Janss
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Ashley Siniard
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Chris Balak
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Robert Kitchen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Joseph Winarta
- Neurogenomics Division, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | - Roger McCoy
- Arizona State University Sports Medicine, 323 E Veterans Way, Tempe, AZ 85281, USA
| | - Matthew Anastasi
- Arizona State University Sports Medicine, 323 E Veterans Way, Tempe, AZ 85281, USA
| | - Seungchan Kim
- Integrated Cancer Genomics, TGen, 445 N. 5th St., Phoenix, AZ 85004, USA
| | | | | |
Collapse
|
38
|
RNY (YRNA)-derived small RNAs regulate cell death and inflammation in monocytes/macrophages. Cell Death Dis 2017; 8:e2530. [PMID: 28055017 PMCID: PMC5386355 DOI: 10.1038/cddis.2016.429] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 01/01/2023]
Abstract
The recent discovery of new classes of small RNAs has opened unknown territories to explore new regulations of physiopathological events. We have recently demonstrated that RNY (or Y RNA)-derived small RNAs (referred to as s-RNYs) are an independent class of clinical biomarkers to detect coronary artery lesions and are associated with atherosclerosis burden. Here, we have studied the role of s-RNYs in human and mouse monocytes/macrophages and have shown that in lipid-laden monocytes/macrophages s-RNY expression is timely correlated to the activation of both NF-κB and caspase 3-dependent cell death pathways. Loss- or gain-of-function experiments demonstrated that s-RNYs activate caspase 3 and NF-κB signaling pathways ultimately promoting cell death and inflammatory responses. As, in atherosclerosis, Ro60-associated s-RNYs generated by apoptotic macrophages are released in the blood of patients, we have investigated the extracellular function of the s-RNY/Ro60 complex. Our data demonstrated that s-RNY/Ro60 complex induces caspase 3-dependent cell death and NF-κB-dependent inflammation, when added to the medium of cultured monocytes/macrophages. Finally, we have shown that s-RNY function is mediated by Toll-like receptor 7 (TLR7). Indeed using chloroquine, which disrupts signaling of endosome-localized TLRs 3, 7, 8 and 9 or the more specific TLR7/9 antagonist, the phosphorothioated oligonucleotide IRS954, we blocked the effect of either intracellular or extracellular s-RNYs. These results position s-RNYs as relevant novel functional molecules that impacts on macrophage physiopathology, indicating their potential role as mediators of inflammatory diseases, such as atherosclerosis.
Collapse
|
39
|
Zhao J, Schnitzler GR, Iyer LK, Aronovitz MJ, Baur WE, Karas RH. MicroRNA-Offset RNA Alters Gene Expression and Cell Proliferation. PLoS One 2016; 11:e0156772. [PMID: 27276022 PMCID: PMC4898817 DOI: 10.1371/journal.pone.0156772] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/19/2016] [Indexed: 11/29/2022] Open
Abstract
MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We demonstrate that endogenous or over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. We report that there is a “seed region” of moR-21 as well as a “seed match region” in the target gene 3’UTR that are indispensable for moR-21-mediated gene down-regulation. We further demonstrate that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. Taken together, these findings provide the first evidence that microRNA offset RNA alters gene expression and is biologically active.
Collapse
Affiliation(s)
- Jin Zhao
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Gavin R. Schnitzler
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Lakshmanan K. Iyer
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Mark J. Aronovitz
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Wendy E. Baur
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Richard H. Karas
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
- * E-mail:
| |
Collapse
|
40
|
Tao S, Liu YB, Zhou ZW, Lian B, Li H, Li JP, Zhou SF. miR-3646 promotes cell proliferation, migration, and invasion via regulating G2/M transition in human breast cancer cells. Am J Transl Res 2016; 8:1659-1677. [PMID: 27186291 PMCID: PMC4859896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are often located in genomic breakpoint regions and play a critical role in regulating a variety of the cellular processes in human cancer. miR-3646 has been reported to take part in tumorigenic progression in breast and bladder cancer, but its potential functions and exact mechanistic roles in breast cancer are still unclear. The objective of this study was to investigate the role of miR-3646 in breast cancer growth and metastasis using both bioinformatic and experimental approaches. Before starting the bench work, we conducted a bioinformatic study to predict the target genes regulated by miR-3646 using a panel of different algorithms. The results showed that miR-3646 might regulate a large number of genes that are related to cell growth, proliferation, metabolis, transport, and apoptosis and some were cancer-related genes. We found that the expression level of miR-3646 was significantly upregulated in breast cancer cells and tissues compared with normal breast cells and no tumor tissues. Subsequently, the MTT and colony formation assay results showed that up-regulation of miR-3646 promoted the cell viability and proliferation. Our results also showed that down-regulation of miR-3646 arrested the cells in G2/M phase in MCF7 and MDA-MB-231 cells which was accompanied by the down-regulation of CDK1/CDC2 and cyclin B1 and upregulation of p21Waf1/Cip1, p27 Kip1, and p53, suggesting that down-regulation of miR-3646 induces G2/M arrest through activation of the p53/p21/CDC2/cyclin B1 pathway. In addition, overexpression of miR-3646 promoted migration and invasion of MCF7 and MDA-MB-231 cells. Taken together, miR-3646 is a potential oncogene in breast cancer and it may represent a new niomarker in the diagnosis and prediction of prognosis and therapeutic response.
Collapse
Affiliation(s)
- Shuang Tao
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Yao-Bang Liu
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Zhi-Wei Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, Texas Tech University, Health Sciences CenterAmarillo, Texas, USA
| | - Bin Lian
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Hong Li
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Jin-Ping Li
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South FloridaTampa, Florida, USA
| |
Collapse
|
41
|
Victoria B, Dhahbi JM, Nunez Lopez YO, Spinel L, Atamna H, Spindler SR, Masternak MM. Circulating microRNA signature of genotype-by-age interactions in the long-lived Ames dwarf mouse. Aging Cell 2015; 14:1055-66. [PMID: 26176567 PMCID: PMC4693471 DOI: 10.1111/acel.12373] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2015] [Indexed: 11/29/2022] Open
Abstract
Recent evidence demonstrates that serum levels of specific miRNAs significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long‐lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype‐specific changes in the circulating levels of 21 miRNAs during aging [genotype‐by‐age interaction (GbA)]. Genotype‐by‐age miRNAs showed four distinct expression patterns and significant overtargeting of transcripts involved in age‐related processes. Functional enrichment analysis of putative and validated miRNA targets highlighted cellular processes such as tumor suppression, anti‐inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long‐lived mouse suggests CR‐like and CR‐independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs modulated by age in the long‐lived Ames mouse.
Collapse
Affiliation(s)
- Berta Victoria
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida 6900 Lake Nona Blvd. Orlando FL 32827 USA
| | - Joseph M. Dhahbi
- Department of Biochemistry University of California at Riverside Riverside CA 92521 USA
- Center for Genetics Childrens Hospital Oakland Research Institute Oakland CA 94609 USA
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes Florida Hospital 301 E. Princeton Street Orlando FL 2804 USA
| | - Lina Spinel
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida 6900 Lake Nona Blvd. Orlando FL 32827 USA
| | - Hani Atamna
- Department of Medical Education California Northstate University Elk Grove CA USA
| | - Stephen R. Spindler
- Department of Biochemistry University of California at Riverside Riverside CA 92521 USA
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida 6900 Lake Nona Blvd. Orlando FL 32827 USA
- Department of Head and Neck Surgery The Greater Poland Cancer Centre 15 Garbary St. 61‐866 Poznan Poland
| |
Collapse
|
42
|
Koo J, Cabarcas-Petroski S, Petrie JL, Diette N, White RJ, Schramm L. Induction of proto-oncogene BRF2 in breast cancer cells by the dietary soybean isoflavone daidzein. BMC Cancer 2015; 15:905. [PMID: 26573593 PMCID: PMC4647806 DOI: 10.1186/s12885-015-1914-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/06/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND BRF2 is a transcription factor required for synthesis of a small group of non-coding RNAs by RNA polymerase III. Overexpression of BRF2 can transform human mammary epithelial cells. In both breast and lung cancers, the BRF2 gene is amplified and overexpressed and may serve as an oncogenic driver. Furthermore, elevated BRF2 can be independently prognostic of unfavorable survival. Dietary soy isoflavones increase metastasis to lungs in a model of breast cancer and a recent study reported significantly increased cell proliferation in breast cancer patients who used soy supplementation. The soy isoflavone daidzein is a major food-derived phytoestrogen that is structurally similar to estrogen. The putative estrogenic effect of soy raises concern that high consumption of soy foods by breast cancer patients may increase tumor growth. METHODS Expression of BRF2 RNA and protein was assayed in ER-positive or -negative human breast cancer cells after exposure to daidzein. We also measured mRNA stability, promoter methylation and response to the demethylating agent 5-azacytidine. In addition, expression was compared between mice fed diets enriched or deprived of isoflavones. RESULTS We demonstrate that the soy isoflavone daidzein specifically stimulates expression of BRF2 in ER-positive breast cancer cells, as well as the related factor BRF1. Induction is accompanied by increased levels of non-coding RNAs that are regulated by BRF2 and BRF1. Daidzein treatment stabilizes BRF2 and BRF1 mRNAs and selectively decreases methylation of the BRF2 promoter. Functional significance of demethylation is supported by induction of BRF2 by the methyltransferase inhibitor 5-azacytidine. None of these effects are observed in an ER-negative breast cancer line, when tested in parallel with ER-positive breast cancer cells. In vivo relevance is suggested by the significantly elevated levels of BRF2 mRNA detected in female mice fed a high-isoflavone commercial diet. In striking contrast, BRF2 and BRF1 mRNA levels are suppressed in matched male mice fed the same isoflavone-enriched diet. CONCLUSIONS The BRF2 gene that is implicated in cancer can be induced in human breast cancer cells by the isoflavone daidzein, through promoter demethylation and/or mRNA stabilization. Dietary isoflavones may also induce BRF2 in female mice, whereas the converse occurs in males.
Collapse
Affiliation(s)
- Jana Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | | | - John L Petrie
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Nicole Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - Robert J White
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Laura Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA.
| |
Collapse
|
43
|
Katsuda T, Ochiya T. Molecular signatures of mesenchymal stem cell-derived extracellular vesicle-mediated tissue repair. Stem Cell Res Ther 2015; 6:212. [PMID: 26560482 PMCID: PMC4642616 DOI: 10.1186/s13287-015-0214-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) play important roles in intercellular communications via their content molecules, and mimic, at least in part, the roles that are played by their originating cells. Consistent with this notion, an increasing number of reports have suggested that EVs derived from mesenchymal stem cells (MSCs), which are therapeutically beneficial to a wide range of diseases, can serve as drugs to treat multiple diseases. EVs contain a variety of molecules, including proteins, microRNAs, and mRNAs, and are associated with biological processes in a content molecule-dependent manner. In this article, we review the latest reports regarding the therapeutic potential of MSC-EVs by focusing on the underlying molecular mechanisms of their effects. Specifically, we feature the effects of MSC-EVs in terms of their content molecules and of the tissue recovery processes endowed by these molecules.
Collapse
Affiliation(s)
- Takeshi Katsuda
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| |
Collapse
|
44
|
Matullo G, Naccarati A, Pardini B. MicroRNA expression profiling in bladder cancer: the challenge of next-generation sequencing in tissues and biofluids. Int J Cancer 2015; 138:2334-45. [PMID: 26489968 DOI: 10.1002/ijc.29895] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 10/09/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
Abstract
Bladder cancer (BC) is a heterogeneous disease characterized by a high recurrence rate that necessitates continuous cystoscopic surveillance. MicroRNAs (miRNAs) are detectable in tissues and biofluids such as plasma/serum and urine. They represent promising biomarkers with potential not only for detecting BC but also informing on prognosis and monitoring treatment response. In this review, the many aspects of the application of next-generation sequencing (NGS) to evaluate miRNA expression in BC is discussed, including technical issues as well as a comparison with results obtained by qRT-PCR. The available studies investigating miRNA profiling in BC by NGS are described, with particular attention to the potential applicability on biofluids. Altered miRNA levels have been observed in BC tissues by NGS, but these results so far only partially overlapped among studies and with previous data obtained by qRT-PCR. The discrepancies can be ascribed to the small groups of BC patients sequenced. The few available studies on biofluids are mainly focused on implementing RNA isolation and sequencing workflow. Using NGS to analyze miRNAs in biofluids can potentially provide results comparable to tissues with no invasive procedures for the patients. In particular, the analyses performed on exosomes/microvesicles appear to be more informative. Thanks to the improvement of both wet-lab procedures and pipelines/tools for data analyses, NGS studies on biofluids will be performed on a larger scale. MiRNAs detected in urine and serum/plasma will demonstrate their potentiality to describe the variegated scenario of BC and to become relevant clinical markers.
Collapse
Affiliation(s)
- Giuseppe Matullo
- Genomic Variation in Human Population and Complex Diseases Unit, Human Genetics Foundation, Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessio Naccarati
- Molecular and Genetic Epidemiology Unit, Human Genetics Foundation, Turin, Italy
| | - Barbara Pardini
- Genomic Variation in Human Population and Complex Diseases Unit, Human Genetics Foundation, Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| |
Collapse
|
45
|
Systematic integration of molecular profiles identifies miR-22 as a regulator of lipid and folate metabolism in breast cancer cells. Oncogene 2015; 35:2766-76. [PMID: 26477310 DOI: 10.1038/onc.2015.333] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 05/31/2015] [Accepted: 07/06/2015] [Indexed: 12/12/2022]
Abstract
Dysregulated microRNA (miRNA) mediate malignant phenotypes, including metabolic reprogramming. By performing an integrative analysis of miRNA and metabolome data for the NCI-60 cell line panel, we identified an miRNA cluster strongly associated with both c-Myc expression and global metabolic variation. Within this cluster the cancer-associated and cardioprotective miR-22 was shown to repress fatty acid synthesis and elongation in tumour cells by targeting ATP citrate lyase and fatty acid elongase 6, as well as impairing mitochondrial one-carbon metabolism by suppression of methylene tetrahydrofolate dehydrogenase/cyclohydrolase. Across several data sets, expression of these target genes were associated with poorer outcomes in breast cancer patients. Importantly, a beneficial effect of miR-22 on clinical outcomes in breast cancer was shown to depend on the expression levels of the identified target genes, demonstrating the relevance of miRNA/mRNA interactions to disease progression in vivo. Our systematic analysis establishes miR-22 as a novel regulator of tumour cell metabolism, a function that could contribute to the role of this miRNA in cellular differentiation and cancer development. Moreover, we provide a paradigmatic example of effect modification in outcome analysis as a consequence of miRNA-directed gene targeting, a phenomenon that could be exploited to improve patient prognosis and treatment.
Collapse
|
46
|
Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015; 31:613-626. [PMID: 26453491 DOI: 10.1016/j.tig.2015.09.002] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
Collapse
Affiliation(s)
- T Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - P Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - K Eilbeck
- Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - J T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - M S McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A Singer
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA
| | - J H Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
47
|
Martinez BV, Dhahbi JM, Lopez YON, Lamperska K, Golusinski P, Luczewski L, Kolenda T, Atamna H, Spindler SR, Golusinski W, Masternak MM. Circulating small non-coding RNA signature in head and neck squamous cell carcinoma. Oncotarget 2015; 6:19246-63. [PMID: 26057471 PMCID: PMC4662488 DOI: 10.18632/oncotarget.4266] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 12/23/2022] Open
Abstract
The Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common human cancer, causing 350,000 individuals die worldwide each year. The overall prognosis in HNSCC patients has not significantly changed for the last decade. Complete understanding of the molecular mechanisms in HNSCC carcinogenesis could allow an earlier diagnosis and the use of more specific and effective therapies. In the present study we used deep sequencing to characterize small non-coding RNAs (sncRNAs) in serum from HNSCC patients and healthy donors. We identified, for the first time, a multi-marker signature of 3 major classes of circulating sncRNAs in HNSCC, revealing the presence of circulating novel and known miRNAs, and tRNA- and YRNA-derived small RNAs that were significantly deregulated in the sera of HNSCC patients compared to healthy controls. By implementing a triple-filtering approach we identified a subset of highly biologically relevant miRNA-mRNA interactions and we demonstrated that the same genes/pathways affected by somatic mutations in cancer are affected by changes in the abundance of miRNAs. Therefore, one important conclusion from our work is that during cancer development, there seems to be a convergence of oncogenic processes driven by somatic mutations and/or miRNA regulation affecting key cellular pathways.
Collapse
Affiliation(s)
- Berta Victoria Martinez
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine Orlando, FL, USA
| | - Joseph M. Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL, USA
| | - Katarzyna Lamperska
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Paweł Golusinski
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznan, Poland
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Lukasz Luczewski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Kolenda
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Hani Atamna
- Department of Medical Education, California Northstate University, Elk Grove, CA, USA
| | - Stephen R. Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Michal M. Masternak
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine Orlando, FL, USA
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
48
|
Kowalski MP, Krude T. Functional roles of non-coding Y RNAs. Int J Biochem Cell Biol 2015; 66:20-9. [PMID: 26159929 PMCID: PMC4726728 DOI: 10.1016/j.biocel.2015.07.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 12/20/2022]
Abstract
Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs.
Collapse
Affiliation(s)
- Madzia P Kowalski
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
| |
Collapse
|
49
|
Lan G, Yang L, Xie X, Peng L, Wang Y. MicroRNA-490-5p is a novel tumor suppressor targeting c-FOS in human bladder cancer. Arch Med Sci 2015; 11:561-9. [PMID: 26170849 PMCID: PMC4495152 DOI: 10.5114/aoms.2015.52359] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 04/15/2013] [Accepted: 07/25/2013] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Recent studies have demonstrated the critical roles of micro-RNAs in tumorigenesis and tumor progression. Here, we describe the regulation and function of miR-490-5p in bladder cancer. MATERIAL AND METHODS Paired tissue samples were collected from bladder cancer patients (n = 20). Real-time PCR revealed that miR-490-5p expression was significantly down-regulated in human bladder cancer tissues and cells. Also there was an inverse relationship between the expression level of miR-490-5p and the pathological grade of bladder cancer. Western blotting was performed to detect the expression levels of c-FOS and TET1 in 6 matched tumor tissue samples and 4 bladder cell lines. Furthermore, to better understand the underlying mechanisms of miR-490-5p, we conducted gain and loss of function analysis by transfecting bladder cancer T24 cells with chemically synthesized miR-490-5p mimics and inhibitor, respectively. RESULTS We found that overexpression of miR-490-5p in T24 cells could inhibit cell proliferation and invasion and induce cell apoptosis. Conversely, suppression of miR-490-5p expression induced cell proliferation and invasion, while it inhibited cell apoptosis. In addition, our bioinformatics prediction and experimental data showed that c-FOS was a potential target of miR-490-5p. The expression level of c-FOS was significantly decreased after miR-490-5p overexpression and significantly increased after miR-490-5p suppression, indicating that c-FOS was a target of miR-490-5p. CONCLUSIONS These findings suggest that miR-490-5p is a novel tumor suppressor, contributing to the carcinogenesis of bladder cancer by targeting c-FOS.
Collapse
Affiliation(s)
- Gongbin Lan
- Department of Kidney Transplantation, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Luoyan Yang
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xubiao Xie
- Department of Kidney Transplantation, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Longkai Peng
- Department of Kidney Transplantation, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yi Wang
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
50
|
A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients. Sci Rep 2015; 5:10438. [PMID: 26039282 PMCID: PMC4453922 DOI: 10.1038/srep10438] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/13/2015] [Indexed: 01/01/2023] Open
Abstract
Although formalin fixed paraffin embedded (FFPE) tissue is a major biological source in cancer research, it is challenging to work with due to macromolecular fragmentation and nucleic acid crosslinking. Therefore, it is important to characterise the quality of data that can be obtained from FFPE samples. We have compared three independent platforms (next generation sequencing, microarray and NanoString) for profiling microRNAs (miRNAs) using clinical FFPE samples from hepatoblastoma (HB) patients. The number of detected miRNAs ranged from 228 to 345 (median=294) using the next generation sequencing platform, whereas 79 to 125 (median=112) miRNAs were identified using microarrays in three HB samples, including technical replicates. NanoString identified 299 to 372 miRNAs in two samples. Between the platforms, we observed high reproducibility and significant levels of shared detection. However, for commonly detected miRNAs, a strong correlation between platforms was not observed. Analysis of 10 additional HB samples with NanoString identified significantly overlapping miRNA expression profiles, and an alternative pattern was identified in a poorly differentiated HB with an aggressive phenotype. This investigation serves as a roadmap for future studies investigating miRNA expression in clinical FFPE samples, and as a guideline for the selection of an appropriate platform.
Collapse
|