1
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Zhang G, Zhu Y, Tan Y, Chen B, Shan S, Zhang G, Lu J. Higher expression of pseudouridine synthase 7 promotes non-small cell lung cancer progression and suggests a poor prognosis. J Cardiothorac Surg 2023; 18:222. [PMID: 37420297 DOI: 10.1186/s13019-023-02332-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/29/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Lung cancer is currently the second most common cancer, and non-small cell lung cancer accounts for about 85% of cases. NSCLC has not been studied for pseudouridine synthase 7 (PUS), a member of the PUS family that is associated with cancer development. Here, we focused on the role and clinical significance of PUS7 in non-small cell lung cancer. AIM To explore the role of PUS7 in NSCLC and its clinical significance. METHODS We downloaded datasets from the TCGA database and CPTAC database. In normal bronchial epithelial cells as well as NSCLC cell lines, RT-PCR and Western blot were used to quantify PUS7 expression. The role of PUS7 in NSCLC has been investigated by CCK8, migration assay, migration assay, and flow cytometry. PUS7 expression in tumor tissues was detected by immunohistochemical staining, and we evaluated the influence of PUS7 expression on the prognosis of NSCLC patients after surgery using Cox regression analysis, both univariate and multivariate. RESULTS NSCLC cell lines and tissues expressed high levels of PUS7, and PUS7 was found to influence the proliferation, migration, and invasion of cancer cells without affecting their apoptosis. There was a worse prognosis for NSCLC patients who have higher PUS7 expression, suggesting that PUS7 was an independent indicator of prognosis (P = .05).
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Affiliation(s)
- Guihong Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd street, No. 58, Guangzhou, Guangdong, 510080, China
| | - Yongde Zhu
- Emergency Department, Hainan Province Nongken Sanya Hospital, Jiefang 4th Road, No. 1154, Sanya, Hainan, 571159, China
| | - Yonghuang Tan
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd street, No. 58, Guangzhou, Guangdong, 510080, China
| | - Biao Chen
- Department of Thoracic Surgery, Cancer Center, Sun Yat-sen University, Dongfeng East Road, No. 651, Guangzhou, Guangdong, 510060, China
| | - Shichao Shan
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd street, No. 58, Guangzhou, Guangdong, 510080, China
| | - Gengyu Zhang
- First School of Clinical Medicine, Guangdong Medical University, Wenming East Road, No. 2, Zhanjiang, Guangdong, 524023, China
| | - Jianjun Lu
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd street, No. 58, Guangzhou, Guangdong, 510080, China.
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2
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Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2023:10.1007/s12033-023-00792-1. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Cellular RNAs, both coding and noncoding are adorned by > 100 chemical modifications, which impact various facets of RNA metabolism and gene expression. Very often derailments in these modifications are associated with a plethora of human diseases. One of the most oldest of such modification is pseudouridylation of RNA, wherein uridine is converted to a pseudouridine (Ψ) via an isomerization reaction. When discovered, Ψ was referred to as the 'fifth nucleotide' and is chemically distinct from uridine and any other known nucleotides. Experimental evidence accumulated over the past six decades, coupled together with the recent technological advances in pseudouridine detection, suggest the presence of pseudouridine on messenger RNA, as well as on diverse classes of non-coding RNA in human cells. RNA pseudouridylation has widespread effects on cellular RNA metabolism and gene expression, primarily via stabilizing RNA conformations and destabilizing interactions with RNA-binding proteins. However, much remains to be understood about the RNA targets and their recognition by the pseudouridylation machinery, the regulation of RNA pseudouridylation, and its crosstalk with other RNA modifications and gene regulatory processes. In this review, we summarize the mechanism and molecular machinery involved in depositing pseudouridine on target RNAs, molecular functions of RNA pseudouridylation, tools to detect pseudouridines, the role of RNA pseudouridylation in human diseases like cancer, and finally, the potential of pseudouridine to serve as a biomarker and as an attractive therapeutic target.
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Affiliation(s)
- Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Kumar Pranav Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India.
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3
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Barozzi C, Zacchini F, Corradini AG, Morara M, Serra M, De Sanctis V, Bertorelli R, Dassi E, Montanaro L. Alterations of ribosomal RNA pseudouridylation in human breast cancer. NAR Cancer 2023; 5:zcad026. [PMID: 37260601 PMCID: PMC10227372 DOI: 10.1093/narcan/zcad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and they are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.
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Affiliation(s)
- Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Federico Zacchini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Angelo Gianluca Corradini
- Unit of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Monica Morara
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Margherita Serra
- Unit of Breast Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
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4
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Keszthelyi TM, Tory K. The importance of pseudouridylation: human disorders related to the fifth nucleoside. Biol Futur 2023:10.1007/s42977-023-00158-3. [PMID: 37000312 DOI: 10.1007/s42977-023-00158-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Pseudouridylation is one of the most abundant RNA modifications in eukaryotes, making pseudouridine known as the "fifth nucleoside." This highly conserved alteration affects all non-coding and coding RNA types. Its role and importance have been increasingly widely researched, especially considering that its absence or damage leads to serious hereditary diseases. Here, we summarize the human genetic disorders described to date that are related to the participants of the pseudouridylation process.
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Affiliation(s)
| | - Kálmán Tory
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
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5
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Zhang Q, Liu X, Zou Z, Zhou B. Evidence from a meta-analysis for the prognostic and clinicopathological importance of DKC1 in malignancies. Future Oncol 2023; 19:473-484. [PMID: 36876511 DOI: 10.2217/fon-2022-1125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Aim: We conducted a meta-analysis to evaluate the prognostic and clinicopathological relevance of DKC1 in various cancers. Methods: We searched Web of Science, Embase, PubMed, Wanfang and CNKI. Stata SE15.1 was used to calculate the hazard ratio and relative risk with 95% CIs to assess the possible correlations between DKC1 expression levels and overall and disease-free survival, as well as with clinicopathological parameters. Results: We included nine studies, with a total of 2574 patients. There was a meaningful link between elevated DKC1 and poorer disease-free (p < 0.001) and overall survival (p < 0.001). Also, it was linked to advanced tumor node metastasis stage (p = 0.005). Conclusion: High DKC1 expression was predictive of worse prognosis and poorer clinicopathological parameters.
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Affiliation(s)
- Qin Zhang
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.,Nanchang University, Nanchang, Jiangxi, China
| | - Xiaohan Liu
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.,Nanchang University, Nanchang, Jiangxi, China
| | - Zhenhong Zou
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Bin Zhou
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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6
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Zhang L, Zhang Y, Zhang S, Qiu L, Zhang Y, Zhou Y, Han J, Xie J. Translational Regulation by eIFs and RNA Modifications in Cancer. Genes (Basel) 2022; 13:2050. [PMID: 36360287 PMCID: PMC9690228 DOI: 10.3390/genes13112050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/04/2023] Open
Abstract
Translation is a fundamental process in all living organisms that involves the decoding of genetic information in mRNA by ribosomes and translation factors. The dysregulation of mRNA translation is a common feature of tumorigenesis. Protein expression reflects the total outcome of multiple regulatory mechanisms that change the metabolism of mRNA pathways from synthesis to degradation. Accumulated evidence has clarified the role of an increasing amount of mRNA modifications at each phase of the pathway, resulting in translational output. Translation machinery is directly affected by mRNA modifications, influencing translation initiation, elongation, and termination or altering mRNA abundance and subcellular localization. In this review, we focus on the translation initiation factors associated with cancer as well as several important RNA modifications, for which we describe their association with cancer.
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Affiliation(s)
- Linzhu Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- The Third People’s Hospital of Chengdu, Clinical College of Southwest Jiao Tong University, Chengdu 610014, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Zhou
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiang Xie
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- The Third People’s Hospital of Chengdu, Clinical College of Southwest Jiao Tong University, Chengdu 610014, China
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7
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Different Approaches for the Profiling of Cancer Pathway-Related Genes in Glioblastoma Cells. Int J Mol Sci 2022; 23:ijms231810883. [PMID: 36142793 PMCID: PMC9504477 DOI: 10.3390/ijms231810883] [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: 08/05/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
Deregulation of signalling pathways that regulate cell growth, survival, metabolism, and migration can frequently lead to the progression of cancer. Brain tumours are a large group of malignancies characterised by inter- and intratumoral heterogeneity, with glioblastoma (GBM) being the most aggressive and fatal. The present study aimed to characterise the expression of cancer pathway-related genes (n = 84) in glial tumour cell lines (A172, SW1088, and T98G). The transcriptomic data obtained by the qRT-PCR method were compared to different control groups, and the most appropriate control for subsequent interpretation of the obtained results was chosen. We analysed three widely used control groups (non-glioma cells) in glioblastoma research: Human Dermal Fibroblasts (HDFa), Normal Human Astrocytes (NHA), and commercially available mRNAs extracted from healthy human brain tissues (hRNA). The gene expression profiles of individual glioblastoma cell lines may vary due to the selection of a different control group to correlate with. Moreover, we present the original multicriterial decision making (MCDM) for the possible characterization of gene expression profiles. We observed deregulation of 75 genes out of 78 tested in the A172 cell line, while T98G and SW1088 cells exhibited changes in 72 genes. By comparing the delta cycle threshold value of the tumour groups to the mean value of the three controls, only changes in the expression of 26 genes belonging to the following pathways were identified: angiogenesis FGF2; apoptosis APAF1, CFLAR, XIAP; cellular senescence BM1, ETS2, IGFBP5, IGFBP7, SOD1, TBX2; DNA damage and repair ERCC5, PPP1R15A; epithelial to mesenchymal transition SNAI3, SOX10; hypoxia ADM, ARNT, LDHA; metabolism ATP5A1, COX5A, CPT2, PFKL, UQCRFS1; telomeres and telomerase PINX1, TINF2, TNKS, and TNKS2. We identified a human astrocyte cell line and normal human brain tissue as the appropriate control group for an in vitro model, despite the small sample size. A different method of assessing gene expression levels produced the same disparities, highlighting the need for caution when interpreting the accuracy of tumorigenesis markers.
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8
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Zacchini F, Venturi G, De Sanctis V, Bertorelli R, Ceccarelli C, Santini D, Taffurelli M, Penzo M, Treré D, Inga A, Dassi E, Montanaro L. Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence. Genome Biol 2022; 23:177. [PMID: 35996163 PMCID: PMC9394076 DOI: 10.1186/s13059-022-02746-3] [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: 12/23/2021] [Accepted: 08/11/2022] [Indexed: 12/05/2022] Open
Abstract
Background Dyskerin is a nuclear protein involved in H/ACA box snoRNA-guided uridine modification of RNA. In humans, its defective function is associated with cancer development and induces specific post-transcriptional alterations of gene expression. In this study, we seek to unbiasedly identify mRNAs regulated by dyskerin in human breast cancer-derived cells. Results We find that dyskerin depletion affects the expression and the association with polysomes of selected mRNA isoforms characterized by the retention of H/ACA box snoRNA-containing introns. These snoRNA retaining transcripts (snoRTs) are bound by dyskerin in the cytoplasm in the form of shorter 3′ snoRT fragments. We then characterize the whole cytoplasmic dyskerin RNA interactome and find both H/ACA box snoRTs and protein-coding transcripts which may be targeted by the snoRTs’ guide properties. Since a fraction of these protein-coding transcripts is involved in the nuclear hormone receptor binding, we test to see if this specific activity is affected by dyskerin. Obtained results indicate that dyskerin dysregulation may alter the dependence on nuclear hormone receptor ligands in breast cancer cells. These results are paralleled by consistent observations on the outcome of primary breast cancer patients stratified according to their tumor hormonal status. Accordingly, experiments in nude mice show that the reduction of dyskerin levels in estrogen-dependent cells favors xenograft development in the absence of estrogen supplementation. Conclusions Our work suggests a cytoplasmic function for dyskerin which could affect mRNA post-transcriptional networks relevant for nuclear hormone receptor functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02746-3.
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Affiliation(s)
- Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Giulia Venturi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Veronica De Sanctis
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Roberto Bertorelli
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Claudio Ceccarelli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Donatella Santini
- Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Mario Taffurelli
- Unità Operativa di Chirurgia Senologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy
| | - Marianna Penzo
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Davide Treré
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Alberto Inga
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Erik Dassi
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy. .,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.
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9
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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10
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Barozzi C, Zacchini F, Asghar S, Montanaro L. Ribosomal RNA Pseudouridylation: Will Newly Available Methods Finally Define the Contribution of This Modification to Human Ribosome Plasticity? Front Genet 2022; 13:920987. [PMID: 35719370 PMCID: PMC9198423 DOI: 10.3389/fgene.2022.920987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
In human rRNA, at least 104 specific uridine residues are modified to pseudouridine. Many of these pseudouridylation sites are located within functionally important ribosomal domains and can influence ribosomal functional features. Until recently, available methods failed to reliably quantify the level of modification at each specific rRNA site. Therefore, information obtained so far only partially explained the degree of regulation of pseudouridylation in different physiological and pathological conditions. In this focused review, we provide a summary of the methods that are now available for the study of rRNA pseudouridylation, discussing the perspectives that newly developed approaches are offering.
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Affiliation(s)
- Chiara Barozzi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Sidra Asghar
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- *Correspondence: Lorenzo Montanaro,
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11
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Liu W, Jiang H, Li Y. Silencing circular RNA-friend leukemia virus integration 1 restrained malignancy of CC cells and oxaliplatin resistance by disturbing dyskeratosis congenita 1. Open Life Sci 2022; 17:563-576. [PMID: 35647294 PMCID: PMC9123302 DOI: 10.1515/biol-2022-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
Circular-RNA friend leukemia virus integration 1 (circ-FLI1; hsa_circ_0000370) is a noninvasive biomarker for the diagnosis of colon carcinoma (CC). Herein, we intended to investigate its functions and competing endogenous RNA (ceRNA) mechanisms in CC cells. In terms of expression status, circ-FLI1 was abnormally upregulated in CC patients’ tumors and cells, paralleled with DKC1 upregulation and miR-197-3p downregulation. Most strikingly, there was a direct target relationship between miR-197-3p and circ-FLI1 or DKC1 based on the starbase database, dual-luciferase reporter assay, and RNA immunoprecipitation. Functionally, the colony formation assay, MTS method, fluorescence-activated cell sorting method, cell cycle and apoptosis assays, and transwell assays were performed, and the results revealed that interfering circ-FLI1 and re-expressing miR-197-3p could restrict colony formation, cell viability, cell cycle progression, and migration/invasion of CC cells with apoptosis rate elevation; besides, they promoted oxaliplatin (L-OHP)-induced cell viability inhibition. Furthermore, there were counteractive effects between circ-FLI1 silencing and miR-197-3p depletion, miR-197-3p overexpression and DKC1 restoration on regulating CC cell functions and L-OHP resistance. With a xenograft tumor model, the anti-growth role of circ-FLI1 silencing was also found in vivo with or without L-OHP treatment. Collectively, we demonstrated that circ-FLI1 might confer L-OHP resistance and malignant progression of CC presumably through the circ-FLI1/miR-197-3p/DKC1 ceRNA axis.
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Affiliation(s)
- Weipeng Liu
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
| | - Hong Jiang
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
| | - Yuanqiang Li
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
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12
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Dyskerin Downregulation Can Induce ER Stress and Promote Autophagy via AKT-mTOR Signaling Deregulation. Biomedicines 2022; 10:biomedicines10051092. [PMID: 35625829 PMCID: PMC9138296 DOI: 10.3390/biomedicines10051092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
Dyskerin is an evolutionarily conserved nucleolar protein implicated in a wide range of fundamental biological roles, including telomere maintenance and ribosome biogenesis. Germline mutations of DKC1, the human gene encoding dyskerin, cause the hereditary disorders known as X-linked dyskeratosis congenita (X-DC). Moreover, dyskerin is upregulated in several cancers. Due to the pleiotropic functions of dyskerin, the X-DC clinical features overlap with those of both telomeropathies and ribosomopathies. In this paper, we evaluate the telomerase-independent effects of dyskerin depletion on cellular physiology by using inducible DCK1 knockdown. This system allows the downregulation of DKC1 expression within a short timeframe. We report that, in these cellular systems, dyskerin depletion induces the accumulation of unfolded/misfolded proteins in the endoplasmic reticulum, which in turn induces the activation of the PERK branch of the unfolded protein response. We also demonstrate that the PERK-eIF2a-ATF4-CHOP signaling pathway, activated by dyskerin downregulation, triggers a functional autophagic flux through the inhibition of the PI3K/AKT/mTOR pathway. By revealing a novel unpredicted connection between the loss of dyskerin, autophagy and UPR, our results establish a firm link between the lowering of dyskerin levels and the activation of the ER stress response, that plays a key role in the pathogenesis of several diseases.
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13
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Role of main RNA modifications in cancer: N 6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct Target Ther 2022; 7:142. [PMID: 35484099 PMCID: PMC9051163 DOI: 10.1038/s41392-022-01003-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N6-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.
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14
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Xu Y, Zhang M, Zhang Q, Yu X, Sun Z, He Y, Guo W. Role of Main RNA Methylation in Hepatocellular Carcinoma: N6-Methyladenosine, 5-Methylcytosine, and N1-Methyladenosine. Front Cell Dev Biol 2021; 9:767668. [PMID: 34917614 PMCID: PMC8671007 DOI: 10.3389/fcell.2021.767668] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
RNA methylation is considered a significant epigenetic modification, a process that does not alter gene sequence but may play a necessary role in multiple biological processes, such as gene expression, genome editing, and cellular differentiation. With advances in RNA detection, various forms of RNA methylation can be found, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), and 5-methylcytosine (m5C). Emerging reports confirm that dysregulation of RNA methylation gives rise to a variety of human diseases, particularly hepatocellular carcinoma. We will summarize essential regulators of RNA methylation and biological functions of these modifications in coding and noncoding RNAs. In conclusion, we highlight complex molecular mechanisms of m6A, m5C, and m1A associated with hepatocellular carcinoma and hope this review might provide therapeutic potent of RNA methylation to clinical research.
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Affiliation(s)
- Yating Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Menggang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Qiyao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Zongzong Sun
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
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15
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Ranhem C, Larsson GL, Lindqvist D, Sorbe B, Karlsson MG, Farnebo M, Hellman K, Kovaleska L, Kashuba E, Andersson S. Evaluation of dyskerin expression and the Cajal body protein WRAP53β as potential prognostic markers for patients with primary vaginal carcinoma. Oncol Lett 2021; 23:30. [PMID: 34868367 PMCID: PMC8630817 DOI: 10.3892/ol.2021.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/30/2021] [Indexed: 11/06/2022] Open
Abstract
Primary vaginal cancer (PVC) is a rare gynaecological malignancy, which, at present, lacks appropriate biomarkers for prognosis. The proteins dyskerin and WD repeat containing antisense to TP53 (WRAP53β), both of which exert their functions in the telomerase holoenzyme complex, have been shown to be upregulated in different cancer types. These proteins have also been proposed as prognostic markers in some types of cancer. The aim of the present study was to examine the expression patterns of dyskerin and WRAP53β in patients with PVC. Moreover, as part of a search for effective biomarkers to evaluate prognosis in PVC, the expression of these two proteins and their potential association with clinical variables and survival were also evaluated. The expression of dyskerin and WRAP53β was assessed in PVC tumour samples from 68 patients using immunohistochemistry. The majority of tumour samples showed low and moderate expression levels of dyskerin. Upregulation of dyskerin in tumour samples was significantly associated with a shorter survival time and a poorer cancer-specific survival rate. WRAP53β was also expressed in most of the cells but was not significantly associated with clinical variables or survival. This study demonstrates that upregulation of dyskerin is significantly associated with poor prognosis. Thus, dyskerin may serve as a promising prognostic marker and a potential putative therapeutic target in PVC.
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Affiliation(s)
- Cecilia Ranhem
- Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.,Centre for Clinical Research Region Västmanland, Uppsala University, Västmanlands Hospital Västerås, 721 89 Västerås, Sweden
| | - Gabriella Lillsunde Larsson
- School of Health and Medical Sciences, Örebro University, Campus USÖ, 701 82 Örebro, Sweden.,Department of Laboratory Medicine, Örebro University Hospital, 701 85 Örebro, Sweden
| | - David Lindqvist
- Department of Radiation Sciences, Umeå Universitet, 901 87 Umeå, Sweden
| | - Bengt Sorbe
- Department of Oncology, Örebro University Hospital, 701 85 Örebro, Sweden
| | - Mats G Karlsson
- School of Medical Sciences, Örebro University, 701 85 Örebro, Sweden
| | - Marianne Farnebo
- Department of Bioscience and Nutrition, Karolinska Institutet, 141 83 Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kristina Hellman
- Department of Oncology-Pathology, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Larysa Kovaleska
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of National Academy of Sciences of Ukraine, 03022 Kiev, Ukraine
| | - Elena Kashuba
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of National Academy of Sciences of Ukraine, 03022 Kiev, Ukraine.,Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sonia Andersson
- Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
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16
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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17
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Berdasco M, Esteller M. Towards a druggable epitranscriptome: Compounds that target RNA modifications in cancer. Br J Pharmacol 2021; 179:2868-2889. [PMID: 34185879 DOI: 10.1111/bph.15604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022] Open
Abstract
Epitranscriptomics is an exciting emerging area that studies biochemical modifications of RNA. The field has been opened up by the technical efforts of the last decade to characterize and quantify RNA modifications, and this has led to a map of post-transcriptional RNA marks in normal cell fate and development. However, the scientific interest has been fuelled by the discovery of aberrant epitranscriptomes associated with human diseases, mainly cancer. The challenge is now to see whether epitrancriptomics offers mechanisms that can be effectively targeted by low MW compounds and are thus druggable. In this review, we will describe the principal RNA modifications (with a focus on mRNA), summarize the latest scientific evidence of their dysregulation in cancer and provide an overview of the state-of-the-art drug discovery to target the epitranscriptome. Finally, we will discuss the principal challenges in the field of chemical biology and drug development to increase the potential of targeted-RNA for clinical benefit.
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Affiliation(s)
- María Berdasco
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC), Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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18
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Destefanis E, Avşar G, Groza P, Romitelli A, Torrini S, Pir P, Conticello SG, Aguilo F, Dassi E. A mark of disease: how mRNA modifications shape genetic and acquired pathologies. RNA (NEW YORK, N.Y.) 2021; 27:367-389. [PMID: 33376192 PMCID: PMC7962492 DOI: 10.1261/rna.077271.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). In mRNAs the deposition, removal, and recognition of chemical marks by writers, erasers and readers influence their structure, localization, stability, and translation. In turn, this modulates key molecular and cellular processes such as RNA metabolism, cell cycle, apoptosis, and others. Unsurprisingly, given their relevance for cellular and organismal functions, alterations of epitranscriptomic marks have been observed in a broad range of human diseases, including cancer, neurological and metabolic disorders. Here, we will review the major types of mRNA modifications and editing processes in conjunction with the enzymes involved in their metabolism and describe their impact on human diseases. We present the current knowledge in an updated catalog. We will also discuss the emerging evidence on the crosstalk of epitranscriptomic marks and what this interplay could imply for the dynamics of mRNA modifications. Understanding how this complex regulatory layer can affect the course of human pathologies will ultimately lead to its exploitation toward novel epitranscriptomic therapeutic strategies.
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Affiliation(s)
- Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
| | - Gülben Avşar
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Paula Groza
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Antonia Romitelli
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Serena Torrini
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Pınar Pir
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Silvestro G Conticello
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Francesca Aguilo
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
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19
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Affiliation(s)
- Seung Hun Han
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
| | - Junho Choe
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
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20
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Akincilar SC, Chan CHT, Ng QF, Fidan K, Tergaonkar V. Non-canonical roles of canonical telomere binding proteins in cancers. Cell Mol Life Sci 2021; 78:4235-4257. [PMID: 33599797 PMCID: PMC8164586 DOI: 10.1007/s00018-021-03783-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/28/2020] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
Reactivation of telomerase is a major hallmark observed in 90% of all cancers. Yet paradoxically, enhanced telomerase activity does not correlate with telomere length and cancers often possess short telomeres; suggestive of supplementary non-canonical roles that telomerase might play in the development of cancer. Moreover, studies have shown that aberrant expression of shelterin proteins coupled with their release from shortening telomeres can further promote cancer by mechanisms independent of their telomeric role. While targeting telomerase activity appears to be an attractive therapeutic option, this approach has failed in clinical trials due to undesirable cytotoxic effects on stem cells. To circumvent this concern, an alternative strategy could be to target the molecules involved in the non-canonical functions of telomeric proteins. In this review, we will focus on emerging evidence that has demonstrated the non-canonical roles of telomeric proteins and their impact on tumorigenesis. Furthermore, we aim to address current knowledge gaps in telomeric protein functions and propose future research approaches that can be undertaken to achieve this.
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Affiliation(s)
- Semih Can Akincilar
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61, Biopolis Drive, Singapore, 138673, Singapore
| | - Claire Hian Tzer Chan
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61, Biopolis Drive, Singapore, 138673, Singapore
| | - Qin Feng Ng
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61, Biopolis Drive, Singapore, 138673, Singapore
| | - Kerem Fidan
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61, Biopolis Drive, Singapore, 138673, Singapore
| | - Vinay Tergaonkar
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61, Biopolis Drive, Singapore, 138673, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
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21
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Nombela P, Miguel-López B, Blanco S. The role of m 6A, m 5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities. Mol Cancer 2021; 20:18. [PMID: 33461542 PMCID: PMC7812662 DOI: 10.1186/s12943-020-01263-w] [Citation(s) in RCA: 243] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.
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Affiliation(s)
- Paz Nombela
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, 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, 37007, Salamanca, Spain. .,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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22
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Alnafakh R, Saretzki G, Midgley A, Flynn J, Kamal AM, Dobson L, Natarajan P, Stringfellow H, Martin-Hirsch P, DeCruze SB, Coupland SE, Hapangama DK. Aberrant Dyskerin Expression Is Related to Proliferation and Poor Survival in Endometrial Cancer. Cancers (Basel) 2021; 13:cancers13020273. [PMID: 33450922 PMCID: PMC7828388 DOI: 10.3390/cancers13020273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Telomeres are the protective caps at the ends of chromosomes, and they are maintained by an enzyme called telomerase. Telomerase activity allows rapid reproduction of the cells (proliferation) of the lining of the womb (endometrium). Telomerase levels are high in cancers in general, including in endometrial cancer. Dyskerin is one of the main components of the telomerase enzyme. While the other main components of telomerase have been studied in endometrial cancer, there are no previous studies on dyskerin in the endometrium. Our study shows that dyskerin levels are significantly lower in endometrial cancer and levels are linked to the survival of women. Experimentally increasing dyskerin protein in endometrial cells in the laboratory reduces the rate of cell proliferation. Consequently, we propose that dyskerin may be a regulator of endometrial cancer cell proliferation, and further studies are required to test if it can be targeted to develop new therapies for endometrial cancer. Abstract Dyskerin is a core-component of the telomerase holo-enzyme, which elongates telomeres. Telomerase is involved in endometrial epithelial cell proliferation. Most endometrial cancers (ECs) have high telomerase activity; however, dyskerin expression in human healthy endometrium or in endometrial pathologies has not been investigated yet. We aimed to examine the expression, prognostic relevance, and functional role of dyskerin in human EC. Endometrial samples from a cohort of 175 women were examined with immunohistochemistry, immunoblotting, and qPCR. The EC cells were transfected with Myc-DDK-DKC1 plasmid and the effect of dyskerin overexpression on EC cell proliferation was assessed by flow cytometry. Human endometrium expresses dyskerin (DKC1) and dyskerin protein levels are significantly reduced in ECs when compared with healthy postmenopausal endometrium. Low dyskerin immunoscores were potentially associated with worse outcomes, suggesting a possible prognostic relevance. Cancer Genome Atlas (TCGA) ECs dataset (n = 589) was also interrogated. The TCGA dataset further confirmed changes in DKC1 expression in EC with prognostic significance. Transient dyskerin overexpression had a negative effect on EC cell proliferation. Our data demonstrates a role for dyskerin in normal endometrium for the first time and confirms aberrant expression with possible prognostic relevance in EC. Interventions aimed at modulating dyskerin levels may provide novel therapeutic options in EC.
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Affiliation(s)
- Rafah Alnafakh
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Department of Pathology, Al-Hilla Teaching Hospital, Babil, Iraq
| | - Gabriele Saretzki
- Biosciences Institute, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne NE4 5PL, UK;
| | - Angela Midgley
- Experimental Arthritis Treatment Centre for Children, Institute in the Park, Department of Women’s and Children’s Health, University of Liverpool, Liverpool L12 2AP, UK;
| | | | - Areege M. Kamal
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Pathology Department, Oncology Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Lucy Dobson
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
| | - Purushothaman Natarajan
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
| | - Helen Stringfellow
- Lancashire Teaching Hospital NHS Trust, Preston PR2 9HT, UK; (H.S.); (P.M.-H.)
| | | | - Shandya B. DeCruze
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
| | - Sarah E. Coupland
- Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK;
| | - Dharani K. Hapangama
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Correspondence:
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23
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Stockert JA, Weil R, Yadav KK, Kyprianou N, Tewari AK. Pseudouridine as a novel biomarker in prostate cancer. Urol Oncol 2021; 39:63-71. [PMID: 32712138 PMCID: PMC7880613 DOI: 10.1016/j.urolonc.2020.06.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 01/25/2023]
Abstract
Epitranscriptomic analysis has recently led to the profiling of modified nucleosides in cancer cell biological matrices, helping to elucidate their functional roles in cancer and reigniting interest in exploring their use as potential markers of cancer development and progression. Pseudouridine, one of the most well-known and the most abundant of the RNA nucleotide modifications, is the C5-glycoside isomer of uridine and its distinctive physiochemical properties allows it to perform many essential functions. Pseudouridine functionally (a) confers rigidity to local RNA structure by enhancing RNA stacking, engaging in a cooperative effect on neighboring nucleosides that overall contributes to RNA stabilization (b) refines the structure of tRNAs, which influences their decoding activity (c) facilitates the accuracy of decoding and proofreading during translation and efficiency of peptide bond formation, thus collectively improving the fidelity of protein biosynthesis and (e) dynamically regulates mRNA coding and translation. Biochemical synthesis of pseudouridine is carried out by pseudouridine synthases. In this review we discuss the evidence supporting an association between elevated pseudouridine levels with the incidence and progression of human prostate cancer and the translational significance of the value of this modified nucleotide as a novel biomarker in prostate cancer progression to advanced disease.
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Affiliation(s)
- Jennifer A Stockert
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Rachel Weil
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Kamlesh K Yadav
- Department of Engineering Medicine, Texas A&M Health Science Center College of Medicine, Houston, TX 77030
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, NY 10029.
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
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DKC1 Overexpression Induces a More Aggressive Cellular Behavior and Increases Intrinsic Ribosomal Activity in Immortalized Mammary Gland Cells. Cancers (Basel) 2020; 12:cancers12123512. [PMID: 33255756 PMCID: PMC7760958 DOI: 10.3390/cancers12123512] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Dyskerin is a nucleolar protein involved in the modification and processing of ribosomal RNA and in the stabilization of the telomerase RNA component. In several human tumors, including breast cancer, dyskerin overexpression is found related to patients’ worse prognosis. Our aim was to study this phenomenon at the molecular and cellular levels. We firstly confirmed the correlation between high dyskerin expression with patients’ shorter survival. Then, through the generation of cellular models of increased dyskerin expression, we found that increasing dyskerin levels conferred a more aggressive phenotype and increased intrinsic ribosomal activity only in cells derived from normal breast epithelium. Our study provides evidence on the prognostic and bio-pathological relevance of the overexpression of dyskerin in breast carcinoma. A possible mechanistic explanation of the effects of dyskerin overexpression, involving specific ribosomal RNA modification and consequent increased ribosomal activity, is also provided. Abstract Dyskerin is a nucleolar protein involved in the small nucleolar RNA (snoRNA)-guided pseudouridylation of specific uridines on ribosomal RNA (rRNA), and in the stabilization of the telomerase RNA component (hTR). Loss of function mutations in DKC1 causes X-linked dyskeratosis congenita, which is characterized by a failure of proliferating tissues and increased susceptibility to cancer. However, several tumors show dyskerin overexpression. We observed that patients with primary breast cancers with high dyskerin levels are more frequently characterized by shorter survival rates and positive lymph node status than those with tumors with a lower dyskerin expression. To functionally characterize the effects of high dyskerin expression, we generated stably overexpressing DKC1 models finding that increased dyskerin levels conferred a more aggressive cellular phenotype in untransformed immortalized MCF10A cells. Contextually, DKC1 overexpression led to an upregulation of some snoRNAs, including SNORA67 and a significantly increased U1445 modification on 18S rRNA, the known target of SNORA67. Lastly, we found that dyskerin overexpression strongly enhanced the synthetic activity of ribosomes increasing translational efficiency in MCF10A. Altogether, our results indicate that dyskerin may sustain the neoplastic phenotype from an early stage in breast cancer endowing ribosomes with an augmented translation efficiency.
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De Nicola I, Guerrieri AN, Penzo M, Ceccarelli C, De Leo A, Trerè D, Montanaro L. Combined expression levels of KDM2A and KDM2B correlate with nucleolar size and prognosis in primary breast carcinomas. Histol Histopathol 2020; 35:1181-1187. [PMID: 32901907 DOI: 10.14670/hh-18-248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ribosome biogenesis is a fine-tuned cellular process and its deregulation is linked to cancer progression: tumors characterized by an intense ribosome biogenesis often display a more aggressive behavior. Ribosomal RNA (rRNA) synthesis is controlled at several levels, the higher one being the epigenetic regulation of the condensation of chromatin portions containing rRNA genes. KDM2A and KDM2B (Lysine (K)-specific demethylase 2A / B) are histone demethylases modulating the accessibility of ribosomal genes, thereby regulating their transcription. Both enzymes are able to demethylate lysins at relevant sites (e.g. K4, K36) on histone H3. We previously demonstrated that KDM2B is one of the factors regulating ribosome biogenesis in human breast cancer. In this study we aimed to define the combined contribution of KDM2A and KDM2B to breast cancer outcome. KDM2A and KDM2B mRNA levels, nucleolar area as a marker of ribosome biogenesis, and patients' prognosis were retrospectively assessed in a series of primary breast carcinomas. We observed that tumors characterized by reduced levels of both KDM2A and KDM2B displayed a particularly aggressive clinical behavior and increased nucleolar size. Our results suggest that KDM2A and KDM2B may cooperate in regulating ribosome biogenesis thus influencing the biological behavior and clinical outcome of human breast cancers.
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Affiliation(s)
- Igor De Nicola
- S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Ania Naila Guerrieri
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Marianna Penzo
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Claudio Ceccarelli
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Antonio De Leo
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy.,Pathology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Davide Trerè
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty medicine (DIMES), Alma Mater Studiorum - University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum - University of Bologna, Bologna, Italy.
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26
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Elsharawy KA, Mohammed OJ, Aleskandarany MA, Hyder A, El-Gammal HL, Abou-Dobara MI, Green AR, Dalton LW, Rakha EA. The nucleolar-related protein Dyskerin pseudouridine synthase 1 (DKC1) predicts poor prognosis in breast cancer. Br J Cancer 2020; 123:1543-1552. [PMID: 32868896 PMCID: PMC7653035 DOI: 10.1038/s41416-020-01045-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022] Open
Abstract
Background Hypertrophy of the nucleolus is a distinctive cytological feature of malignant cells and corresponds to aggressive behaviour. This study aimed to identify the key gene associated with nucleolar prominence (NP) in breast cancer (BC) and determine its prognostic significance. Methods From The Cancer Genome Atlas (TCGA) cohort, digital whole slide images identified cancers having NP served as label and an information theory algorithm was applied to find which mRNA gene best explained NP. Dyskerin Pseudouridine Synthase 1 (DKC1) was identified. DKC1 expression was assessed using mRNA data of Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1980) and TCGA (n = 855). DKC1 protein expression was assessed using immunohistochemistry in Nottingham BC cohort (n = 943). Results Nuclear and nucleolar expressions of DKC1 protein were significantly associated with higher tumour grade (p < 0.0001), high nucleolar score (p < 0.001) and poor Nottingham Prognostic Index (p < 0.0001). High DKC1 expression was associated with shorter BC-specific survival (BCSS). In multivariate analysis, DKC1 mRNA and protein expressions were independent risk factors for BCSS (p < 0.01). Conclusion DKC1 expression is strongly correlated with NP and its overexpression in BC is associated with unfavourable clinicopathological characteristics and poor outcome. This has been a detailed example in the correlation of phenotype with genotype.
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Affiliation(s)
- Khloud A Elsharawy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.,Faculty of Science, Damietta University, Damietta, Egypt
| | - Omar J Mohammed
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Mohammed A Aleskandarany
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Ayman Hyder
- Faculty of Science, Damietta University, Damietta, Egypt
| | | | | | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Leslie W Dalton
- Department of Histopathology, South Austin Hospital, Austin, TX, USA
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.
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27
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Janin M, Coll-SanMartin L, Esteller M. Disruption of the RNA modifications that target the ribosome translation machinery in human cancer. Mol Cancer 2020; 19:70. [PMID: 32241281 PMCID: PMC7114786 DOI: 10.1186/s12943-020-01192-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic changes deregulate RNA and protein expression in cancer cells. In this regard, tumors exhibit an abnormal proteome in comparison to the corresponding normal tissues. Translation control is a crucial step in the regulation of gene expression regulation under normal and pathological conditions that ultimately determines cellular fate. In this context, evidence shows that transfer and ribosomal RNA (tRNA and rRNA) modifications affect the efficacy and fidelity of translation. The number of RNA modifications increases with the complexity of organisms, suggesting an evolutionary diversification of the possibilities for fine-tuning the functions of coding and non-coding RNAs. In this review, we focus on alterations of modifications of transfer and ribosomal RNA that affect translation in human cancer. This variation in the RNA modification status can be the result of altered modifier expression (writers, readers or erasers), but also due to components of the machineries (C/D or H/ACA boxes) or alterations of proteins involved in modifier expression. Broadening our understanding of the mechanisms by which site-specific modifications modulate ribosome activity in the context of tumorigenesis will enable us to enrich our knowledge about how ribosomes can influence cell fate and form the basis of new therapeutic opportunities.
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Affiliation(s)
- Maxime Janin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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28
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Xu Y, Ruggero D. The Role of Translation Control in Tumorigenesis and Its Therapeutic Implications. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033420] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As a convergent mechanism downstream of most oncogenic signals, control of mRNA translation has emerged as a key driver in establishing and tuning gene expression at specific steps in cancer development. Translation control is the most energetically expensive molecular process in the cell that needs to be modulated upon adaption to limited cellular resources, such as cellular stress. It thereby serves as the Achilles’ heel for cancer cells, particularly in response to changes in the microenvironment as well as to nutrient and metabolic shifts characteristic of cancer cell growth and metastasis. In this review, we discuss emerging discoveries that reveal how cancer cells modulate the translation machinery to adapt to oncogenic stress, the mechanisms that guide mRNA translation specificity in cancer, and how this selective mode of gene regulation provides advantages for cancer progression. We also provide an overview of promising preclinical and clinical efforts aimed at targeting the unique vulnerabilities of cancer cells that rely on the remodeling of mRNA translation for their infinite growth and survival.
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Affiliation(s)
- Yichen Xu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
| | - Davide Ruggero
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
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29
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Huang H, Weng H, Deng X, Chen J. RNA Modifications in Cancer: Functions, Mechanisms, and Therapeutic Implications. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033357] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over 170 chemical modifications have been identified in protein-coding and noncoding RNAs and shown to exhibit broad impacts on gene expression. Dysregulation of RNA modifications caused by aberrant expression of or mutations in RNA modifiers aberrantly reprograms the epitranscriptome and skews global gene expression, which in turn leads to tumorigenesis and drug resistance. Here we review current knowledge of the functions and underlying mechanisms of aberrant RNA modifications in human cancers, particularly several common RNA modifications, including N6-methyladenosine (m6A), A-to-I editing, pseudouridine (ψ), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), N1-methyladenosine (m1A), and N4-acetylcytidine (ac4C), providing insights into therapeutic implications of targeting RNA modifications and the associated machineries for cancer therapy.
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Affiliation(s)
- Huilin Huang
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Hengyou Weng
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Xiaolan Deng
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
| | - Jianjun Chen
- Department of Systems Biology and The Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California 91010, USA
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30
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Targeting the Human 80S Ribosome in Cancer: From Structure to Function and Drug Design for Innovative Adjuvant Therapeutic Strategies. Cells 2020; 9:cells9030629. [PMID: 32151059 PMCID: PMC7140421 DOI: 10.3390/cells9030629] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
The human 80S ribosome is the cellular nucleoprotein nanomachine in charge of protein synthesis that is profoundly affected during cancer transformation by oncogenic proteins and provides cancerous proliferating cells with proteins and therefore biomass. Indeed, cancer is associated with an increase in ribosome biogenesis and mutations in several ribosomal proteins genes are found in ribosomopathies, which are congenital diseases that display an elevated risk of cancer. Ribosomes and their biogenesis therefore represent attractive anti-cancer targets and several strategies are being developed to identify efficient and specific drugs. Homoharringtonine (HHT) is the only direct ribosome inhibitor currently used in clinics for cancer treatments, although many classical chemotherapeutic drugs also appear to impact on protein synthesis. Here we review the role of the human ribosome as a medical target in cancer, and how functional and structural analysis combined with chemical synthesis of new inhibitors can synergize. The possible existence of oncoribosomes is also discussed. The emerging idea is that targeting the human ribosome could not only allow the interference with cancer cell addiction towards protein synthesis and possibly induce their death but may also be highly valuable to decrease the levels of oncogenic proteins that display a high turnover rate (MYC, MCL1). Cryo-electron microscopy (cryo-EM) is an advanced method that allows the visualization of human ribosome complexes with factors and bound inhibitors to improve our understanding of their functioning mechanisms mode. Cryo-EM structures could greatly assist the foundation phase of a novel drug-design strategy. One goal would be to identify new specific and active molecules targeting the ribosome in cancer such as derivatives of cycloheximide, a well-known ribosome inhibitor.
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Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types. Cells 2020; 9:cells9020387. [PMID: 32046192 PMCID: PMC7072173 DOI: 10.3390/cells9020387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs involved in RNA modification and processing. Approximately half of the so far identified snoRNA genes map within the intronic regions of host genes, and their expression, as well as the expression of their host genes, is dependent on transcript splicing and maturation. Growing evidence indicates that mutations and/or deregulations that affect snoRNAs, as well as host genes, play a significant role in oncogenesis. Among the possible factors underlying snoRNA/host gene expression deregulation is copy number alteration (CNA). We analyzed the data available in The Cancer Genome Atlas database, relative to CNA and expression of 295 snoRNA/host gene couples in 10 cancer types, to understand whether the genetic or expression alteration of snoRNAs and their matched host genes would have overlapping trends. Our results show that, counterintuitively, copy number and expression alterations of snoRNAs and matched host genes are not necessarily coupled. In addition, some snoRNA/host genes are mutated and overexpressed recurrently in multiple cancer types. Our findings suggest that the differential contribution to cancer development of both snoRNAs and host genes should always be considered, and that snoRNAs and their host genes may contribute to cancer development in conjunction or independently.
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32
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Esteve-Puig R, Bueno-Costa A, Esteller M. Writers, readers and erasers of RNA modifications in cancer. Cancer Lett 2020; 474:127-137. [PMID: 31991154 DOI: 10.1016/j.canlet.2020.01.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 02/08/2023]
Abstract
Although cancer was originally considered a disease driven only by genetic mutations, it has now been proven that it is also an epigenetic disease driven by DNA hypermethylation-associated silencing of tumor suppressor genes and aberrant histone modifications. Very recently, a third component has emerged: the so-called epitranscriptome understood as the chemical modifications of RNA that regulate and alter the activity of RNA molecules. In this regard, the study of genetic and epigenetic disruption of the RNA-modifying proteins is gaining momentum in advancing our understanding of cancer biology. Furthermore, the development of epitranscriptomic anticancer drugs could lead to new promising and unexpected therapeutic strategies for oncology in the coming years.
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Affiliation(s)
- Rosaura Esteve-Puig
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Alberto Bueno-Costa
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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33
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Weeks SE, Metge BJ, Samant RS. The nucleolus: a central response hub for the stressors that drive cancer progression. Cell Mol Life Sci 2019; 76:4511-4524. [PMID: 31338556 PMCID: PMC6841648 DOI: 10.1007/s00018-019-03231-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/25/2019] [Accepted: 07/15/2019] [Indexed: 01/17/2023]
Abstract
The nucleolus is a sub-nuclear body known primarily for its role in ribosome biogenesis. Increased number and/or size of nucleoli have historically been used by pathologists as a prognostic indicator of cancerous lesions. This increase in nucleolar number and/or size is classically attributed to the increased need for protein synthesis in cancer cells. However, evidences suggest that the nucleolus plays critical roles in many cellular functions in both normal cell biology and disease pathologies, including cancer. As new functions of the nucleolus are elucidated, there is mounting evidence to support the role of the nucleolus in regulating additional cellular functions, particularly response to cellular stressors, maintenance of genome stability, and DNA damage repair, as well as the regulation of gene expression and biogenesis of several ribonucleoproteins. This review highlights the central role of the nucleolus in carcinogenesis and cancer progression and discusses how cancer cells may become "addicted" to nucleolar functions.
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Affiliation(s)
- Shannon E Weeks
- Department of Pathology, University of Alabama at Birmingham, WTI 320E, 1824 6th Ave South, Birmingham, AL, 35233, USA
| | - Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, WTI 320E, 1824 6th Ave South, Birmingham, AL, 35233, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, WTI 320E, 1824 6th Ave South, Birmingham, AL, 35233, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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Tzelepis K, Rausch O, Kouzarides T. RNA-modifying enzymes and their function in a chromatin context. Nat Struct Mol Biol 2019; 26:858-862. [PMID: 31582848 PMCID: PMC7613430 DOI: 10.1038/s41594-019-0312-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/30/2019] [Indexed: 12/29/2022]
Abstract
Exciting research has connected specific RNA modifications to chromatin, providing evidence for co-transcriptional deposition and function in gene regulation. Here we review insights gained from studying the co-transcriptional roles of RNA modifications, and their influence in normal and disease contexts. We also discuss how the availability of novel technical approaches could raise the translational potential of targeting RNA-modifying enzymes for the treatment of disease.
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Affiliation(s)
- Konstantinos Tzelepis
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Oliver Rausch
- Storm Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | - Tony Kouzarides
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
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Subedi P, Nembrini S, An Q, Zhu Y, Peng H, Yeh F, Cole SA, Rhoades DA, Lee ET, Zhao J. Telomere length and cancer mortality in American Indians: the Strong Heart Study. GeroScience 2019; 41:351-361. [PMID: 31230193 DOI: 10.1007/s11357-019-00080-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022] Open
Abstract
The objective of this study was to investigate whether leukocyte telomere length (LTL) predicts the risk for cancer mortality among American Indians participating in the Strong Heart Study (1989-1991). Participants (aged 45-74 years) were followed annually until December 2015 to collect information on morbidity/mortality. LTL was measured by qPCR using genomic DNA isolated from peripheral blood. The association between LTL and risk for cancer mortality was examined using a multivariable Cox proportional hazard model, adjusting for age, gender, education, study site, smoking, alcohol use, physical activity, systolic blood pressure, fasting blood glucose, obesity, and low- and high-density lipoprotein. Of 1945 participants (mean age 56.10 ± 8.17 at baseline, 57% women) followed for an average 20.5 years, 220 died of cancer. Results showed that longer LTL at baseline significantly predicts an increased risk of cancer death among females (HR 1.57, 95% CI 1.08-2.30), but not males (HR 0.74, 95% CI 0.49-1.12) (p for interaction 0.009). Specifically, compared with the women with the longest LTL (fourth quartile), those in the third, second, and first quartiles showed 53%, 41%, and 44% reduced risk for cancer death, respectively. The findings highlight the importance of sex-specific analysis in future telomere research.
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Affiliation(s)
- Pooja Subedi
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA
| | - Stefano Nembrini
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA
| | - Qiang An
- Department of Orthopaedics and Rehabilitation, University of Iowa Health Care, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, 01066 JPP, Iowa City, IA, 52242, USA
| | - Yun Zhu
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA
| | - Hao Peng
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA.,Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Fawn Yeh
- College of Public Health, University of Oklahoma Health Sciences Center, 801 N.E. 13th Street, Oklahoma City, OK, 73104, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | - Dorothy A Rhoades
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 655 Research Parkway, Oklahoma City, OK, 73104, USA
| | - Elisa T Lee
- College of Public Health, University of Oklahoma Health Sciences Center, 801 N.E. 13th Street, Oklahoma City, OK, 73104, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions, College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA.
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Watanabe M, Yamamoto G, Fujiyoshi K, Akagi Y, Kakuta M, Nishimura Y, Akagi K. Development of metachronous rectal cancers in a young man with dyskeratosis congenita: a case report. J Med Case Rep 2019; 13:117. [PMID: 31027506 PMCID: PMC6486685 DOI: 10.1186/s13256-019-2044-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/07/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND DKC1 (dyskerin pseudouridine synthase 1) is a causative gene for X-linked dyskeratosis congenita. Approximately 8% of patients with dyskeratosis congenita have malignancy, but information about the development of malignancy in patients with dyskeratosis congenita is limited. CASE PRESENTATION A young Japanese patient with bone marrow failure developed metachronous rectal adenocarcinomas at the ages of 16 and 18 years. He had no family history of cancer. Microsatellite instability testing with rectal tumor tissue demonstrated low-level microsatellite instability. To clarify whether any cancer susceptibility genes were involved in the development of rectal cancer, RNA sequencing was performed. Cancer-related genes were assessed, and a c.361A>G (p.Ser121Gly) germline variant was detected in DKC1. The same missense variant was previously reported in two patients with dyskeratosis congenita as a pathogenic variant, but those patients did not develop malignancies. CONCLUSIONS Our patient developed rectal cancer at an early age of onset compared with the previously reported typical onset age of patients with dyskeratosis congenita. DKC1 might be involved in predisposition to colorectal cancer in young adulthood; therefore, appropriate surveillance may be considered.
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Affiliation(s)
- Motoko Watanabe
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | | | - Yoshito Akagi
- Department of Surgery, Kurume University, Fukuoka, Japan
| | - Miho Kakuta
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Yoji Nishimura
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - Kiwamu Akagi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan.
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Miao FA, Chu K, Chen HR, Zhang M, Shi PC, Bai J, You YP. Increased DKC1 expression in glioma and its significance in tumor cell proliferation, migration and invasion. Invest New Drugs 2019; 37:1177-1186. [PMID: 30847721 DOI: 10.1007/s10637-019-00748-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/15/2019] [Indexed: 11/25/2022]
Abstract
The dyskeratosis congenita 1 (DKC1) gene is located on the X chromosome at Xq28. Dyskerin encoded by the DKC1 gene is associated with the formation of certain small RNAs and the telomerase activity. Inherited mutations in DKC1 inactivate the dyskerin and causes dyskeratosis congenital, which is characterized by skin defects, hematopoiesis failure, and increased susceptibility to cancer. DKC1 reportedly up-regulates in several human cancers, including renal cell carcinoma and prostate cancer. Dyskerin is deregulated in B-chronic lymphocytic leukemia and breast carcinomas, but its expression and function in glioma have hardly been investigated. Hence, we were prompted to collect tissue samples and implement cell experiments. Our study reveals that DKC1 expression is significantly increased in the pathological tissues of glioma compared with that in normal tissues. The increased staining of DKC1 is related to the World Health Organization stages of tumors. DKC1 knockdown also significantly inhibits glioma cell growth by altering the expression of cell cycle-relative molecules to arrest at the G1 phase. In the transwell chamber, DKC1 knockdown glioma cells exhibit low motility. Consistent with classic oncogenic pathways, N-cadherin, HIF-1α, and MMP2 expression levels are lower compared with those of the control group. Therefore, DKC1 up-regulation in gliomas is common and necessary for extensive tumor growth. The phenotype of glioma cell lines after DKC1 down-regulation suggests its use as a valuable clinical treatment strategy.
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Affiliation(s)
- Fa-An Miao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 211100, Jiangsu Province, China
- Department of Neurosurgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Kun Chu
- Department of Neurosurgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Hai-Rong Chen
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Meng Zhang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Pei-Cong Shi
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China.
| | - Yong-Ping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 211100, Jiangsu Province, China.
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 221002, Jiangsu Province, China.
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Dinescu S, Ignat S, Lazar AD, Constantin C, Neagu M, Costache M. Epitranscriptomic Signatures in lncRNAs and Their Possible Roles in Cancer. Genes (Basel) 2019; 10:genes10010052. [PMID: 30654440 PMCID: PMC6356509 DOI: 10.3390/genes10010052] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
In contrast to the amazing exponential growth in knowledge related to long non-coding RNAs (lncRNAs) involved in cell homeostasis or dysregulated pathological states, little is known so far about the links between the chemical modifications occurring in lncRNAs and their function. Generally, ncRNAs are post-transcriptional regulators of gene expression, but RNA modifications occurring in lncRNAs generate an additional layer of gene expression control. Chemical modifications that have been reported in correlation with lncRNAs include m⁶A, m⁵C and pseudouridylation. Up to date, several chemically modified long non-coding transcripts have been identified and associated with different pathologies, including cancers. This review presents the current level of knowledge on the most studied cancer-related lncRNAs, such as the metastasis associated lung adenocarcinoma transcript 1 (MALAT1), the Hox transcript antisense intergenic RNA (HOTAIR), or the X-inactive specific transcript (XIST), as well as more recently discovered forms, and their potential roles in different types of cancer. Understanding how these RNA modifications occur, and the correlation between lncRNA changes in structure and function, may open up new therapeutic possibilities in cancer.
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Affiliation(s)
- Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Simona Ignat
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Andreea Daniela Lazar
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Carolina Constantin
- Immunology Department, "Victor Babes" National Institute of Pathology, 050096 Bucharest, Romania.
| | - Monica Neagu
- Immunology Department, "Victor Babes" National Institute of Pathology, 050096 Bucharest, Romania.
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
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Turning Uridines around: Role of rRNA Pseudouridylation in Ribosome Biogenesis and Ribosomal Function. Biomolecules 2018; 8:biom8020038. [PMID: 29874862 PMCID: PMC6023024 DOI: 10.3390/biom8020038] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 01/09/2023] Open
Abstract
Ribosomal RNA (rRNA) is extensively edited through base methylation and acetylation, 2'-O-ribose methylation and uridine isomerization. In human rRNA, 95 uridines are predicted to by modified to pseudouridine by ribonucleoprotein complexes sharing four core proteins and differing for a RNA sequence guiding the complex to specific residues to be modified. Most pseudouridylation sites are placed within functionally important ribosomal domains and can influence ribosomal functional features. Information obtained so far only partially explained the degree of regulation and the consequences of pseudouridylation on ribosomal structure and function in different physiological and pathological conditions. This short review focuses on the available evidence in this topic, highlighting open questions in the field and perspectives that the development of emerging techniques is offering.
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40
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Angrisani A, Matrone N, Belli V, Vicidomini R, Di Maio N, Turano M, Scialò F, Netti PA, Porcellini A, Furia M. A functional connection between dyskerin and energy metabolism. Redox Biol 2017; 14:557-565. [PMID: 29132127 PMCID: PMC5684492 DOI: 10.1016/j.redox.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/12/2017] [Accepted: 11/03/2017] [Indexed: 02/06/2023] Open
Abstract
The human DKC1 gene encodes dyskerin, an evolutionarily conserved nuclear protein whose overexpression represents a common trait of many types of aggressive sporadic cancers. As a crucial component of the nuclear H/ACA snoRNP complexes, dyskerin is involved in a variety of essential processes, including telomere maintenance, splicing efficiency, ribosome biogenesis, snoRNAs stabilization and stress response. Although multiple minor dyskerin splicing isoforms have been identified, their functions remain to be defined. Considering that low-abundance splice variants could contribute to the wide functional repertoire attributed to dyskerin, possibly having more specialized tasks or playing significant roles in changing cell status, we investigated in more detail the biological roles of a truncated dyskerin isoform that lacks the C-terminal nuclear localization signal and shows a prevalent cytoplasmic localization. Here we show that this dyskerin variant can boost energy metabolism and improve respiration, ultimately conferring a ROS adaptive response and a growth advantage to cells. These results reveal an unexpected involvement of DKC1 in energy metabolism, highlighting a previously underscored role in the regulation of metabolic cell homeostasis. Human dyskerin is an evolutionary conserved component of nuclear H/ACA snoRNPs. The functional role of a truncated dyskerin isoform (Iso3) is analyzed. Iso3 overexpression boosts energy metabolism and induces a ROS adaptive response. Iso3 connects dyskerin with mitochondrial functionality and redox homeostasis.
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Affiliation(s)
- Alberto Angrisani
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy.
| | - Nunzia Matrone
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Valentina Belli
- Istituto Italiano di Tecnologia, IIT@CRIB, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy
| | - Rosario Vicidomini
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Nunzia Di Maio
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Mimmo Turano
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Filippo Scialò
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, University of Newcastle, Newcastle-upon-Tyne NE4 5PL, United Kingdom
| | - Paolo Antonio Netti
- Istituto Italiano di Tecnologia, IIT@CRIB, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; Centro di Ricerca Interdipartimentale sui Biomateriali CRIB, Università di Napoli Federico II, Piazzale Tecchio 80, 80125 Napoli, Italy
| | - Antonio Porcellini
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Maria Furia
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy; Centro di Ricerca Interdipartimentale sui Biomateriali CRIB, Università di Napoli Federico II, Piazzale Tecchio 80, 80125 Napoli, Italy.
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RNA Pseudouridylation in Physiology and Medicine: For Better and for Worse. Genes (Basel) 2017; 8:genes8110301. [PMID: 29104216 PMCID: PMC5704214 DOI: 10.3390/genes8110301] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022] Open
Abstract
Pseudouridine is the most abundant modification found in RNA. Today, thanks to next-generation sequencing techniques used in the detection of RNA modifications, pseudouridylation sites have been described in most eukaryotic RNA classes. In the present review, we will first consider the available information on the functional roles of pseudouridine(s) in different RNA species. We will then focus on how alterations in the pseudouridylation process may be connected with a series of human pathologies, including inherited disorders, cancer, diabetes, and viral infections. Finally, we will discuss how the availability of novel technical approaches are likely to increase the knowledge in this field.
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Ibáñez-Cabellos JS, Pérez-Machado G, Seco-Cervera M, Berenguer-Pascual E, García-Giménez JL, Pallardó FV. Acute telomerase components depletion triggers oxidative stress as an early event previous to telomeric shortening. Redox Biol 2017; 14:398-408. [PMID: 29055871 PMCID: PMC5650655 DOI: 10.1016/j.redox.2017.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 01/13/2023] Open
Abstract
Loss of function of dyskerin (DKC1), NOP10 and TIN2 are responsible for different inheritance patterns of Dyskeratosis congenita (DC; ORPHA1775). They are key components of telomerase (DKC1 and NOP10) and shelterin (TIN2), and play an important role in telomere homeostasis. They participate in several fundamental cellular processes by contributing to Dyskeratosis congenita through mechanisms that are not fully understood. Presence of oxidative stress was postulated to result from telomerase ablation. However, the resulting disturbed redox status can promote telomere attrition by generating a vicious circle, which promotes cellular senescence. This fact prompted us to study if acute loss of DKC1, NOP10 and TINF2 can promote redox disequilibrium as an early event when telomere shortening has not yet taken place. We generated siRNA-mediated (DKC1, NOP10 and TINF2) cell lines by RNA interference, which was confirmed by mRNA and protein expression analyses. No telomere shortening occurred in any silenced cell line. Depletion of H/ACA ribonucleoproteins DKC1 and NOP10 diminished telomerase activity via TERC down-regulation, and produced alterations in pseudouridylation and ribosomal biogenesis. An increase in the GSSG/GSH ratio, carbonylated proteins and oxidized peroxiredoxin-6 was observed, in addition to MnSOD and TRX1 overexpression in the siRNA DC cells. Likewise, high PARylation levels and high PARP1 protein expression were detected. In contrast, the silenced TINF2 cells did not alter any evaluated oxidative stress marker. Altogether these findings lead us to conclude that loss of DKC1 and NOP10 functions induces oxidative stress in a telomere shortening independent manner. Transient silencing of DKC1 and NOP10 genes produce oxidative stress. Cells depleted of DKC1 and NOP10 are susceptible to DNA damage. Acute DKC1 and NOP10 depletion disrupts RNA maturation. Oxidative stress is an early event previous to telomere shortening.
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Affiliation(s)
- José Santiago Ibáñez-Cabellos
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Giselle Pérez-Machado
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Marta Seco-Cervera
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Ester Berenguer-Pascual
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain.
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
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Henras AK, Plisson-Chastang C, Humbert O, Romeo Y, Henry Y. Synthesis, Function, and Heterogeneity of snoRNA-Guided Posttranscriptional Nucleoside Modifications in Eukaryotic Ribosomal RNAs. Enzymes 2017; 41:169-213. [PMID: 28601222 DOI: 10.1016/bs.enz.2017.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity. Strikingly, recent quantitative nucleoside modification profiling methods have revealed that a subset of modification sites is not always fully modified. The finding of such ribosome heterogeneity is in line with the concept of specialized ribosomes that could preferentially translate specific mRNAs. This emerging concept is supported by findings that some human diseases are caused by defects in the rRNA modification machinery correlated with a significant alteration of IRES-dependent translation.
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
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Çalışkan Can E, Atalay MC, Miser Salihoğlu E, Yalçıntaş Arslan Ü, Şimşek HB, Yardım Akaydın S. Normal and Tumour Tissue mRNA Expressions of Telomerase Complex Genes in Several Types of Cancer. Balkan Med J 2017; 34:269-274. [PMID: 28443573 PMCID: PMC5450868 DOI: 10.4274/balkanmedj.2015.1616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Aims: To investigate the changes in mRNA expression levels of telomerase-related significant proteins in several types of cancer. Methods: Human telomerase reverse transcriptase, pontin, reptin and dyskerin expressions were measured in normal and tumour tissues obtained from 26 patients with colorectal, breast and gastric cancers, using the real-time reverse transcriptase-polymerase chain reaction method. Results: For all patients, no significant difference was found in mRNA expressions of human telomerase reverse transcriptase and dyskerin (p>0.05), although their levels in tumour tissues were found to be higher than in normal tissues. However, pontin and reptin mRNA expressions were significantly higher in tumour tissues than in normal tissues (p<0.01). While human telomerase reverse transcriptase showed a high correlation with only pontin (p<0.001) in normal tissues, high positive correlations were observed between human telomerase reverse transcriptase with pontin (p<0.005), reptin (p<0.01) and dyskerin (p<0.01) in tumour tissues. Conclusion: The increased mRNA expressions of all four genes in tumour tissues may suggest a role in cancer development. Correlations of pontin, reptin and dyskerin with human telomerase reverse transcriptase support the hypotheses describing their roles in telomerase complexes.
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Affiliation(s)
- Emel Çalışkan Can
- Department of Biochemistry, Gazi University School of Pharmacy, Ankara, Turkey
| | - M Can Atalay
- Department of General Surgery, Ankara Oncology Training and Research Hospital, Ankara, Turkey
| | - Ece Miser Salihoğlu
- Department of Biochemistry, Gazi University School of Pharmacy, Ankara, Turkey
| | - Ülkü Yalçıntaş Arslan
- Department of Medical Oncology, Ankara Oncology Training and Research Hospital, Ankara, Turkey
| | - H Bolkan Şimşek
- Department of Biochemistry, Gazi University School of Pharmacy, Ankara, Turkey
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The importance of being (slightly) modified: The role of rRNA editing on gene expression control and its connections with cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:330-338. [PMID: 27815156 DOI: 10.1016/j.bbcan.2016.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/12/2016] [Accepted: 10/30/2016] [Indexed: 12/22/2022]
Abstract
In human ribosomal RNAs, over 200 residues are modified by specific, RNA-driven enzymatic complexes or stand-alone, RNA-independent enzymes. In most cases, modification sites are placed in specific positions within important functional areas of the ribosome. Some evidence indicates that the altered control in ribosomal RNA modifications may affect ribosomal function during mRNA translation. Here we provide an overview of the connections linking ribosomal RNA modifications to ribosome function, and suggest how aberrant modifications may affect the control of the expression of key cancer genes, thus contributing to tumor development. In addition, the future perspectives in this field are discussed.
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Abstract
Telomerase activity is responsible for the maintenance of chromosome end structures (telomeres) and cancer cell immortality in most human malignancies, making telomerase an attractive therapeutic target. The rationale for targeting components of the telomerase holoenzyme has been strengthened by accumulating evidence indicating that these molecules have extra-telomeric functions in tumour cell survival and proliferation. This Review discusses current knowledge of the biogenesis, structure and multiple functions of telomerase-associated molecules intertwined with recent advances in drug discovery approaches. We also describe the fertile ground available for the pursuit of next-generation small-molecule inhibitors of telomerase.
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Affiliation(s)
- Greg M Arndt
- Australian Cancer Research Foundation (ACRF) Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Karen L MacKenzie
- Personalised Medicine Program, Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
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Penzo M, Ludovini V, Treré D, Siggillino A, Vannucci J, Bellezza G, Crinò L, Montanaro L. Dyskerin and TERC expression may condition survival in lung cancer patients. Oncotarget 2016; 6:21755-60. [PMID: 26301749 PMCID: PMC4673301 DOI: 10.18632/oncotarget.4580] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/06/2015] [Indexed: 12/13/2022] Open
Abstract
Dyskerin mediates both the modification of uridine on ribosomal and small nuclear RNAs and the stabilization of the telomerase RNA component (TERC). In human tumors dyskerin expression was found to be associated with both rRNA modification and TERC levels. Moreover, dyskerin overexpression has been linked to unfavorable prognosis in a variety of tumor types, however an explanation for the latter association is not available. To clarify this point, we analyzed the connection between dyskerin expression, TERC levels and clinical outcome in two series of primary lung cancers, differing for the presence of TERC gene amplification, a genetic alteration inducing strong TERC overexpression. TERC levels were significantly higher in tumors bearing TERC gene amplification (P = 0.017). In addition, the well-established association between dyskerin expression and TERC levels was observed only in the series without TERC gene amplification (P = 0.003), while it was not present in TERC amplified tumors (P = 0.929). Similarly, the association between dyskerin expression and survival was found in cases not bearing TERC gene amplification (P = 0.009) and was not observed in TERC amplified tumors (P = 0.584). These results indicate that the influence of dyskerin expression on tumor clinical outcome is linked to its role on the maintenance of high levels of TERC.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, I-40138, Italy
| | - Vienna Ludovini
- Department of Medical Oncology, S. Maria della Misericordia Hospital, Perugia, I-06156, Italy
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, I-40138, Italy
| | - Annamaria Siggillino
- Department of Medical Oncology, S. Maria della Misericordia Hospital, Perugia, I-06156, Italy
| | - Jacopo Vannucci
- Department of Thoracic Surgery, University of Perugia, Perugia, I-06156, Italy
| | - Guido Bellezza
- Institute of Pathological Anatomy and Histology, University of Perugia, Perugia, I-06156, Italy
| | - Lucio Crinò
- Department of Medical Oncology, S. Maria della Misericordia Hospital, Perugia, I-06156, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, I-40138, Italy
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Panero J, Stella F, Schutz N, Fantl DB, Slavutsky I. Differential Expression of Non-Shelterin Genes Associated with High Telomerase Levels and Telomere Shortening in Plasma Cell Disorders. PLoS One 2015; 10:e0137972. [PMID: 26366868 PMCID: PMC4569359 DOI: 10.1371/journal.pone.0137972] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/24/2015] [Indexed: 12/25/2022] Open
Abstract
Telomerase, shelterin proteins and various interacting factors, named non-shelterin proteins, are involved in the regulation of telomere length (TL). Altered expression of any of these telomere-associated genes can lead to telomere dysfunction, causing genomic instability and disease development. In this study, we investigated the expression profile of a set of non-shelterin genes involved in essential processes such as replication (RPA1), DNA damage repair pathways (MRE11-RAD50-NBS1) and stabilization of telomerase complex (DKC1), in 35 patients with monoclonal gammopathy of undetermined significance (MGUS) and 40 cases with multiple myeloma (MM). Results were correlated with hTERT expression, TL and clinical parameters. Overall, a significant increase in DKC1, RAD50, MRE11, NBS1 and RPA1 expression along with an upregulation of hTERT in MM compared with MGUS was observed (p≤0.032). Interestingly, in both entities high mRNA levels of non-shelterin genes were associated with short TLs and increased hTERT expression. Significant differences were observed for DKC1 in MM (p ≤0.026), suggesting an important role for this gene in the maintenance of short telomeres by telomerase in myeloma plasma cells. With regard to clinical associations, we observed a significant increase in DKC1, RAD50, MRE11 and RPA1 expression in MM cases with high bone marrow infiltration (p≤0.03) and a tendency towards cases with advanced ISS stage, providing the first evidence of non-shelterin genes associated to risk factors in MM. Taken together, our findings bring new insights into the intricate mechanisms by which telomere-associated proteins collaborate in the maintenance of plasma cells immortalization and suggest a role for the upregulation of these genes in the progression of the disease.
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Affiliation(s)
- Julieta Panero
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
- * E-mail:
| | - Flavia Stella
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Natalia Schutz
- Departamento de Clínica Médica, Sección Hematología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Dorotea Beatriz Fantl
- Departamento de Clínica Médica, Sección Hematología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Irma Slavutsky
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
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Penzo M, Rocchi L, Brugiere S, Carnicelli D, Onofrillo C, Couté Y, Brigotti M, Montanaro L. Human ribosomes from cells with reduced dyskerin levels are intrinsically altered in translation. FASEB J 2015; 29:3472-82. [PMID: 25934701 DOI: 10.1096/fj.15-270991] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/21/2015] [Indexed: 12/19/2022]
Abstract
Dyskerin is a pseudouridine (ψ) synthase involved in fundamental cellular processes including uridine modification in rRNA and small nuclear RNA and telomere stabilization. Dyskerin functions are altered in X-linked dyskeratosis congenita (X-DC) and cancer. Dyskerin's role in rRNA pseudouridylation has been suggested to underlie the alterations in mRNA translation described in cells lacking dyskerin function, although relevant direct evidences are currently lacking. Our purpose was to establish definitely whether defective dyskerin function might determine an intrinsic ribosomal defect leading to an altered synthetic activity. Therefore, ribosomes from dyskerin-depleted human cells were purified and 1) added to a controlled reticulocyte cell-free system devoid of ribosomes to study mRNA translation; 2) analyzed for protein contamination and composition by mass spectrometry, 3) analyzed for global pseudouridylation levels. Ribosomes purified from dyskerin-depleted cells showed altered translational fidelity and internal ribosome entry site (IRES)-mediated translation. These ribosomes displayed reduced uridine modification, whereas they were not different in terms of protein contamination or ribosomal protein composition with respect to ribosomes from matched control cells with full dyskerin activity. In conclusion, lack of dyskerin function in human cells induces a defect in rRNA uridine modification, which is sufficient to alter ribosome activity.
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Affiliation(s)
- Marianna Penzo
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Laura Rocchi
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Sabine Brugiere
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Domenica Carnicelli
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Carmine Onofrillo
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Yohann Couté
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Maurizio Brigotti
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
| | - Lorenzo Montanaro
- *Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum-Università di Bologna, Bologna, Italy; University Grenoble Alpes, Commissariat à l'Énergie Atomique, Institut Régional de Travail Social, and Institut National de la Santé et de la Recherche Médicale, Biologie à Grande Echelle, Grenoble, France
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50
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von Stedingk K, De Preter K, Vandesompele J, Noguera R, Øra I, Koster J, Versteeg R, Påhlman S, Lindgren D, Axelson H. Individual patient risk stratification of high-risk neuroblastomas using a two-gene score suited for clinical use. Int J Cancer 2015; 137:868-77. [PMID: 25652004 DOI: 10.1002/ijc.29461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/08/2015] [Indexed: 11/11/2022]
Abstract
Several gene expression-based prognostic signatures have been described in neuroblastoma, but none have successfully been applied in the clinic. Here we have developed a clinically applicable prognostic gene signature, both with regards to number of genes and analysis platform. Importantly, it does not require comparison between patients and is applicable amongst high-risk patients. The signature is based on a two-gene score (R-score) with prognostic power in high-stage tumours (stage 4 and/or MYCN-amplified diagnosed after 18 months of age). QPCR-based and array-based analyses of matched cDNAs confirmed cross platform (array-qPCR) transferability. We also defined a fixed cut-off value identifying prognostically differing subsets of high-risk patients on an individual patient basis. This gene expression signature independently contributes to the current neuroblastoma classification system, and if prospectively validated could provide further stratification of high-risk patients, and potential upfront identification of a group of patients that are in need of new/additional treatment regimens.
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Affiliation(s)
- Kristoffer von Stedingk
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Katleen De Preter
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Ingrid Øra
- Department of Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Sven Påhlman
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David Lindgren
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Håkan Axelson
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
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