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Gaspari L, Haouzi D, Gennetier A, Granes G, Soler A, Sultan C, Paris F, Hamamah S. Transgenerational Transmission of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Effects in Human Granulosa Cells: The Role of MicroRNAs. Int J Mol Sci 2024; 25:1144. [PMID: 38256218 PMCID: PMC10816780 DOI: 10.3390/ijms25021144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Endocrine-disrupting chemicals (EDCs) might contribute to the increase in female-specific cancers in Western countries. 2,3,7,8-tetrachlordibenzo-p-dioxin (TCDD) is considered the "prototypical toxicant" to study EDCs' effects on reproductive health. Epigenetic regulation by small noncoding RNAs (sncRNAs), such as microRNAs (miRNA), is crucial for controlling cancer development. The aim of this study was to analyze transcriptional activity and sncRNA expression changes in the KGN cell line after acute (3 h) and chronic (72 h) exposure to 10 nM TCDD in order to determine whether sncRNAs' deregulation may contribute to transmitting TCDD effects to the subsequent cell generations (day 9 and day 14 after chronic exposure). Using Affymetrix GeneChip miRNA 4.0 arrays, 109 sncRNAs were found to be differentially expressed (fold change < -2 or >2; p-value < 0.05) between cells exposed or not (control) to TCDD for 3 h and 72 h and on day 9 and day 14 after chronic exposure. Ingenuity Pathway Analysis predicted that following the acute and chronic exposure of KGN cells, sncRNAs linked to cellular development, growth and proliferation were downregulated, and those linked to cancer promotion were upregulated on day 9 and day 14. These results indicated that TCDD-induced sncRNA dysregulation may have transgenerational cancer-promoting effects.
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Affiliation(s)
- Laura Gaspari
- Unité d’Endocrinologie-Gynécologie Pédiatrique, Service de Pédiatrie, Hôpital Arnaud-de-Villeneuve, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (L.G.); (C.S.)
- Centre de Référence Maladies Rares du Développement Génital, Constitutif Sud, Hôpital Lapeyronie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
| | - Delphine Haouzi
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
- Département de Biologie de la Reproduction et DPI (ART/PGD), Hôpital A. de Villeneuve, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
| | - Aurélie Gennetier
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
| | - Gaby Granes
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
| | - Alexandra Soler
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
- Global ART Innovation Network (GAIN), 34295 Montpellier, France
| | - Charles Sultan
- Unité d’Endocrinologie-Gynécologie Pédiatrique, Service de Pédiatrie, Hôpital Arnaud-de-Villeneuve, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (L.G.); (C.S.)
| | - Françoise Paris
- Unité d’Endocrinologie-Gynécologie Pédiatrique, Service de Pédiatrie, Hôpital Arnaud-de-Villeneuve, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (L.G.); (C.S.)
- Centre de Référence Maladies Rares du Développement Génital, Constitutif Sud, Hôpital Lapeyronie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
| | - Samir Hamamah
- INSERM U 1203, Développement Embryonnaire Fertilité Environnement, Université de Montpellier, INSERM, 34295 Montpellier, France (A.S.)
- Département de Biologie de la Reproduction et DPI (ART/PGD), Hôpital A. de Villeneuve, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
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Gawade K, Raczynska KD. Imprinted small nucleolar RNAs: Missing link in development and disease? WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1818. [PMID: 37722601 DOI: 10.1002/wrna.1818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
The 14q32.2 (DLK1-DIO3) and 15q11-q13 (SNURF-SNRPN) imprinted gene loci harbor the largest known small nucleolar RNA clusters expressed from the respective maternal and paternal alleles. Recent studies have demonstrated significant roles for the 15q11-q13 located SNORD115-SNORD116 C/D box snoRNAs in Prader-Willi syndrome (PWS), a neurodevelopmental disorder. Even though the effect of SNORD116 deletion is apparent in the PWS phenotype, similar effects of a SNORD113-SNORD114 cluster deletion from the 14q32.2 locus in Kagami-Ogata syndrome (KOS14) and upregulation in Temple syndrome (TS14) remain to be explored. Moreover, apart from their probable involvement in neurodevelopmental disorders, snoRNAs from the SNORD113-SNORD114 cluster have been implicated in multiple biological processes, including pluripotency, development, cancers, and RNA modifications. Here we summarize the current understanding of the system to explore the possibility of a link between developmental disorders and C/D box snoRNA expression from the imprinted 14q32.2 locus. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Processing > Processing of Small RNAs.
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Affiliation(s)
- Kishor Gawade
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Katarzyna D Raczynska
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, Poznan, Poland
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3
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Smatti MK, Al-Sarraj YA, Albagha O, Yassine HM. Genome-wide association study identifies several loci for HEV seropositivity. iScience 2023; 26:107586. [PMID: 37664632 PMCID: PMC10470371 DOI: 10.1016/j.isci.2023.107586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/22/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Hepatitis E viral (HEV) infection imposes a heavy global health burden. The variability in the prevalence of serological markers of HEV infection between different ethnic groups proposes a host genetic influence. Here, we report genetic polymorphisms associated with anti-HEV antibody positivity and level using binary- and quantitative-trait genome-wide association studies (GWAS) on a population from Qatar (n = 5829). We identified a region in 12p11.1 (lead SNP: rs559856097, allele: A, p = 2.3 × 10-10) significantly associated with anti-HEV antibodies level. This intergenic variant is located near SNORD112, a small nucleolar RNA (snoRNA). Additional gene-set and pathway enrichment analyses highlighted a strong correlation with anti-viral response-related pathways, including IFNs (alpha/beta) and interleukin-21 (IL-21) signaling. This is the first GWAS on the response to HEV infection. Further replication and functional experimentation are warranted to validate these findings.
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Affiliation(s)
- Maria K. Smatti
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Yasser A. Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Omar Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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5
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Pellegrino S, Dent KC, Spikes T, Warren AJ. Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution. Nucleic Acids Res 2023; 51:4043-4054. [PMID: 36951107 PMCID: PMC10164566 DOI: 10.1093/nar/gkad194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the inability to accurately visualise these modifications has limited mechanistic understanding of the role of these modifications in ribosome function. Here we report the 2.15 Å resolution cryo-EM reconstruction of the human 40S ribosomal subunit. We directly visualise post-transcriptional modifications within the 18S rRNA and four post-translational modifications of ribosomal proteins. Additionally, we interpret the solvation shells in the core regions of the 40S ribosomal subunit and reveal how potassium and magnesium ions establish both universally conserved and eukaryote-specific coordination to promote the stabilisation and folding of key ribosomal elements. This work provides unprecedented structural details for the human 40S ribosomal subunit that will serve as an important reference for unravelling the functional role of ribosomal RNA modifications.
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Affiliation(s)
- Simone Pellegrino
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Kyle C Dent
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Tobias Spikes
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alan J Warren
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
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6
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FUS regulates a subset of snoRNA expression and modulates the level of rRNA modifications. Sci Rep 2023; 13:2974. [PMID: 36806717 PMCID: PMC9941101 DOI: 10.1038/s41598-023-30068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this work, we show that FUS depletion results in the differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2'-O methylation (2'-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2'-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2'-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and progression.
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Huang W, Sun YM, Pan Q, Fang K, Chen XT, Zeng ZC, Chen TQ, Zhu SX, Huang LB, Luo XQ, Wang WT, Chen YQ. The snoRNA-like lncRNA LNC-SNO49AB drives leukemia by activating the RNA-editing enzyme ADAR1. Cell Discov 2022; 8:117. [PMID: 36316318 PMCID: PMC9622897 DOI: 10.1038/s41421-022-00460-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/18/2022] [Indexed: 01/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are usually 5' capped and 3' polyadenylated, similar to most typical mRNAs. However, recent studies revealed a type of snoRNA-related lncRNA with unique structures, leading to questions on how they are processed and how they work. Here, we identify a novel snoRNA-related lncRNA named LNC-SNO49AB containing two C/D box snoRNA sequences, SNORD49A and SNORD49B; and show that LNC-SNO49AB represents an unreported type of lncRNA with a 5'-end m7G and a 3'-end snoRNA structure. LNC-SNO49AB was found highly expressed in leukemia patient samples, and silencing LNC-SNO49AB dramatically suppressed leukemia progression in vitro and in vivo. Subcellular location indicated that the LNC-SNO49AB is mainly located in nucleolus and interacted with the nucleolar protein fibrillarin. However, we found that LNC-SNO49AB does not play a role in 2'-O-methylation regulation, a classical function of snoRNA; instead, its snoRNA structure affected the lncRNA stability. We further demonstrated that LNC-SNO49AB could directly bind to the adenosine deaminase acting on RNA 1(ADAR1) and promoted its homodimerization followed by a high RNA A-to-I editing activity. Transcriptome profiling shows that LNC-SNO49AB and ADAR1 knockdown respectively share very similar patterns of RNA modification change in downstream signaling pathways, especially in cell cycle pathways. These findings suggest a previously unknown class of snoRNA-related lncRNAs, which function via a manner in nucleolus independently on snoRNA-guide rRNA modification. This is the first report that a lncRNA regulates genome-wide RNA A-to-I editing by enhancing ADAR1 dimerization to facilitate hematopoietic malignancy, suggesting that LNC-SNO49AB may be a novel target in therapy directed to leukemia.
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Affiliation(s)
- Wei Huang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yu-Meng Sun
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Qi Pan
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Ke Fang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xiao-Tong Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Zhan-Cheng Zeng
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tian-Qi Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Shun-Xin Zhu
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Li-Bin Huang
- grid.412615.50000 0004 1803 6239The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xue-Qun Luo
- grid.412615.50000 0004 1803 6239The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Wen-Tao Wang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yue-Qin Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
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Kumari A, Rahaman A, Zeng XA, Farooq MA, Huang Y, Yao R, Ali M, Ishrat R, Ali R. Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease. Front Neurosci 2022; 16:966877. [PMID: 35958988 PMCID: PMC9359077 DOI: 10.3389/fnins.2022.966877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022] Open
Abstract
Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention.
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Affiliation(s)
- Ankita Kumari
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- Abdul Rahaman
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- *Correspondence: Xin-An Zeng
| | - Muhammad Adil Farooq
- Institute of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Yanyan Huang
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Murtaza Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Romana Ishrat
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Romana Ishrat
| | - Rafat Ali
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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9
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Small noncoding RNAs play superior roles in maintaining hematopoietic stem cell homeostasis. BLOOD SCIENCE 2022; 4:125-132. [DOI: 10.1097/bs9.0000000000000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
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10
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Yang T, Shen J. Small nucleolar RNAs and SNHGs in the intestinal mucosal barrier: Emerging insights and current roles. J Adv Res 2022; 46:75-85. [PMID: 35700920 PMCID: PMC10105082 DOI: 10.1016/j.jare.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Previous studies have focused on the involvement of small nucleolar RNAs (snoRNAs) and SNHGs in tumor cell proliferation, apoptosis, invasion, and metastasis via multiple pathways, including phosphatidylinositol-3-kinase/protein kinase B (PI3K/AKT), Wnt/β catenin, and mitogen-activated protein kinase (MAPK). These molecular mechanisms affect the integrity of the intestinal mucosal barrier. AIM OF REVIEW Current evidence regarding snoRNAs and SNHGs in the context of the mucosal barrier and modulation of homeostasis is fragmented. In this review, we collate the established information on snoRNAs and SNHGs as well as discuss the major pathways affecting the mucosal barrier. KEY SCIENTIFIC CONCEPTS OF REVIEW Intestinal mucosal immunity, microflora, and the physical barrier are altered in non-neoplastic diseases such as inflammatory bowel diseases. Dysregulated snoRNAs and SNHGs may impact the intestinal mucosal barrier to promote the pathogenesis and progression of multiple diseases. SnoRNAs or SNHGs has been shown to be associated with poor disease behaviors, indicating that they may be exploited as prognostic biomarkers. Additionally, clarifying the complicated interactions between snoRNAs or SNHGs and the mucosal barrier may provide novel insights for the therapeutic treatment targeting strengthen the intestinal mucosal barrier.
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Affiliation(s)
- Tian Yang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center. Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai 200127, China; Shanghai Institute of Digestive Disease, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center. Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai 200127, China; Shanghai Institute of Digestive Disease, China.
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11
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snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology. Cell Death Dis 2022; 8:259. [PMID: 35552378 PMCID: PMC9098889 DOI: 10.1038/s41420-022-01056-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Small nucleolar RNAs (snoRNAs), a type of non-coding RNA, are widely present in the nucleoli of eukaryotic cells and play an important role in rRNA modification. With the recent increase in research on snoRNAs, new evidence has emerged indicating that snoRNAs also participate in tRNA and mRNA modification. Studies suggest that numerous snoRNAs, including tumor-promoting and tumor-suppressing snoRNAs, are not only dysregulated in tumors but also show associations with clinical prognosis. In this review, we summarize the reported functions of snoRNAs and the possible mechanisms underlying their role in tumorigenesis and cancer development to guide the snoRNA-based clinical diagnosis and treatment of cancer in the future.
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12
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Han C, Sun LY, Luo XQ, Pan Q, Sun YM, Zeng ZC, Chen TQ, Huang W, Fang K, Wang WT, Chen YQ. Chromatin-associated orphan snoRNA regulates DNA damage-mediated differentiation via a non-canonical complex. Cell Rep 2022; 38:110421. [PMID: 35354054 DOI: 10.1016/j.celrep.2022.110421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/04/2021] [Accepted: 01/31/2022] [Indexed: 12/21/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are commonly acknowledged as a class of homogeneous non-coding RNAs that guide ribosomal RNA modifications. However, snoRNAs referred to as orphans have largely unknown functions. Here, we systematically profile chromatin-associated snoRNAs (casnoRNAs) in mammalian cells and identify a subgroup of orphan casnoRNAs responding to DNA damage stress, among which SNORA73 shows the most marked reduction in chromatin enrichment. Downregulated SNORA73 maintains cancer genome stability and differentiation block in hematopoietic malignancy. Mechanistically, casnoRNA the 5' end non-canonical structure of SNORA73 is critical for its function and binding to poly (ADP-ribose) polymerase 1 (PARP1). SNORA73 inhibits PARP1 auto-PARylation to affect cancer genome stability by forming a small nucleolar ribonucleoprotein (snoRNP) with PARP1 and canonical H/ACA proteins DKC1/NHP2. Our findings reveal the role of an orphan snoRNA serving as casnoRNA and highlights a link between non-canonical structure of snoRNA and their functional diversity.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xue-Qun Luo
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qi Pan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhan-Cheng Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Tian-Qi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Ke Fang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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13
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Rastorgueva E, Liamina D, Panchenko I, Iurova E, Beloborodov E, Pogodina E, Dmitrii S, Slesarev S, Saenko Y. The effect of chromosome abnormalities on expression of SnoRNA in radioresistant and radiosensitive cell lines after irradiation. Cancer Biomark 2022; 34:545-553. [PMID: 35275519 DOI: 10.3233/cbm-210092] [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: 11/02/2022]
Abstract
In this paper, we have studied the role of chromosomal abnormalities in the expression of small nucleolar RNAs (snoRNAs) of radioresistant (K562) and radiosensitive (HL-60) leukemia cell line. Cells were exposed to an X-ray dose of 4 Gy. SnoRNA expression was investigated using NGS sequencing. The distribution of expressed snoRNAs on chromosomes has been found to be different for two cell lines. The most significant differences in the expression of snoRNAs were found in the K562 cell line based on the analysis of the dynamics of log2fc values. The type of clustering, the number and type of snoRNAs slightly differed in the chromosomes with trisomy and monosomy and had a pronounced difference in pairs with marker chromosomes in both cell lines. In this study, we have demonstrated that chromosomal abnormalities alter the expression of snoRNA after irradiation. Trisomies and monosomies do not have such a noticeable effect on the expression of snoRNAs as the presence of marker chromosomes.
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Affiliation(s)
- Eugenia Rastorgueva
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian.,Department of General and Clinical Pharmacology and Microbiology, Faculty of Medicine, Ulyanovsk State University, Ulyanovsk, Russian
| | - Daria Liamina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Ivan Panchenko
- Second Surgical Department, Ulyanovsk Oncology Center, Ulyanovsk, Russian
| | - Elena Iurova
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgenii Beloborodov
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgeniya Pogodina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sugak Dmitrii
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sergei Slesarev
- Department of Biology, Ecology and Natural Resources Management, Faculty of Ecology, Ulyanovsk State University, Ulyanovsk, Russia
| | - Yury Saenko
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
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14
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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15
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Calvo Sánchez J, Köhn M. Small but Mighty-The Emerging Role of snoRNAs in Hematological Malignancies. Noncoding RNA 2021; 7:68. [PMID: 34842767 PMCID: PMC8629011 DOI: 10.3390/ncrna7040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Over recent years, the long known class of small nucleolar RNAs (snoRNAs) have gained interest among the scientific community, especially in the clinical context. The main molecular role of this interesting family of non-coding RNAs is to serve as scaffolding RNAs to mediate site-specific RNA modification of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). With the development of new sequencing techniques and sophisticated analysis pipelines, new members of the snoRNA family were identified and global expression patterns in disease backgrounds could be determined. We will herein shed light on the current research progress in snoRNA biology and their clinical role by influencing disease outcome in hematological diseases. Astonishingly, in recent studies snoRNAs emerged as potent biomarkers in a variety of these clinical setups, which is also highlighted by the frequent deregulation of snoRNA levels in the hema-oncological context. However, research is only starting to reveal how snoRNAs might influence cellular functions and the connected disease hallmarks in hematological malignancies.
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Affiliation(s)
| | - Marcel Köhn
- Junior Research Group ‘RBPs and ncRNAs in Human Diseases’, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Saale, Germany;
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16
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Small nucleolar RNA is potential as a novel player in leukemogenesis and clinical application. BLOOD SCIENCE 2021; 3:122-131. [PMID: 35402848 PMCID: PMC8975097 DOI: 10.1097/bs9.0000000000000091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
Lack of clarity of the mechanisms that underlie leukemogenesis obstructs the diagnosis, prognosis, and treatment of leukemia. Research has found that small nuclear RNA (snoRNA) plays an essential role in leukemia. These small non-coding RNAs are involved in ribosome biogenesis, including the 2′-O-methylation and pseudouridylation of precursor ribosomal RNA (pre-rRNA), and pre-rRNA splicing. Recently, many snoRNAs were found to be orphans that have no predictable RNA modification targets, but these RNAs have always been found to be located in different subcellular organelles, and they play diverse roles. Using high-throughput technology, snoRNA expression profiles have been revealed in leukemia, and some of the deregulated snoRNAs may regulate the cell cycle, differentiation, proliferation, and apoptosis in leukemic cells and confer drug resistance during leukemia treatment. In this review, we discuss the expression profiles and functions of snoRNAs, particularly orphan snoRNAs, in leukemia. It is possible that the dysregulated snoRNAs are promising diagnosis and prognosis markers for leukemia, which may serve as potential therapeutic targets in leukemia treatment.
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17
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Fazi F, Fatica A. Regulation of Ribosome Function by RNA Modifications in Hematopoietic Development and Leukemia: It Is Not Only a Matter of m 6A. Int J Mol Sci 2021; 22:ijms22094755. [PMID: 33946178 PMCID: PMC8125340 DOI: 10.3390/ijms22094755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Growth and maturation of hematopoietic stem cells (HSCs) are largely controlled at both transcriptional and post-transcriptional levels. In particular, hematopoietic development requires a tight control of protein synthesis. Furthermore, translational deregulation strongly contributes to hematopoietic malignancies. Researchers have recently identified a new layer of gene expression regulation that consists of chemical modification of RNA species, which led to the birth of the epitranscriptomics field. RNA modifications provide an additional level of control in hematopoietic development by acting as post-transcriptional regulators of lineage-specific genetic programs. Other reviews have already described the important role of the N6-methylation of adenosine (m6A) within mRNA species in regulating hematopoietic differentiation and diseases. The aim of this review is to summarize the current status of the role of RNA modifications in the regulation of ribosome function, beyond m6A. In particular, we discuss the importance of RNA modifications in tRNA and rRNA molecules. By balancing translational rate and fidelity, they play an important role in regulating normal and malignant hematopoietic development.
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Affiliation(s)
- Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, 00165 Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
- Correspondence: (F.F.); (A.F.)
| | - Alessandro Fatica
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, 00165 Rome, Italy
- Correspondence: (F.F.); (A.F.)
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18
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miR-139-5p Regulates the Proliferation of Acute Promyelocytic Leukemia Cells by Targeting MNT. JOURNAL OF ONCOLOGY 2021; 2021:5522051. [PMID: 33953744 PMCID: PMC8064781 DOI: 10.1155/2021/5522051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Acute promyelocytic leukemia (APL) patients with progressive leukocytosis are more likely to have various complications and poor outcomes. However, the regulatory roles of microRNAs in the leukocytosis of APL have not been clarified. Our study aims to evaluate the effects of miRNAs on leukocytosis during induction therapy of APL patients and explore its potential mechanisms. During induction treatment, patients with white blood cell count higher than 10 × 109/L were divided into leukocytosis group and others were nonleukocytosis group. Using microarray assays, we found that miR-139-5p was significantly downregulated in the leukocytosis group. Elevated expression of miR-139-5p inhibited the proliferation of NB4 cells by arresting the cell cycle and inducing apoptosis. We further identified that MNT was a target of miR-139-5p. miR-139-5p significantly inhibited the proliferation, invasion, and migration function of NB4 cells through targeting MNT. Strategies for regulating miR-139-5p or MNT expression might provide new therapeutic approaches for progressive leukocytosis in APL.
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19
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Rodriguez PD, Paculova H, Kogut S, Heath J, Schjerven H, Frietze S. Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22052683. [PMID: 33799946 PMCID: PMC7961854 DOI: 10.3390/ijms22052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Jessica Heath
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Department of Pediatrics, University of Vermont, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Correspondence:
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20
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021; 11:jkaa014. [PMID: 33561224 PMCID: PMC7849908 DOI: 10.1093/g3journal/jkaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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21
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021. [PMID: 33561224 DOI: 10.1093/g3journal/jkaa014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA.,The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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22
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Elsharawy KA, Althobiti M, Mohammed OJ, Aljohani AI, Toss MS, Green AR, Rakha EA. Nucleolar protein 10 (NOP10) predicts poor prognosis in invasive breast cancer. Breast Cancer Res Treat 2020; 185:615-627. [PMID: 33161513 PMCID: PMC7920889 DOI: 10.1007/s10549-020-05999-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/26/2020] [Indexed: 01/16/2023]
Abstract
Purpose Nucleolar protein 10 (NOP10) is required for ribosome biogenesis and telomere maintenance and plays a key role in carcinogenesis. This study aims to evaluate the clinical and prognostic significance of NOP10 in breast cancer (BC). Methods NOP10 expression was assessed at mRNA level employing the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (n = 1980) and Cancer Genome Atlas (TCGA) BC cohorts (n = 854). Protein expression was evaluated on tissue microarray of a large BC cohort (n = 1081) using immunohistochemistry. The correlation between NOP10 expression, clinicopathological parameters and patient outcome was assessed. Results NOP10 expression was detected in the nucleus and nucleolus of the tumour cells. At the transcriptomic and proteomic levels, NOP10 was significantly associated with aggressive BC features including high tumour grade, high nucleolar score and poor Nottingham Prognostic Index. High NOP10 protein expression was an independent predictor of poor outcome in the whole cohort and in triple-negative BC (TNBC) class (p = 0.002 & p = 0.014, respectively). In chemotherapy- treated patients, high NOP10 protein expression was significantly associated with shorter survival (p = 0.03) and was predictive of higher risk of death (p = 0.028) and development of distant metastasis (p = 0.02) independent of tumour size, nodal stage and tumour grade. Conclusion High NOP10 expression is a poor prognostic biomarker in BC and its expression can help in predicting chemotherapy resistance. Functional assessments are necessary to decipher the underlying mechanisms and to reveal its potential therapeutic values in various BC subtypes especially in the aggressive TNBC class. Electronic supplementary material The online version of this article (doi:10.1007/s10549-020-05999-3) contains supplementary material, which is available to authorized users.
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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
| | - Maryam Althobiti
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.,Department of Clinical Laboratory Science, College of Applied Medical Science, Shaqra University, Shaqra, Saudi Arabia
| | - 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
| | - Abrar I Aljohani
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | - 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
| | - 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. .,Division of Cancer and Stem Cell, University of Nottingham, City Hospital Campus, Hucknall Road, Nottingham, NG5 1PB, UK.
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23
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Hu S, Chen X, Xu X, Zheng C, Huang W, Zhou Y, Akuetteh PDP, Yang H, Shi K, Chen B, Zhang Q. STRAP as a New Therapeutic Target for Poor Prognosis of Pancreatic Ductal Adenocarcinoma Patients Mainly Caused by TP53 Mutation. Front Oncol 2020; 10:594224. [PMID: 33134183 PMCID: PMC7550692 DOI: 10.3389/fonc.2020.594224] [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: 08/12/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a high mortality rate and poor prognosis. KRAS, TP53, CDKN2A, and SMAD4 are driver genes of PDAC and 30-75% patients have mutations in at least two of these four genes. Herein, we analyzed the relationship between these genes and prognosis of 762 patients in the absence of coexisting mutations, using data from three independent public datasets. Interestingly, we found that compared with mutations in other driver genes, TP53 mutation plays a significant role in leading to poor prognosis of PDAC. Additionally, we found that snoRNA-mediated rRNA maturation was responsible for the progression of cancer in PDAC patients with TP53 mutations. Inhibition of STRAP, which regulates the localization of SMN complexes and further affects the assembly of snoRNP, can effectively reduce maturation of rRNA and significantly suppress progression of TP53-mutant or low p53 expression pancreatic cancer cells in vitro and in vivo. Our study highlighted the actual contribution rate of driver genes to patient prognosis, enriching traditional understanding of the relationship between these genes and PDAC. We also provided a possible mechanism and a new target to combat progression of TP53-mutant PDAC patients.
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Affiliation(s)
- Shanshan Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangxiang Xu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chenlei Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenqian Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Percy David Papa Akuetteh
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongbao Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Keqing Shi
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bicheng Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiyu Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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24
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Non-coding RNAs in Brain Tumors, the Contribution of lncRNAs, circRNAs, and snoRNAs to Cancer Development-Their Diagnostic and Therapeutic Potential. Int J Mol Sci 2020; 21:ijms21197001. [PMID: 32977537 PMCID: PMC7582339 DOI: 10.3390/ijms21197001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/17/2022] Open
Abstract
Brain tumors are one of the most frightening ailments that afflict human beings worldwide. They are among the most lethal of all adult and pediatric solid tumors. The unique cell-intrinsic and microenvironmental properties of neural tissues are some of the most critical obstacles that researchers face in the diagnosis and treatment of brain tumors. Intensifying the search for potential new molecular markers in order to develop new effective treatments for patients might resolve this issue. Recently, the world of non-coding RNAs (ncRNAs) has become a field of intensive research since the discovery of their essential impact on carcinogenesis. Some of the most promising diagnostic and therapeutic regulatory RNAs are long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small nucleolar RNAs (snoRNAs). Many recent reports indicate the important role of these molecules in brain tumor development, as well as their implications in metastasis. In the following review, we summarize the current state of knowledge about regulatory RNAs, namely lncRNA, circRNAs, and snoRNAs, and their impact on the development of brain tumors in children and adults with particular emphasis on malignant primary brain tumors-gliomas and medulloblastomas (MB). We also provide an overview of how these different ncRNAs may act as biomarkers in these tumors and we present their potential clinical implications.
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25
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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26
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Håkansson KEJ, Goossens EAC, Trompet S, van Ingen E, de Vries MR, van der Kwast RVCT, Ripa RS, Kastrup J, Hohensinner PJ, Kaun C, Wojta J, Böhringer S, Le Cessie S, Jukema JW, Quax PHA, Nossent AY. Genetic associations and regulation of expression indicate an independent role for 14q32 snoRNAs in human cardiovascular disease. Cardiovasc Res 2020; 115:1519-1532. [PMID: 30544252 DOI: 10.1093/cvr/cvy309] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/11/2018] [Indexed: 01/12/2023] Open
Abstract
AIMS We have shown that 14q32 microRNAs are highly involved in vascular remodelling and cardiovascular disease. However, the 14q32 locus also encodes 41 'orphan' small nucleolar RNAs (snoRNAs). We aimed to gather evidence for an independent role for 14q32 snoRNAs in human cardiovascular disease. METHODS AND RESULTS We performed a lookup of the 14q32 region within the dataset of a genome wide association scan in 5244 participants of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER). Single nucleotide polymorphisms (SNPs) in the snoRNA-cluster were significantly associated with heart failure. These snoRNA-cluster SNPs were not linked to SNPs in the microRNA-cluster or in MEG3, indicating that snoRNAs modify the risk of cardiovascular disease independently. We looked at expression of 14q32 snoRNAs throughout the human cardio-vasculature. Expression profiles of the 14q32 snoRNAs appeared highly vessel specific. When we compared expression levels of 14q32 snoRNAs in human vena saphena magna (VSM) with those in failed VSM-coronary bypasses, we found that 14q32 snoRNAs were up-regulated. SNORD113.2, which showed a 17-fold up-regulation in failed bypasses, was also up-regulated two-fold in plasma samples drawn from patients with ST-elevation myocardial infarction directly after hospitalization compared with 30 days after start of treatment. However, fitting with the genomic associations, 14q32 snoRNA expression was highest in failing human hearts. In vitro studies show that the 14q32 snoRNAs bind predominantly to methyl-transferase Fibrillarin, indicating that they act through canonical mechanisms, but on non-canonical RNA targets. The canonical C/D-box snoRNA seed sequences were highly conserved between humans and mice. CONCLUSION 14q32 snoRNAs appear to play an independent role in cardiovascular pathology. 14q32 snoRNAs are specifically regulated throughout the human vasculature and their expression is up-regulated during cardiovascular disease. Our data demonstrate that snoRNAs merit increased effort and attention in future basic and clinical cardiovascular research.
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Affiliation(s)
- Kjell E J Håkansson
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Reginald V C T van der Kwast
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Rasmus S Ripa
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | - Jens Kastrup
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | | | - Christoph Kaun
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Johann Wojta
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Stefan Böhringer
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia Le Cessie
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Ludwig Boltzmann Cluster for Cardiovascular Research, Vienna, Austria
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27
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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28
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Shi H, Chai P, Jia R, Fan X. Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation. Mol Cancer 2020; 19:78. [PMID: 32303268 PMCID: PMC7164178 DOI: 10.1186/s12943-020-01194-6] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
RNA modifications can be added or removed by a variety of enzymes that catalyse the necessary reactions, and these modifications play roles in essential molecular mechanisms. The prevalent modifications on mRNA include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), pseudouridine (Ψ), inosine (I), uridine (U) and ribosemethylation (2’-O-Me). Most of these modifications contribute to pre-mRNA splicing, nuclear export, transcript stability and translation initiation in eukaryotic cells. By participating in various physiological processes, RNA modifications also have regulatory roles in the pathogenesis of tumour and non-tumour diseases. We discussed the physiological roles of RNA modifications and associated these roles with disease pathogenesis. Functioning as the bridge between transcription and translation, RNA modifications are vital for the progression of numerous diseases and can even regulate the fate of cancer cells.
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Affiliation(s)
- Hanhan Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
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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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Abstract
RNA plays essential roles in not only translating nucleic acids into proteins, but also in gene regulation, environmental interactions and many human diseases. Nature uses over 150 chemical modifications to decorate RNA and diversify its functions. With the fast-growing RNA research in the burgeoning field of 'epitranscriptome', a term describes post-transcriptional RNA modifications that can dynamically change the transcriptome, it becomes clear that these modifications participate in modulating gene expression and controlling the cell fate, thereby igniting the new interests in RNA-based drug discovery. The dynamics of these RNA chemical modifications is orchestrated by coordinated actions of an array of writer, reader and eraser proteins. Deregulated expression of these RNA modifying proteins can lead to many human diseases including cancer. In this review, we highlight several critical modifications, namely m6A, m1A, m5C, inosine and pseudouridine, in both coding and non-coding RNAs. In parallel, we present a few other cancer-related tRNA and rRNA modifications. We further discuss their roles in cancer promotion or tumour suppression. Understanding the molecular mechanisms underlying the biogenesis and turnover of these RNA modifications will be of great significance in the design and development of novel anticancer drugs.
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Affiliation(s)
- Phensinee Haruehanroengra
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
| | - Ya Ying Zheng
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University , Houston, TX, USA
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University , Houston, TX, USA
| | - Jia Sheng
- Department of Chemistry and the RNA Institute, College of Arts and Science, University at Albany, State University of New York , Albany, NY, USA
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31
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Goustin AS, Thepsuwan P, Kosir MA, Lipovich L. The Growth-Arrest-Specific ( GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers. Noncoding RNA 2019; 5:ncrna5030046. [PMID: 31533355 PMCID: PMC6789762 DOI: 10.3390/ncrna5030046] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading frames (smORFs) that may encode short proteins. Any given lncRNA may have more than one of these functions. This review focuses on one fascinating case—the growth-arrest-specific (GAS)-5 gene, encoding a complicated repertoire of alternatively-spliced lncRNA isoforms. GAS5 is also a host gene of numerous small nucleolar (sno) RNAs, which are processed from its introns. Publications about this lncRNA date back over three decades, covering its role in cell proliferation, cell differentiation, and cancer. The GAS5 story has drawn in contributions from prominent molecular geneticists who attempted to define its tumor suppressor function in mechanistic terms. The evidence suggests that rodent Gas5 and human GAS5 functions may be different, despite the conserved multi-exonic architecture featuring intronic snoRNAs, and positional conservation on syntenic chromosomal regions indicating that the rodent Gas5 gene is the true ortholog of the GAS5 gene in man and other apes. There is no single answer to the molecular mechanism of GAS5 action. Our goal here is to summarize competing, not mutually exclusive, mechanistic explanations of GAS5 function that have compelling experimental support.
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Affiliation(s)
- Anton Scott Goustin
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | | | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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32
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Zhu W, Niu J, He M, Zhang L, Lv X, Liu F, Jiang L, Zhang J, Yu Z, Zhao L, Bi J, Yan Y, Wei Q, Huo H, Fan Y, Chen Y, Ding J, Wei M. SNORD89 promotes stemness phenotype of ovarian cancer cells by regulating Notch1-c-Myc pathway. J Transl Med 2019; 17:259. [PMID: 31395064 PMCID: PMC6686521 DOI: 10.1186/s12967-019-2005-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022] Open
Abstract
Background Ovarian cancer is the leading cause of death in gynecological cancer. Cancer stem cells (CSCs) contribute to the occurrence, progression and resistance. Small nucleolar RNAs (SnoRNAs), a class of small molecule non-coding RNA, involve in the cancer cell stemness and tumorigenesis. Methods In this study, we screened out SNORNAs related to ovarian patient’s prognosis by analyzing the data of 379 cases of ovarian cancer patients in the TCGA database, and analyzed the difference of SNORNAs expression between OVCAR-3 (OV) sphere-forming (OS) cells and OV cells. After overexpression or knockdown SNORD89, the expression of Nanog, CD44, and CD133 was measured by qRT-PCR or flow cytometry analysis in OV, CAOV-3 (CA) and OS cells, respectively. CCK-8 assays, plate clone formation assay and soft agar colony formation assay were carried out to evaluate the changes of cell proliferation and self-renewal ability. Scratch migration assay and trans-well invasion analysis were used for assessing the changes of migration and invasion ability. Results High expression of SNORD89 indicates the poor prognosis of ovarian cancer patients and was associated with patients’ age, therapy outcome. SNORD89 highly expressed in ovarian cancer stem cells. The overexpression of SNORD89 resulted in the increased stemness markers, S phase cell cycle, cell proliferation, invasion and migration ability in OV and CA cells. Conversely, these phenomena were reversed after SNORD89 silencing in OS cells. Further, we found that SNORD89 could upregulate c-Myc and Notch1 expression in mRNA and protein levels. SNORD89 deteriorates the prognosis of ovarian cancer patients by regulating Notch1-c-Myc pathway to promote cell stemness and acts as an oncogene in ovarian tumorigenesis. Consequently, SNORD89 can be a novel prognostic biomarker and therapeutic target for ovarian cancer. Electronic supplementary material The online version of this article (10.1186/s12967-019-2005-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjing Zhu
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Department of Pharmacy, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Jumin Niu
- Shenyang Women's and Children's Hospital, Shenyang, Liaoning, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Liwen Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Xuemei Lv
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Fangxiao Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Longyang Jiang
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Jing Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Jia Bi
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Hong Huo
- Department of Pharmaceutics, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Yue Fan
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China.,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jian Ding
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China. .,Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, People's Republic of China. .,Liaoning Engineering Technology Research Center for the Research, Development and Industrialization of Innovative Peptide Drugs, China Medical University, Shenyang, Liaoning, China.
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Overexpression of SNORA21 suppresses tumorgenesis of gallbladder cancer in vitro and in vivo. Biomed Pharmacother 2019; 118:109266. [PMID: 31401397 DOI: 10.1016/j.biopha.2019.109266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Gallbladder cancer (GBC) ranks fifth in the most common malignancy of the gastrointestinal tract worldwide. It is reported many small nucleolar RNAs (SNORNs) could regulate the progression of GBC. To identify potential therapeutic targets for GBC, we conducted microarray analysis in GBC tissues and adjacent normal tissues. We found that SNORA21 was downregulated most in gallbladder tumor samples. Therefore, this research aimed to investigate the role of SNORA21 during the tumorigenesis of GBC. METHODS The differential expression of SNORNs between GBC tissues and para-carcinoma tissues were examined by microarray analysis and that were confirmed by qRT-PCR. Cell proliferation was tested by CCK-8 and immunofluorescence. Cell apoptosis and cell cycle in GBC were detected by flow cytometry. Expression of proteins in GBC cells was measured by Western-blot. Transwell assay was used for testing the cell migration and invasion. Xenograft tumor model was established to verify the effect of SNORA21 overexpression on GBC in vivo. RESULTS The results revealed that SNORA21 overexpression inhibited the proliferation, migration and invasion of GBC cells. Moreover, overexpression of SNORA21 significantly increased the expression of E-cadherin and decreased the levels of N-cadherin and vimentin. Meanwhile, overexpression of SNORA21 significantly induced apoptosis and G1 arrest of GBC cells. Finally, SNORA21 overexpression significantly suppressed the growth of gallbladder tumors in vivo. CONCLUSION Overexpression of SNORA21 significantly suppressed the tumorigenesis of GBC in vitro and in vivo, which may serve as a potential novel target for the treatment of GBC.
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Liang J, Wen J, Huang Z, Chen XP, Zhang BX, Chu L. Small Nucleolar RNAs: Insight Into Their Function in Cancer. Front Oncol 2019; 9:587. [PMID: 31338327 PMCID: PMC6629867 DOI: 10.3389/fonc.2019.00587] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs divided into two classes: C/D box snoRNAs and H/ACA box snoRNAs. The canonical function of C/D box and H/ACA box snoRNAs are 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. Emerging evidence has demonstrated that snoRNAs are involved in various physiological and pathological cellular processes. Mutations and aberrant expression of snoRNAs have been reported in cell transformation, tumorigenesis, and metastasis, indicating that snoRNAs may serve as biomarkers and/or therapeutic targets of cancer. Hence, further study of the functions and underlying mechanism of snoRNAs is valuable. In this review, we summarize the biogenesis and functions of snoRNAs, as well as the association of snoRNAs in different types of cancers and their potential roles in cancer diagnosis and therapy.
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Affiliation(s)
- Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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35
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Sun Y, Chen E, Li Y, Ye D, Cai Y, Wang Q, Li Q, Zhang X. H/ACA box small nucleolar RNA 7B acts as an oncogene and a potential prognostic biomarker in breast cancer. Cancer Cell Int 2019; 19:125. [PMID: 31168298 PMCID: PMC6509762 DOI: 10.1186/s12935-019-0830-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 04/20/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most frequent malignancy occurring in women worldwide. Emerging evidence indicates that small nucleolar RNAs (snoRNAs) play a role in tumor development. In the current study, we evaluated expression profiles and functions of snoRNAs associated with BC. METHODS We analyzed the expression levels of snoRNAs between breast cancer and normal tissues in TCGA database and found that SNORA7B is upregulated in BC. We confirmed this result in clinical cancer tissues and BC cell lines via qRT-PCR. Then, we investigated clinical significance in public datasets and biological function of SNORA7B using a series of in vitro gain- and loss-of-function experiments. RESULTS SNORA7B expression was significantly upregulated in samples from patients with BC in both public database and our clinical tissues compared to its expression in normal tissues. Meanwhile, patients with high SNORA7B expression have worse prognosis. Inhibition of SNORA7B expression impaired cell growth, proliferation, migration, and invasion via inducing apoptosis. CONCLUSIONS SNORA7B functions as an important oncogenic snoRNA in BC and may serve as a potential prognosis biomarker for BC.
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Affiliation(s)
- Yihan Sun
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Endong Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Yuefeng Li
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Danrong Ye
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Yefeng Cai
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Qingxuan Wang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Quan Li
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
| | - Xiaohua Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 32500 Zhejiang China
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Abstract
While only a small part of the human genome encodes for proteins, biological functions for the so-called junk genome are increasingly being recognized through high-throughput technologies and mechanistic experimental studies. Indeed, novel mechanisms of gene regulation are being discovered that require coordinated interaction between DNA, RNA, and proteins. Therefore, interdisciplinary efforts are still needed to decipher these complex transcriptional networks. In this review, we discuss how non-coding RNAs (ncRNAs) are epigenetically regulated in cancer and metastases and consequently how ncRNAs participate in the sculpting of the epigenetic profile of a cancer cell, thus modulating the expression of other RNA molecules. In the latter case, ncRNAs not only affect the DNA methylation status of certain genomic loci but also interact with histone-modifying complexes, changing the structure of the chromatin itself. We present several examples of epigenetic changes causing aberrant expression of ncRNAs in the context of tumor progression. Interestingly, there are also important epigenetic changes and transcriptional regulatory effects derived from their aberrant expression. As ncRNAs can also be used as biomarkers for diagnosis and prognosis or explored as potential targets, we present insights into the use of ncRNAs for targeted cancer therapy.
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Capomaccio S, Cappelli K, Bazzucchi C, Coletti M, Gialletti R, Moriconi F, Passamonti F, Pepe M, Petrini S, Mecocci S, Silvestrelli M, Pascucci L. Equine Adipose-Derived Mesenchymal Stromal Cells Release Extracellular Vesicles Enclosing Different Subsets of Small RNAs. Stem Cells Int 2019; 2019:4957806. [PMID: 31011332 PMCID: PMC6442443 DOI: 10.1155/2019/4957806] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/13/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Equine adipose-derived mesenchymal stromal cells (e-AdMSC) exhibit attractive proregenerative properties strongly related to the delivery of extracellular vesicles (EVs) that enclose different kinds of molecules including RNAs. In this study, we investigated small RNA content of EVs produced by e-AdMSC with the aim of speculating on their possible biological role. METHODS EVs were obtained by ultracentrifugation of the conditioned medium of e-AdMSC of 4 subjects. Transmission electron microscopy and scanning electron microscopy were performed to assess their size and nanostructure. RNA was isolated, enriched for small RNAs (<200 nt), and sequenced by Illumina technology. After bioinformatic analysis with state-of-the-art pipelines for short sequences, mapped reads were used to describe EV RNA cargo, reporting classes, and abundances. Enrichment analyses were performed to infer involved pathways and functional categories. RESULTS Electron microscopy showed the presence of vesicles ranging in size from 30 to 300 nm and expressing typical markers. RNA analysis revealed that ribosomal RNA was the most abundant fraction, followed by small nucleolar RNAs (snoRNAs, 13.67%). Miscellaneous RNA (misc_RNA) reached 4.57% of the total where Y RNA, RNaseP, and vault RNA represented the main categories. miRNAs were sequenced at a lower level (3.51%) as well as protein-coding genes (1.33%). Pathway analyses on the protein-coding fraction revealed a significant enrichment for the "ribosome" pathway followed by "oxidative phosphorylation." Gene Ontology analysis showed enrichment for terms like "extracellular exosome," "organelle envelope," "RNA binding," and "small molecule metabolic process." The miRNA target pathway analysis revealed the presence of "signaling pathways regulating pluripotency of stem cells" coherent with the source of the samples. CONCLUSION We herein demonstrated that e-AdMSC release EVs enclosing different subsets of small RNAs that potentially regulate a number of biological processes. These findings shed light on the role of EVs in the context of MSC biology.
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Affiliation(s)
- Stefano Capomaccio
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Katia Cappelli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Cinzia Bazzucchi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
| | - Mauro Coletti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Rodolfo Gialletti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Franco Moriconi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Fabrizio Passamonti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Marco Pepe
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Stefano Petrini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Italy
| | - Samanta Mecocci
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Maurizio Silvestrelli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
| | - Luisa Pascucci
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo, 4, 06126 Perugia, Italy
- Centro di Ricerca sul Cavallo Sportivo (CRCS), Università degli Studi di Perugia, Italy
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Sellers ZP, Bolkun L, Kloczko J, Wojtaszewska ML, Lewandowski K, Moniuszko M, Ratajczak MZ, Schneider G. Increased methylation upstream of the MEG3 promotor is observed in acute myeloid leukemia patients with better overall survival. Clin Epigenetics 2019; 11:50. [PMID: 30876483 PMCID: PMC6419839 DOI: 10.1186/s13148-019-0643-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/28/2019] [Indexed: 12/24/2022] Open
Abstract
Background The delta-like non-canonical Notch ligand 1 (DLK1)-maternally expressed 3(MEG3) locus (DLK1-MEG3 locus) plays a critical role in the maintenance and differentiation of hematopoietic stem cells. Accumulating evidence implicates the imprinted genes from this locus, DLK1 and MEG3, in the development and progression of acute myeloid leukemia (AML). However, the contribution of this locus to the treatment response of patients and their survival is unknown. Methods DNA methylation of select CG dinucleotide-containing amplicons (CpG sites) within the DLK1-MEG3 locus and within differentially methylated regions of other imprinted loci was assessed in the mononuclear cells of 45 AML patients by combined bisulfite restriction analysis. Methylation results were compared with patient response to first-round induction therapy and overall survival. Multivariable analysis was employed to identify independent prognostic factors for patient overall survival in AML. Results Increased methylation at CpG sites within the MEG3 promotor region was observed in AML patients having longer overall survival. In addition, patients with shorter overall survival had increased expression of DLK1 and MEG3, and methylation at the MEG3-DMR CpG site inversely correlated with MEG3 expression. Multivariable analysis revealed that methylation at CG9, a non-imprinted CpG site within the MEG3 promotor region which contains a CCCTC-binding factor (CTCF)-binding DNA sequence, is an independent prognostic factor for the overall survival of AML patients. Conclusions The results of our pilot study underscore the importance of the DLK1-MEG3 locus in AML development and progression. We identify CG9 methylation as an independent prognostic factor for AML patient survival, which suggests that distinct miRNA signatures from the DLK1-MEG3 locus could reflect varying degrees of cell stemness and present novel opportunities for personalized therapies in the future. These data provide a foundation for future studies into the role of higher-order chromatin structure at DLK1-MEG3 in AML. Electronic supplementary material The online version of this article (10.1186/s13148-019-0643-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachariah Payne Sellers
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Lukasz Bolkun
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | - Janusz Kloczko
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | | | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, University of Medical Sciences, Poznań, Poland
| | - Marcin Moniuszko
- Department of Allergology, Medical University of Bialystok, Bialystok, Poland.,Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA. .,Department of Regenerative Medicine, Medical University of Warsaw, Warsaw, Poland.
| | - Gabriela Schneider
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA.
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Expression profiling of snoRNAs in normal hematopoiesis and AML. Blood Adv 2019; 2:151-163. [PMID: 29365324 DOI: 10.1182/bloodadvances.2017006668] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. We optimized a next-generation sequencing approach and a custom analysis pipeline to identify and quantify expression of snoRNAs in acute myeloid leukemia (AML) and normal hematopoietic cell populations. We show that snoRNAs are expressed in a lineage- and development-specific fashion during hematopoiesis. The most striking examples involve snoRNAs located in 2 imprinted loci, which are highly expressed in hematopoietic progenitors and downregulated during myeloid differentiation. Although most snoRNAs are expressed at similar levels in AML cells compared with CD34+, a subset of snoRNAs showed consistent differential expression, with the great majority of these being decreased in the AML samples. Analysis of host gene expression, splicing patterns, and whole-genome sequence data for mutational events did not identify transcriptional patterns or genetic alterations that account for these expression differences. These data provide a comprehensive analysis of the snoRNA transcriptome in normal and leukemic cells and should be helpful in the design of studies to define the contribution of snoRNAs to normal and malignant hematopoiesis.
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40
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Srivastava A, Creek DJ. Discovery and Validation of Clinical Biomarkers of Cancer: A Review Combining Metabolomics and Proteomics. Proteomics 2018; 19:e1700448. [PMID: 30353665 DOI: 10.1002/pmic.201700448] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/11/2018] [Indexed: 12/19/2022]
Abstract
Early detection and diagnosis of cancer can allow timely medical intervention, which greatly improves chances of survival and enhances quality of life. Biomarkers play an important role in assisting clinicians and health care providers in cancer diagnosis and treatment follow-up. In spite of years of research and the discovery of thousands of candidate cancer biomarkers, only a few have transitioned to routine usage in the clinic. This review highlights advances in proteomics technologies that have enabled high rates of discovery of candidate cancer biomarkers and evaluates integration with other omics technologies to improve their progress through to validation and clinical translation. Furthermore, it gauges the role of metabolomics technology in cancer biomarker research and assesses it as a complementary tool in aiding cancer biomarker discovery and validation.
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Affiliation(s)
- Anubhav Srivastava
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Darren John Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
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41
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Akhtari FS, Havener TM, Fukudo M, Jack JR, McLeod HL, Wiltshire T, Motsinger-Reif AA. The influence of Neanderthal alleles on cytotoxic response. PeerJ 2018; 6:e5691. [PMID: 30386687 PMCID: PMC6202974 DOI: 10.7717/peerj.5691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
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Affiliation(s)
- Farida S Akhtari
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
| | - Tammy M Havener
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | | | - John R Jack
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
| | - Howard L McLeod
- The DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Tim Wiltshire
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
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2'-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation? Biomolecules 2018; 8:biom8040106. [PMID: 30282949 PMCID: PMC6316387 DOI: 10.3390/biom8040106] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2′-O-Me to the translational capacity of ribosomes has been established. Yet, how 2′-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2′-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2′-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2′-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.
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43
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Merkerova MD, Remesova H, Krejcik Z, Loudova N, Hrustincova A, Szikszai K, Cermak J, Jonasova A, Belickova M. Relationship between Altered miRNA Expression and DNA Methylation of the DLK1-DIO3 Region in Azacitidine-Treated Patients with Myelodysplastic Syndromes and Acute Myeloid Leukemia with Myelodysplasia-Related Changes. Cells 2018; 7:cells7090138. [PMID: 30223454 PMCID: PMC6162661 DOI: 10.3390/cells7090138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
The DLK1–DIO3 region contains a large miRNA cluster, the overexpression of which has previously been associated with myelodysplastic syndromes (MDS). To reveal whether this overexpression is epigenetically regulated, we performed an integrative analysis of miRNA/mRNA expression and DNA methylation of the regulatory sequences in the region (promoter of the MEG3 gene) in CD34+ bone marrow cells from the patients with higher-risk MDS and acute myeloid leukemia with myelodysplasia-related changes (AML-MRC), before and during hypomethylating therapy with azacytidine (AZA). Before treatment, 50% of patients showed significant miRNA/mRNA overexpression in conjunction with a diagnosis of AML-MRC. Importantly, increased level of MEG3 was associated with poor outcome. After AZA treatment, the expression levels were reduced and were closer to those seen in the healthy controls. In half of the patients, we observed significant hypermethylation in a region preceding the MEG3 gene that negatively correlated with expression. Interestingly, this hypermethylation (when found before treatment) was associated with longer progression-free survival after therapy initiation. However, neither expression nor methylation status were associated with future responsiveness to AZA treatment. In conclusion, we correlated expression and methylation changes in the DLK1–DIO3 region, and we propose a complex model for regulation of this region in myelodysplasia.
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Affiliation(s)
| | - Hana Remesova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Nikoleta Loudova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Andrea Hrustincova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Katarina Szikszai
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
| | - Anna Jonasova
- General University Hospital, 128 08 Prague, Czech Republic.
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
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44
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Światowy W, Jagodzińśki PP. Molecules derived from tRNA and snoRNA: Entering the degradome pool. Biomed Pharmacother 2018; 108:36-42. [PMID: 30216797 DOI: 10.1016/j.biopha.2018.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/03/2018] [Accepted: 09/04/2018] [Indexed: 02/02/2023] Open
Abstract
Molecules built of RNA have been the subjects of numerous studies, which have made known new functions and structures that these molecules can create. In recent years, thanks to next-generation sequencing, it is possible to observe very small RNAs and the number of newly discovered RNA molecules is rapidly increasing. Among other small oligonucleotides, structures derived from tRNA and snoRNA molecules have been observed, and these molecules were determined to not be precursors of known RNA molecules. These structures have attracted the attention of researchers because the level of accumulation of tRNA or snoRNA fragments was relatively high. Additionally, other parts of the parent molecules were absent. Derivatives of well-known RNA molecules also have functions that are different from their parent molecules. They are mainly involved in regulating the expression of genetic information in a similar way to miRNA. In addition, some of the miRNAs that have been described are derivatives of tRNA or snoRNA. Most of the research on these newly discovered molecules is based on their detection and on the study of the macro effects that they exert, in the absence of a description of the molecular mechanism by which they arise and work.
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Affiliation(s)
- Witold Światowy
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland.
| | - Paweł P Jagodzińśki
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland
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45
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Tusup M, Kundig T, Pascolo S. Epitranscriptomics of cancer. World J Clin Oncol 2018; 9:42-55. [PMID: 29900123 PMCID: PMC5997933 DOI: 10.5306/wjco.v9.i3.42] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
The functional impact of modifications of cellular RNAs, including mRNAs, miRNAs and lncRNAs, is a field of intense study. The role of such modifications in cancer has started to be elucidated. Diverse and sometimes opposite effects of RNA modifications have been reported. Some RNA modifications promote, while others decrease the growth and invasiveness of cancer. The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine, Pseudouridine, Inosine, 2’O-methylation or methylcytidine in cancer’s RNA. It also highlights the remaining questions and provides hints on research avenues and potential therapeutic applications, whereby modulating dynamic RNA modifications may be a new method to treat cancer.
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Affiliation(s)
- Marina Tusup
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
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46
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SNORD47, a box C/D snoRNA, suppresses tumorigenesis in glioblastoma. Oncotarget 2018; 8:43953-43966. [PMID: 28410200 PMCID: PMC5546453 DOI: 10.18632/oncotarget.16693] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022] Open
Abstract
SNORD47 is a member of the C/D box small nucleolar RNAs, which have been implicated in cancer development. We intended to investigate the therapeutic potential of SNORD47 in glioma. We found that the expression of SNORD47 was downregulated in glioma tissues samples and inversely associated with advanced tumor stage (WHO grade IV). Kaplan-Meier survival analysis revealed that glioma patients with high SNORD47 expression had longer overall survival than those with low SNORD47 expression. SNORD47 suppressed the proliferation of glioma cells and induced G2 phase arrest. In addition, upregulation of SNORD47 suppressed invasion and epithelial-mesenchymal transition in glioma cells, and combination treatment with lenti-SNORD47 could augment the anti-tumor effect of temozolomide. These results showed that SNORD47 acted as a tumor suppressor in glioma, and provided the potential anti-tumor function in glioma treatment.
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47
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Molina-Pinelo S, Salinas A, Moreno-Mata N, Ferrer I, Suarez R, Andrés-León E, Rodríguez-Paredes M, Gutekunst J, Jantus-Lewintre E, Camps C, Carnero A, Paz-Ares L. Impact of DLK1-DIO3 imprinted cluster hypomethylation in smoker patients with lung cancer. Oncotarget 2018; 9:4395-4410. [PMID: 29435111 PMCID: PMC5796982 DOI: 10.18632/oncotarget.10611] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 06/02/2016] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is important for gene expression and genome stability, and its disruption is thought to play a key role in the initiation and progression of cancer and other diseases. The DLK1-DIO3 cluster has been shown to be imprinted in humans, and some of its components are relevant to diverse pathological processes. The purpose of this study was to assess the methylation patterns of the DLK1-DIO3 cluster in patients with lung cancer to study its relevance in the pathogenesis of this disease. We found a characteristic methylation pattern of this cluster in smoking associated lung cancer, as compared to normal lung tissue. This methylation profile is not patent however in lung cancer of never smokers nor in lung tissue of COPD patients. We found 3 deregulated protein-coding genes at this locus: one was hypermethylated (DIO3) and two were hypomethylated (DLK1 and RTL1). Statistically significant differences were also detected in two different families of SNORDs, two miRNA clusters and four lncRNAs (MEG3, MEG8, MEG9 and LINC00524). These findings were validated using data from the cancer genome atlas (TCGA) database. We have then showed an inverse correlation between DNA methylation and expression levels in 5 randomly selected genes. Several targets of miRNAs included in the DLK1-DIO3 cluster have been experimentally verified as tumor suppressors. All of these results suggest that the dysmethylation of the imprinted DLK1-DIO3 cluster could have a relevant role in the pathogenesis of lung cancer in current and former smokers and may be used for diagnostic and/or therapeutic purposes.
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Affiliation(s)
- Sonia Molina-Pinelo
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
- Medical Oncology Department, Hospital Universitario Doce de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- CIBER de Cáncer, Madrid, Spain
| | - Ana Salinas
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
| | - Nicolás Moreno-Mata
- Thoracic Surgery Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Irene Ferrer
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
- Medical Oncology Department, Hospital Universitario Doce de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- CIBER de Cáncer, Madrid, Spain
| | - Rocío Suarez
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
- Medical Oncology Department, Hospital Universitario Doce de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- CIBER de Cáncer, Madrid, Spain
| | - Eduardo Andrés-León
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- University Tumor Center Düsseldorf, University of Düsseldorf, Düsseldorf, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario de Valencia, Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de Valencia, Valencia, Spain
| | - Carlos Camps
- Department of Medicine, University of Valencia, Valencia, Spain
- Department of Medical Oncology, Hospital General Universitario de Valencia, Valencia, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
- CIBER de Cáncer, Madrid, Spain
| | - Luis Paz-Ares
- Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
- Medical Oncology Department, Hospital Universitario Doce de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- CIBER de Cáncer, Madrid, Spain
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Lawrie CH, Armesto M, Fernandez-Mercado M, Arestín M, Manterola L, Goicoechea I, Larrea E, Caffarel MM, Araujo AM, Sole C, Sperga M, Alvarado-Cabrero I, Michal M, Hes O, López JI. Noncoding RNA Expression and Targeted Next-Generation Sequencing Distinguish Tubulocystic Renal Cell Carcinoma (TC-RCC) from Other Renal Neoplasms. J Mol Diagn 2018; 20:34-45. [PMID: 29056573 DOI: 10.1016/j.jmoldx.2017.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/29/2017] [Accepted: 09/13/2017] [Indexed: 01/23/2023] Open
Abstract
Tubulocystic renal cell carcinoma (TC-RCC) is a rare recently described renal neoplasm characterized by gross, microscopic, and immunohistochemical differences from other renal tumor types and was recently classified as a distinct entity. However, this distinction remains controversial particularly because some genetic studies suggest a close relationship with papillary RCC (PRCC). The molecular basis of this disease remains largely unexplored. We therefore performed noncoding (nc) RNA/miRNA expression analysis and targeted next-generation sequencing mutational profiling on 13 TC-RCC cases (11 pure, two mixed TC-RCC/PRCC) and compared with other renal neoplasms. The expression profile of miRNAs and other ncRNAs in TC-RCC was distinct and validated 10 differentially expressed miRNAs by quantitative RT-PCR, including miR-155 and miR-34a, that were significantly down-regulated compared with PRCC cases (n = 22). With the use of targeted next-generation sequencing we identified mutations in 14 different genes, most frequently (>60% of TC-RCC cases) in ABL1 and PDFGRA genes. These mutations were present in <5% of clear cell RCC, PRCC, or chromophobe RCC cases (n > 600) of The Cancer Genome Atlas database. In summary, this study is by far the largest molecular study of TC-RCC cases and the first to investigate either ncRNA expression or their genomic profile. These results add molecular evidence that TC-RCC is indeed a distinct entity from PRCC and other renal neoplasms.
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Affiliation(s)
- Charles H Lawrie
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - María Armesto
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | | | - María Arestín
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - Lorea Manterola
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - Ibai Goicoechea
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - Erika Larrea
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - María M Caffarel
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Angela M Araujo
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - Carla Sole
- Molecular Oncology Group of Biodonostia Research Institute, San Sebastian, Spain
| | - Maris Sperga
- Department of Pathology, Riga Stradins University, Riga, Latvia
| | | | - Michal Michal
- Department of Pathology, Charles University Hospital, Plzen, Czech Republic
| | - Ondrej Hes
- Department of Pathology, Charles University Hospital, Plzen, Czech Republic
| | - José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country, Barakaldo, Bizkaia, Spain; BioCruces Research Institute, Barakaldo, Bizkaia, Spain
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49
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Yang Y, Zhang H, Xie Y, Zhang S, Zhu J, Yin G, Shu G, Zhang Y. Preliminary screening and identification of differentially expressed metastasis-related ncRNAs in ovarian cancer. Oncol Lett 2017; 15:368-374. [PMID: 29387224 PMCID: PMC5769367 DOI: 10.3892/ol.2017.7338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/19/2017] [Indexed: 01/22/2023] Open
Abstract
Ovarian cancer (OC) is an aggressive disease with few valuable biomarkers and effective therapies. In this study, we aimed to elucidate biomarkers associated with OC metastasis into the omentum. We performed comprehensive screening of non-coding RNAs (ncRNAs) between matched primary OC and omental metastasis using the Agilent human lncRNA Array V3.0 microarray. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the microarray results at the mRNA level. Microarray revealed 235 ncRNAs changes, and we validated the top four differential changed genes in an additional 27 paired samples with RT-qPCR. We found that myocardial infarction associated transcript (MIAT) expression increased in the omentum tissue, while small nucleolar RNA, C/D Box 114 cluster (SNORD114) family members SNORD114-10, SNORD114-2 and SNORD114-11 were downregulated when compared with OC tissue. However, there is no significant difference in SNORD114-2 and SNORD114-11 levels. We thus infer that differential expression of MIAT and SNORD114-10 could play an important role during OC metastasis. These ncRNAs might be useful as pre-diagnostic biomarkers at the early stage of cancer metastasis.
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Affiliation(s)
- Yu Yang
- School of Resources Processing and Bioengineering, Central South University, Changsha, Hunan 410006, P.R. China
| | - Hui Zhang
- School of Resources Processing and Bioengineering, Central South University, Changsha, Hunan 410006, P.R. China
| | - Yajiao Xie
- School of Resources Processing and Bioengineering, Central South University, Changsha, Hunan 410006, P.R. China
| | - Shufen Zhang
- Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Junyou Zhu
- Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Gang Yin
- Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Guang Shu
- Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yu Zhang
- Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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50
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Qin Y, Meng L, Fu Y, Quan Z, Ma M, Weng M, Zhang Z, Gao C, Shi X, Han K. SNORA74B gene silencing inhibits gallbladder cancer cells by inducing PHLPP and suppressing Akt/mTOR signaling. Oncotarget 2017; 8:19980-19996. [PMID: 28212545 PMCID: PMC5386738 DOI: 10.18632/oncotarget.15301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/08/2017] [Indexed: 01/17/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been implicated in the development of many cancers. We therefore examined the differential expression of snoRNAs between gallbladder cancer (GBC) tissues and matched adjacent non-tumor tissues using expression microarray analysis with confirmation by quantitative real-time PCR (qRT-PCR). Western blot analysis showed that SNORA74B levels were higher in GBC than non-tumor tissues. SNORA74B expression was positively associated with local invasion, advanced TNM stage, CA19-9 level, and Ki67 expression in patients with GBC, while it was negatively associated with expression of PHLPP, an endogenous Akt inhibitor. Moreover, SNORA74B expression was prognostic for overall survival (OS) and disease-free survival (DFS). Functional studies revealed that silencing SNORA74B in GBC cells using sh-SNORA74B suppressed cell proliferation, induced G1 arrest, and promoted apoptosis. Preliminary molecular investigation revealed that SNORA74B silencing inhibited activation of the AKT/mTOR signaling pathway, while increasing PHLPP expression. PHLPP depletion using shRNA abrogated sh-SNORA74B suppression of GBC cell proliferation, indicating that the antitumor effects of SNORA74B silencing were mediated by PHLPP. These findings define the important role of SNORA74B in cell proliferation, cell cycle, and apoptosis of GBC, and suggest that it may serve as a novel target for GBC treatment.
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Affiliation(s)
- Yiyu Qin
- Clinical College, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China.,Research Centre of Biomedical Technology, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China.,Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Li Meng
- Research Centre of Biomedical Technology, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China
| | - Yang Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhiwei Quan
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Mingzhe Ma
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Mingzhe Weng
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Cuixiang Gao
- Research Centre of Biomedical Technology, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China
| | - Xinghua Shi
- Research Centre of Biomedical Technology, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China
| | - Koulan Han
- Clinical College, Yancheng Institute of Health Sciences, Yancheng, Jiangsu 224000, China
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