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Leung EY, Askarian-Amiri ME, Singleton DC, Ferraro-Peyret C, Joseph WR, Finlay GJ, Broom RJ, Kakadia PM, Bohlander SK, Marshall E, Baguley BC. Derivation of Breast Cancer Cell Lines Under Physiological (5%) Oxygen Concentrations. Front Oncol 2018; 8:425. [PMID: 30370249 PMCID: PMC6194255 DOI: 10.3389/fonc.2018.00425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Most human breast cancer cell lines currently in use were developed and are cultured under ambient (21%) oxygen conditions. While this is convenient in practical terms, higher ambient oxygen could increase oxygen radical production, potentially modulating signaling pathways. We have derived and grown a series of four human breast cancer cell lines under 5% oxygen, and have compared their properties to those of established breast cancer lines growing under ambient oxygen. Methods: Cell lines were characterized in terms of appearance, cellular DNA content, mutation spectrum, hormone receptor status, pathway utilization and drug sensitivity. Results: Three of the four lines (NZBR1, NZBR2, and NZBR4) were triple negative (ER-, PR-, HER2-), with NZBR1 also over-expressing EGFR. NZBR3 was HER2+ and ER+ and also over-expressed EGFR. Cell lines grown in 5% oxygen showed increased expression of the hypoxia-inducible factor 1 (HIF-1) target gene carbonic anhydrase 9 (CA9) and decreased levels of ROS. As determined by protein phosphorylation, NZBR1 showed low AKT pathway utilization while NZBR2 and NZBR4 showed low p70S6K and rpS6 pathway utilization. The lines were characterized for sensitivity to 7-hydroxytamoxifen, doxorubicin, paclitaxel, the PI3K inhibitor BEZ235 and the HER inhibitors lapatinib, afatinib, dacomitinib, and ARRY-380. In some cases they were compared to established breast cancer lines. Of particular note was the high sensitivity of NZBR3 to HER inhibitors. The spectrum of mutations in the NZBR lines was generally similar to that found in commonly used breast cancer cell lines but TP53 mutations were absent and mutations in EVI2B, LRP1B, and PMS2, which have not been reported in other breast cancer lines, were detected. The results suggest that the properties of cell lines developed under low oxygen conditions (5% O2) are similar to those of commonly used breast cancer cell lines. Although reduced ROS production and increased HIF-1 activity under 5% oxygen can potentially influence experimental outcomes, no difference in sensitivity to estrogen or doxorubicin was observed between cell lines cultured in 5 vs. 21% oxygen.
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Affiliation(s)
- Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Dean C Singleton
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Carole Ferraro-Peyret
- Univ Lyon, Claude Bernard University, Cancer Research Center of Lyon, INSERM 1052, CNRS5286, Faculty of Pharmacy, Lyon, France.,Hospices Civils de Lyon, Molecular Biology of Tumors, GHE Hospital, Bron, France
| | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Reuben J Broom
- Auckland City Hospital-Oncology, Grafton, Auckland, New Zealand
| | - Purvi M Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Elaine Marshall
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
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Sarkar D, Oghabian A, Bodiyabadu PK, Joseph WR, Leung EY, Finlay GJ, Baguley BC, Askarian-Amiri ME. Correction: Sarkar, D., et al. Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing. Int. J. Mol. Sci. 2017, 18, 1378. Int J Mol Sci 2018; 19:ijms19051343. [PMID: 29724053 PMCID: PMC5983800 DOI: 10.3390/ijms19051343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Debina Sarkar
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Ali Oghabian
- Institute of Biotechnology, P.O. Box 56 (Viikinkaari 5), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Pasani K Bodiyabadu
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
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Saunus JM, Smart CE, Kutasovic JR, Johnston RL, Kalita-de Croft P, Miranda M, Rozali EN, Vargas AC, Reid LE, Lorsy E, Cocciardi S, Seidens T, McCart Reed AE, Dalley AJ, Wockner LF, Johnson J, Sarkar D, Askarian-Amiri ME, Simpson PT, Khanna KK, Chenevix-Trench G, Al-Ejeh F, Lakhani SR. Multidimensional phenotyping of breast cancer cell lines to guide preclinical research. Breast Cancer Res Treat 2017; 167:289-301. [PMID: 28889351 DOI: 10.1007/s10549-017-4496-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
Abstract
PURPOSE Cell lines are extremely useful tools in breast cancer research. Their key benefits include a high degree of control over experimental variables and reproducibility. However, the advantages must be balanced against the limitations of modelling such a complex disease in vitro. Informed selection of cell line(s) for a given experiment now requires essential knowledge about molecular and phenotypic context in the culture dish. METHODS We performed multidimensional profiling of 36 widely used breast cancer cell lines that were cultured under standardised conditions. Flow cytometry and digital immunohistochemistry were used to compare the expression of 14 classical breast cancer biomarkers related to intrinsic molecular profiles and differentiation states: EpCAM, CD24, CD49f, CD44, ER, AR, HER2, EGFR, E-cadherin, p53, vimentin, and cytokeratins 5, 8/18 and 19. RESULTS This cell-by-cell analysis revealed striking heterogeneity within cultures of individual lines that would be otherwise obscured by analysing cell homogenates, particularly amongst the triple-negative lines. High levels of p53 protein, but not RNA, were associated with somatic mutations (p = 0.008). We also identified new subgroups using the nanoString PanCancer Pathways panel (730 transcripts representing 13 canonical cancer pathways). Unsupervised clustering identified five groups: luminal/HER2, immortalised ('normal'), claudin-low and two basal clusters, distinguished mostly by baseline expression of TGF-beta and PI3-kinase pathway genes. CONCLUSION These features are compared with other published genotype and phenotype information in a user-friendly reference table to help guide selection of the most appropriate models for in vitro and in vivo studies, and as a framework for classifying new patient-derived cancer cell lines and xenografts.
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Affiliation(s)
- Jodi M Saunus
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia.
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
| | - Chanel E Smart
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Department of Pathology, IRCCS San Raffaele Vita-Salute University, Milan, Italy
| | - Jamie R Kutasovic
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Rebecca L Johnston
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Priyakshi Kalita-de Croft
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Mariska Miranda
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Esdy N Rozali
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Lynne E Reid
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Eva Lorsy
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | | | - Tatjana Seidens
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Amy E McCart Reed
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Andrew J Dalley
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Leesa F Wockner
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Julie Johnson
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Debina Sarkar
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Marjan E Askarian-Amiri
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Peter T Simpson
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Fares Al-Ejeh
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Sunil R Lakhani
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- Pathology Queensland, The Royal Brisbane and Women's Hospital, Herston, QLD, Australia
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Leung EY, Askarian-Amiri ME, Sarkar D, Ferraro-Peyret C, Joseph WR, Finlay GJ, Baguley BC. Endocrine Therapy of Estrogen Receptor-Positive Breast Cancer Cells: Early Differential Effects on Stem Cell Markers. Front Oncol 2017; 7:184. [PMID: 28929082 PMCID: PMC5591432 DOI: 10.3389/fonc.2017.00184] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/08/2017] [Indexed: 01/13/2023] Open
Abstract
Introduction Endocrine therapy of breast cancer, which either deprives cancer tissue of estrogen or prevents estrogen pathway signaling, is the most common treatment after surgery and radiotherapy. We have previously shown for the estrogen-responsive MCF-7 cell line that exposure to tamoxifen, or deprivation of estrogen, leads initially to inhibition of cell proliferation, followed after several months by the emergence of resistant sub-lines that are phenotypically different from the parental line. We examined the early responses of MCF-7 cells following either exposure to 4-hydroxytamoxifen or deprivation of estrogen for periods of 2 days–4 weeks. Methods Endocrine-sensitive or -resistant breast cancer cell lines were used to examine the expression of the stem cell gene SOX2, and the Wnt effector genes AXIN2 and DKK1 using quantitative PCR analysis. Breast cancer cell lines were used to assess the anti-proliferative effects (as determined by IC50 values) of Wnt pathway inhibitors LGK974 and IWP-2. Results Hormone therapy led to time-dependent increases of up to 10-fold in SOX2 expression, up to threefold in expression of the Wnt target genes AXIN2 and DKK1, and variable changes in NANOG and OCT4 expression. The cells also showed increased mammosphere formation and increased CD24 surface protein expression. Some but not all hormone-resistant MCF-7 sub-lines, emerging after long-term hormonal stress, showed up to 50-fold increases in SOX2 expression and smaller increases in AXIN2 and DKK1 expression. However, the increase in Wnt target gene expression was not accompanied by an increase in sensitivity to Wnt pathway inhibitors LGK974 and IWP-2. A general trend of lower IC50 values was observed in 3-dimensional spheroid culture conditions (which allowed enrichment of cells with cancer stem cell phenotype) relative to monolayer cultures. The endocrine-resistant cell lines showed no significant increase in sensitivity to Wnt inhibitors. Conclusion Hormone treatment of cultured MCF-7 cells leads within 2 days to increased expression of components of the SOX2 and Wnt pathways and to increased potential for mammosphere formation. We suggest that these responses are indicative of early adaptation to endocrine stress with features of stem cell character and that this facilitates the survival of emerging hormone-resistant cell populations.
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Affiliation(s)
- Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Molecular Medicine and Pathology Department, University of Auckland, Auckland, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Molecular Medicine and Pathology Department, University of Auckland, Auckland, New Zealand
| | - Debina Sarkar
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Molecular Medicine and Pathology Department, University of Auckland, Auckland, New Zealand
| | - Carole Ferraro-Peyret
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Cancer Research Center of Lyon, INSERM 1052, CNRS5286, Lyon, France.,Faculty of Pharmacy, University of Lyon, Claude Bernard Lyon 1 University, Lyon, France.,Molecular Biology of Tumors, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Molecular Medicine and Pathology Department, University of Auckland, Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
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Sarkar D, Oghabian A, Bodiyabadu PK, Joseph WR, Leung EY, Finlay GJ, Baguley BC, Askarian-Amiri ME. Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing. Int J Mol Sci 2017; 18:ijms18071378. [PMID: 28653984 PMCID: PMC5535871 DOI: 10.3390/ijms18071378] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022] Open
Abstract
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation of ANRIL transcripts remains incomplete. Several functions have been associated with ANRIL. In our judgement, studies on ANRIL functionality are premature pending a more complete appreciation of the profusion of isoforms. We found differential expression of ANRIL exons, which indicates that multiple isoforms exist in melanoma cells. In addition to linear isoforms, we identified circular forms of ANRIL (circANRIL). Further characterisation of circANRIL in two patient-derived metastatic melanoma cell lines (NZM7 and NZM37) revealed the existence of a rich assortment of circular isoforms. Moreover, in the two melanoma cell lines investigated, the complements of circANRIL isoforms were almost completely different. Novel exons were also discovered. We also found the family of linear ANRIL was enriched in the nucleus, whilst the circular isoforms were enriched in the cytoplasm and they differed markedly in stability. With respect to the variable processing of circANRIL species, bioinformatic analysis indicated that intronic Arthrobacter luteus (Alu) restriction endonuclease inverted repeats and exon skipping were not involved in selection of back-spliced exon junctions. Based on our findings, we hypothesise that “ANRIL” has wholly distinct dual sets of functions in melanoma. This reveals the dynamic nature of the locus and constitutes a basis for investigating the functions of ANRIL in melanoma.
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Affiliation(s)
- Debina Sarkar
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Ali Oghabian
- Institute of Biotechnology, P.O. Box 56 (Viikinkaari 5), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Pasani K Bodiyabadu
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Rd. Grafton, 1023 Auckland, New Zealand.
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Hansji H, Leung EY, Baguley BC, Finlay GJ, Cameron-Smith D, Figueiredo VC, Askarian-Amiri ME. ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells. Biol Direct 2016; 11:62. [PMID: 27871336 PMCID: PMC5117590 DOI: 10.1186/s13062-016-0165-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development. As developmental genes are often deregulated in cancer, here we have studied its function in breast cancer cell lines. Results Using human breast cancer cell lines, ZFAS1 was found to be expressed in all cell lines tested, albeit at different levels of abundance. Following subcellular fractionation, human ZFAS1 was found in both nucleus and cytoplasm (as is the mouse orthologue) in an isoform-independent manner. Sucrose gradients based on velocity sedimentation were utilised to separate the different components of total cell lysate, and surprisingly ZFAS1 was primarily co-localised with light polysomes. Further investigation into ribosome association through subunit dissociation studies showed that ZFAS1 was predominantly associated with the 40S small ribosomal subunit. The expression levels of ZFAS1 and of mRNAs encoding several ribosomal proteins that have roles in ribosome assembly, production and maturation were tightly correlated. ZFAS1 knockdown significantly reduced RPS6 phosphorylation. Conclusion A large number of lncRNAs associate with ribosomes but the function of the majority of these lncRNAs has not been elucidated. The association of the lncRNA ZFAS1 with a subpopulation of ribosomes and the correlation with expression of mRNAs for ribosomal proteins suggest a ribosome-interacting mechanism pertaining to their assembly or biosynthetic activity. ZFAS1 may represent a new class of lncRNAs which associates with ribosomes to regulate their function. Reviewers This article was reviewed by Christine Vande Velde, Nicola Aceto and Haruhiko Siomi. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0165-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - David Cameron-Smith
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Vandre C Figueiredo
- The Liggins Institute, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand. .,Department of Molecular Medicine and Pathology, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
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Abstract
Recent genomic and transcriptomic analysis has revealed that the majority of the human genome is transcribed as nonprotein-coding RNA. These transcripts, known as long noncoding RNA, have structures similar to those of mRNA. Many of these transcripts are now thought to have regulatory roles in different biological pathways which provide cells with an additional layer of regulatory complexity in gene expression and proteome function in response to stimuli. A wide variety of cellular functions may thus depend on the fine-tuning of interactions between noncoding RNAs and other key molecules in cell signaling networks. Deregulation of many noncoding RNAs is thought to occur in a variety of human diseases, including neoplasia and cancer drug resistance. Here we discuss recent findings on the molecular functions of long noncoding RNAs in cellular pathways mediating resistance to anticancer drugs.
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Affiliation(s)
- Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand. .,Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Graeme Finlay
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
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8
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Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
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Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
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Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
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9
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Hansji H, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Keeping abreast with long non-coding RNAs in mammary gland development and breast cancer. Front Genet 2014; 5:379. [PMID: 25400658 PMCID: PMC4215690 DOI: 10.3389/fgene.2014.00379] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/13/2014] [Indexed: 12/18/2022] Open
Abstract
The majority of the human genome is transcribed, even though only 2% of transcripts encode proteins. Non-coding transcripts were originally dismissed as evolutionary junk or transcriptional noise, but with the development of whole genome technologies, these non-coding RNAs (ncRNAs) are emerging as molecules with vital roles in regulating gene expression. While shorter ncRNAs have been extensively studied, the functional roles of long ncRNAs (lncRNAs) are still being elucidated. Studies over the last decade show that lncRNAs are emerging as new players in a number of diseases including cancer. Potential roles in both oncogenic and tumor suppressive pathways in cancer have been elucidated, but the biological functions of the majority of lncRNAs remain to be identified. Accumulated data are identifying the molecular mechanisms by which lncRNA mediates both structural and functional roles. LncRNA can regulate gene expression at both transcriptional and post-transcriptional levels, including splicing and regulating mRNA processing, transport, and translation. Much current research is aimed at elucidating the function of lncRNAs in breast cancer and mammary gland development, and at identifying the cellular processes influenced by lncRNAs. In this paper we review current knowledge of lncRNAs contributing to these processes and present lncRNA as a new paradigm in breast cancer development.
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Affiliation(s)
- Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand ; Department of Molecular Medicine and Pathology, University of Auckland Auckland, New Zealand
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10
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Askarian-Amiri ME, Seyfoddin V, Smart CE, Wang J, Kim JE, Hansji H, Baguley BC, Finlay GJ, Leung EY. Emerging role of long non-coding RNA SOX2OT in SOX2 regulation in breast cancer. PLoS One 2014; 9:e102140. [PMID: 25006803 PMCID: PMC4090206 DOI: 10.1371/journal.pone.0102140] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/13/2014] [Indexed: 02/02/2023] Open
Abstract
The transcription factor SOX2 is essential for maintaining pluripotency in a variety of stem cells. It has important functions during embryonic development, is involved in cancer stem cell maintenance, and is often deregulated in cancer. The mechanism of SOX2 regulation has yet to be clarified, but the SOX2 gene lies in an intron of a long multi-exon non-coding RNA called SOX2 overlapping transcript (SOX2OT). Here, we show that the expression of SOX2 and SOX2OT is concordant in breast cancer, differentially expressed in estrogen receptor positive and negative breast cancer samples and that both are up-regulated in suspension culture conditions that favor growth of stem cell phenotypes. Importantly, ectopic expression of SOX2OT led to an almost 20-fold increase in SOX2 expression, together with a reduced proliferation and increased breast cancer cell anchorage-independent growth. We propose that SOX2OT plays a key role in the induction and/or maintenance of SOX2 expression in breast cancer.
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Affiliation(s)
| | - Vahid Seyfoddin
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Chanel E. Smart
- University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital Campus, Herston, Queensland, Australia
| | - Jingli Wang
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Ji Eun Kim
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Bruce C. Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Graeme J. Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- * E-mail: (GJF); (EYL)
| | - Euphemia Y. Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- * E-mail: (GJF); (EYL)
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11
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D'mello SAN, Flanagan JU, Green TN, Leung EY, Askarian-Amiri ME, Joseph WR, McCrystal MR, Isaacs RJ, Shaw JHF, Furneaux CE, During MJ, Finlay GJ, Baguley BC, Kalev-Zylinska ML. Evidence That GRIN2A Mutations in Melanoma Correlate with Decreased Survival. Front Oncol 2014; 3:333. [PMID: 24455489 PMCID: PMC3888952 DOI: 10.3389/fonc.2013.00333] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 12/30/2013] [Indexed: 12/17/2022] Open
Abstract
Previous whole-exome sequencing has demonstrated that melanoma tumors harbor mutations in the GRIN2A gene. GRIN2A encodes the regulatory GluN2A subunit of the glutamate-gated N-methyl-d-aspartate receptor (NMDAR), involvement of which in melanoma remains undefined. Here, we sequenced coding exons of GRIN2A in 19 low-passage melanoma cell lines derived from patients with metastatic melanoma. Potential mutation impact was evaluated in silico, including within the GluN2A crystal structure, and clinical correlations were sought. We found that of 19 metastatic melanoma tumors, four (21%) carried five missense mutations in the evolutionarily conserved domains of GRIN2A; two were previously reported. Melanoma cells that carried these mutations were treatment-naïve. Sorting intolerant from tolerant analysis predicted that S349F, G762E, and P1132L would disrupt protein function. When modeled into the crystal structure of GluN2A, G762E was seen to potentially alter GluN1-GluN2A interactions and ligand binding, implying disruption to NMDAR functionality. Patients whose tumors carried non-synonymous GRIN2A mutations had faster disease progression and shorter overall survival (P < 0.05). This was in contrast to the BRAF V600E mutation, found in 58% of tumors but showing no correlation with clinical outcome (P = 0.963). Although numbers of patients in this study are small, and firm conclusions about the association between GRIN2A mutations and poor clinical outcome cannot be drawn, our results highlight the high prevalence of GRIN2A mutations in metastatic melanoma and suggest for the first time that mutated NMDARs impact melanoma progression.
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Affiliation(s)
- Stacey Ann N D'mello
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland , Auckland , New Zealand
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, University of Auckland , Auckland , New Zealand ; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland , Auckland , New Zealand
| | - Taryn N Green
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland , Auckland , New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland , Auckland , New Zealand
| | | | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland , Auckland , New Zealand
| | - Michael R McCrystal
- Department of Clinical Oncology, Auckland District Health Board , Auckland , New Zealand ; Canopy Cancer Care, Mercy Hospital , Auckland , New Zealand
| | - Richard J Isaacs
- Regional Cancer Treatment Service, Palmerston North Public Hospital , Palmerston North , New Zealand
| | | | | | - Matthew J During
- Department of Molecular Virology, Immunology and Medical Genetics, Neuroscience and Neurological Surgery, Ohio State University , Columbus, OH , USA ; Centre for Brain Research, University of Auckland , Auckland , New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland , Auckland , New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland , Auckland , New Zealand
| | - Maggie L Kalev-Zylinska
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland , Auckland , New Zealand ; LabPlus Haematology, Auckland District Health Board , Auckland , New Zealand
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12
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Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 2011; 17:878-891. [PMID: 21460236 PMCID: PMC3078737 DOI: 10.1261/rna.2528811] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 02/15/2011] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized to play major regulatory roles in development and disease. To identify novel regulators in breast biology, we identified differentially regulated lncRNAs during mouse mammary development. Among the highest and most differentially expressed was a transcript (Zfas1) antisense to the 5' end of the protein-coding gene Znfx1. In vivo, Zfas1 RNA is localized within the ducts and alveoli of the mammary gland. Zfas1 intronically hosts three previously undescribed C/D box snoRNAs (SNORDs): Snord12, Snord12b, and Snord12c. In contrast to the general assumption that noncoding SNORD-host transcripts function only as vehicles to generate snoRNAs, knockdown of Zfas1 in a mammary epithelial cell line resulted in increased cellular proliferation and differentiation, while not substantially altering the levels of the SNORDs. In support of an independent function, we also found that Zfas1 is extremely stable, with a half-life >16 h. Expression analysis of the SNORDs revealed these were expressed at different levels, likely a result of distinct structures conferring differential stability. While there is relatively low primary sequence conservation between Zfas1 and its syntenic human ortholog ZFAS1, their predicted secondary structures have similar features. Like Zfas1, ZFAS1 is highly expressed in the mammary gland and is down-regulated in breast tumors compared to normal tissue. We propose a functional role for Zfas1/ ZFAS1 in the regulation of alveolar development and epithelial cell differentiation in the mammary gland, which, together with its dysregulation in human breast cancer, suggests ZFAS1 as a putative tumor suppressor gene.
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13
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Mercer TR, Dinger ME, Bracken CP, Kolle G, Szubert JM, Korbie DJ, Askarian-Amiri ME, Gardiner BB, Goodall GJ, Grimmond SM, Mattick JS. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res 2010; 20:1639-50. [PMID: 21045082 DOI: 10.1101/gr.112128.110] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.
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Affiliation(s)
- Tim R Mercer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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14
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Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 2009; 15:2013-2027. [PMID: 19767420 PMCID: PMC2764477 DOI: 10.1261/rna.1705309] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 08/18/2009] [Indexed: 05/28/2023]
Abstract
The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2, is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2, Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot, an isoform of Sox2ot transcribed from a distal HCE located >500 kb upstream of Sox2, was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development.
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Affiliation(s)
- Paulo P Amaral
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia,QLD 4072, Australia
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15
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Poole ES, Young DJ, Askarian-Amiri ME, Scarlett DJG, Tate WP. Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome. Cell Res 2007; 17:591-607. [PMID: 17621307 DOI: 10.1038/cr.2007.56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to span the decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site crafted for a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide, the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein that results in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial termination complex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stop codon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix alpha5. The anticodon loop also makes contact with the base following the stop codon that is known to strongly influence termination efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. The mRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflect structural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiased SELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in its different binding conformations within the active centre of the ribosome.
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Affiliation(s)
- Elizabeth S Poole
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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16
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Poole ES, Askarian-Amiri ME, Major LL, McCaughan KK, Scarlett DJG, Wilson DN, Tate WP. Molecular Mimicry in the Decoding of Translational Stop Signals. ACTA ACUST UNITED AC 2003; 74:83-121. [PMID: 14510074 DOI: 10.1016/s0079-6603(03)01011-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Molecular mimicry was a concept that was revived as we understood more about the ligands that bound to the active center of the ribosome, and the characteristics of the active center itself. It has been particularly useful for the termination phase of protein synthesis, because for many years this major process seemed not only to be out of step) with the initiation and elongation phases but also there were no common features of the process between eubacteria and eukaryotes. As the facts that supported molecular mimicry emerged, it was seen that the protein factors that facilitated polypeptide chain release when the decoding of an mRNA was complete had common features with the ligands involved in the other phases. Moreover, now common features and mechanisms began to emerge between the eubacterial and eukaryotic RFs and suddenly there seemed to be remarkable synergy between the external ligands and commonality in at least some features of the mechanistic prnciples. Almost 10 years after molecular mimicry took hold as a framework concept, we can now see that this idea is probably too simple. For example, structural mimicry can be apparent if there are extensive conformational changes either in the ribosome active center or in the ligand itself or, most likely, both. Early indications are that the bacterial RF may indeed undergo extensive conformational changes from its solution structure to achieve this accommodation. Thus, as important if not more important than structural and functional mimicry among the ligands, might be their accomodation of a common single active center made up of at least three parts to carry out a complex series of reactions. One part of the ribosomal active center is committed to decoding, a second is committed to the chemistry of putting the protein together and releasing it, and a third part, perhaps residing in the subdomains, is committed to binding ligands so that they can perform their respective single or multiple functions. It might be more accurate to regard the decoding RF as the cuckoo taking over the nest that was crafted and honed through evolution by another, the tRNA. A somewhat ungainly RF, perhaps bigger in dimensions than the tRNA, is able, nevertheless, like the cuckoo, to maneuvre into the nest. Perhaps it pushes the nest a little out of shape, but is still able to use the site for its own functions of stop signal decoding and for facilitating the release of the polypeptide. The term molecular mimicry has been dominant in the literature for a period of important advances in the understanding of protein synthesis. When the first structures of the ribosome appeared, the concept survived and was seen to be valid still. Now, we are at the stage of understanding the more detailed molecular interactions between ligands and the rRNA in particular, and how subtle changes in localized spatial orientations of atoms occur within these interactions. The simplicity of the original concept of mimicry will inevitably be blurred by this more detailed analysis. Nevertheless, it has provided a significant set of principles that allowed development of experimental programs to enhance our understanding of the dynamic events at this remarkable active site at the interface between the two subunits of this fascinating cell organelle, the ribosome.
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Affiliation(s)
- Elizabeth S Poole
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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17
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Askarian-Amiri ME, Pel HJ, Guévremont D, McCaughan KK, Poole ES, Sumpter VG, Tate WP. Functional characterization of yeast mitochondrial release factor 1. J Biol Chem 2000; 275:17241-8. [PMID: 10748224 DOI: 10.1074/jbc.m910448199] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast Saccharomyces cerevisiae mitochondrial release factor was expressed from the cloned MRF1 gene, purified from inclusion bodies, and refolded to give functional activity. The gene encoded a factor with release activity that recognized cognate stop codons in a termination assay with mitochondrial ribosomes and in an assay with Escherichia coli ribosomes. The noncognate stop codon, UGA, encoding tryptophan in mitochondria, was recognized weakly in the heterologous assay. The mitochondrial release factor 1 protein bound to bacterial ribosomes and formed a cross-link with the stop codon within a mRNA bound in a termination complex. The affinity was strongly dependent on the identity of stop signal. Two alleles of MRF1 that contained point mutations in a release factor 1 specific region of the primary structure and that in vivo compensated for mutations in the decoding site rRNA of mitochondrial ribosomes were cloned, and the expressed proteins were purified and refolded. The variant proteins showed impaired binding to the ribosome compared with mitochondrial release factor 1. This structural region in release factors is likely to be involved in codon-dependent specific ribosomal interactions.
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Affiliation(s)
- M E Askarian-Amiri
- Department of Biochemistry and Centre for Gene Research, University of Otago, P. O. Box 56, 9015 Dunedin, New Zealand
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