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El-Helkan B, Emam M, Mohanad M, Fathy S, Zekri AR, Ahmed OS. Long non-coding RNAs as novel prognostic biomarkers for breast cancer in Egyptian women. Sci Rep 2022; 12:19498. [PMID: 36376369 PMCID: PMC9663553 DOI: 10.1038/s41598-022-23938-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Breast cancer (BC), the most common type of malignant tumor, is the leading cause of death, having the highest incidence rate among women. The lack of early diagnostic tools is one of the clinical obstacles for BC treatment. The current study was designed to evaluate a panel of long non-coding RNAs (lncRNAs) BC040587, HOTAIR, MALAT1, CCAT1, CCAT2, PVT1, UCA1, SPRY4-IT1, PANDAR, and AK058003-and two mRNAs (SNCG, BDNF) as novel prognostic biomarkers for BC. This study was ethically approved by the Institutional Review Board of the National Cancer Institute, Cairo University. Our study included 75 women recently diagnosed with BC and 25 healthy women as normal controls. Patients were divided into three groups: 24 with benign breast diseases, 28 with metastatic breast cancer (MBC, stage IV), and 23 with non-metastatic breast cancer (NMBC, stage III). LncRNA and mRNA expression levels were measured in patient plasma using quantitative real-time PCR. We found that 10 lncRNAs (BCO40587, HOTAIR, PVT1, CCAT2, PANDAR, CCAT1, UCA1, SPRY4-IT1, AK058003, and MALAT1) and both mRNAs demonstrated at least a 2-fold change in expression with a more than 95% probability of significance. BCO40587 and SNCG were significantly up-regulated in MBC and NMBC patients (3.2- and 4-fold, respectively) compared with normal controls. The expression of UCA1 was repressed by 1.78-fold in MBC and NMBC patients compared with those with benign diseases. SPRY4-IT1 was down-regulated by 1.45-fold in MBC patients compared with NMBC and benign disease patients. Up-regulation of lncRNAs plays an important role in BC development. SNCG and BCO40587 may be potential prognostic markers for BC.The organization number is IORG0003381 (IRB No: IRB00004025).
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Affiliation(s)
- Basma El-Helkan
- grid.7269.a0000 0004 0621 1570Department of Biochemistry, Faculty of Science-Ain Shams University, Cairo, Egypt
| | - Manal Emam
- grid.7269.a0000 0004 0621 1570Department of Biochemistry, Faculty of Science-Ain Shams University, Cairo, Egypt
| | - Marwa Mohanad
- grid.440875.a0000 0004 1765 2064College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October ,Giza, Egypt
| | - Shadia Fathy
- grid.7269.a0000 0004 0621 1570Department of Biochemistry, Faculty of Science-Ain Shams University, Cairo, Egypt
| | - Abdel Rahman Zekri
- grid.7776.10000 0004 0639 9286Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ola S. Ahmed
- grid.7776.10000 0004 0639 9286Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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Yan L, Wang S, Li Y, Tognetti L, Tan R, Zeng K, Pianigiani E, Mi X, Li H, Fimiani M, Rubegni P. Retraction: SNHG5 promotes proliferation and induces apoptosis in melanoma by sponging miR-155. RSC Adv 2022; 12:25279. [PMID: 36199334 PMCID: PMC9450005 DOI: 10.1039/d2ra90086f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Retraction of ‘SNHG5 promotes proliferation and induces apoptosis in melanoma by sponging miR-155’ by Lu Yan et al., RSC Adv., 2018, 8, 6160–6168, https://doi.org/10.1039/C7RA12520H.
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Affiliation(s)
- Lu Yan
- Department of Dermatology, Zhujiang Hospital of Southern Medical University, Guangzhou, 510000, China
| | - Suihai Wang
- School of Biotechnology, Southern Medical University, Guangzhou, 510000, China
| | - Yue Li
- Department of Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, China
| | - Linda Tognetti
- Department of Medical, Surgical and Neuro Sciences, Section of Dermatology, University of Siena, Policlinico Le Scotte Viale Bracci, Siena, 53100, Italy
| | - Rui Tan
- Department of Dermatology, Zhujiang Hospital of Southern Medical University, Guangzhou, 510000, China
| | - Kang Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, China
| | - Elisa Pianigiani
- Department of Medical, Surgical and Neuro Sciences, Section of Dermatology, University of Siena, Policlinico Le Scotte Viale Bracci, Siena, 53100, Italy
| | - Xiangbin Mi
- Department of Dermatology, Zhujiang Hospital of Southern Medical University, Guangzhou, 510000, China
| | - Hui Li
- Department of Dermatology, Zhujiang Hospital of Southern Medical University, Guangzhou, 510000, China
| | - Michele Fimiani
- Department of Medical, Surgical and Neuro Sciences, Section of Dermatology, University of Siena, Policlinico Le Scotte Viale Bracci, Siena, 53100, Italy
| | - Pietro Rubegni
- Department of Medical, Surgical and Neuro Sciences, Section of Dermatology, University of Siena, Policlinico Le Scotte Viale Bracci, Siena, 53100, Italy
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Traversa D, Simonetti G, Tolomeo D, Visci G, Macchia G, Ghetti M, Martinelli G, Kristensen LS, Storlazzi CT. Unravelling similarities and differences in the role of circular and linear PVT1 in cancer and human disease. Br J Cancer 2021; 126:835-850. [PMID: 34754096 PMCID: PMC8927338 DOI: 10.1038/s41416-021-01584-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
The plasmacytoma variant translocation 1 (PVT1) is a long non-coding RNA gene involved in human disease, mainly in cancer onset/progression. Although widely analysed, its biological roles need to be further clarified. Notably, functional studies on PVT1 are complicated by the occurrence of multiple transcript variants, linear and circular, which generate technical issues in the experimental procedures used to evaluate its impact on human disease. Among the many PVT1 transcripts, the linear PVT1 (lncPVT1) and the circular hsa_circ_0001821 (circPVT1) are frequently reported to perform similar pathologic and pro-tumorigenic functions when overexpressed. The stimulation of cell proliferation, invasion and drug resistance, cell metabolism regulation, and apoptosis inhibition is controlled through multiple targets, including MYC, p21, STAT3, vimentin, cadherins, the PI3K/AKT, HK2, BCL2, and CASP3. However, some of this evidence may originate from an incorrect evaluation of these transcripts as two separate molecules, as they share the lncPVT1 exon-2 sequence. We here summarise lncPVT1/circPVT1 functions by mainly focusing on shared pathways, pointing out the potential bias that may exist when the biological role of each transcript is analysed. These considerations may improve the knowledge about lncPVT1/circPVT1 and their specific targets, which deserve further studies due to their diagnostic, prognostic, and therapeutic potential.
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Affiliation(s)
- Debora Traversa
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Doron Tolomeo
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Grazia Visci
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Gemma Macchia
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Martina Ghetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
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Videira A, Beckedorff FC, daSilva LF, Verjovski-Almeida S. PVT1 signals an androgen-dependent transcriptional repression program in prostate cancer cells and a set of the repressed genes predicts high-risk tumors. Cell Commun Signal 2021; 19:5. [PMID: 33430890 PMCID: PMC7798249 DOI: 10.1186/s12964-020-00691-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 12/01/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Androgen receptor (AR) and polycomb repressive complex 2 (PRC2) are known to co-occupy the loci of genes that are downregulated by androgen-stimulus. Long intergenic non-coding RNA (lincRNA) PVT1 is an overexpressed oncogene that is associated with AR in LNCaP prostate cancer cells, and with PRC2 in HeLa and many other types of cancer cells. The possible involvement of PVT1 in mediating androgen-induced gene expression downregulation in prostate cancer has not been explored. METHODS LNCaP cell line was used. Native RNA-binding-protein immunoprecipitation with anti-AR or anti-EZH2 was followed by RT-qPCR with primers for PVT1. Knockdown of PVT1 with specific GapmeRs (or a control with scrambled GapmeR) was followed by differentially expressed genes (DEGs) determination with Agilent microarrays and with Significance Analysis of Microarrays statistical test. DEGs were tested as a tumor risk classifier with a machine learning Random Forest algorithm run with gene expression data from all TCGA-PRAD (prostate adenocarcinoma) tumors as input. ChIP-qPCR was performed for histone marks at the promoter of one DEG. RESULTS We show that PVT1 knockdown in androgen-stimulated LNCaP cells caused statistically significant expression upregulation/downregulation of hundreds of genes. Interestingly, PVT1 knockdown caused upregulation of 160 genes that were repressed by androgen, including a significantly enriched set of tumor suppressor genes, and among them FAS, NOV/CCN3, BMF, HRK, IFIT2, AJUBA, DRAIC and TNFRSF21. A 121-gene-set (out of the 160) was able to correctly predict the classification of all 293 intermediate- and high-risk TCGA-PRAD tumors, with a mean ROC area under the curve AUC = 0.89 ± 0.04, pointing to the relevance of these genes in cancer aggressiveness. Native RIP-qPCR in LNCaP showed that PVT1 was associated with EZH2, a component of PRC2. PVT1 knockdown followed by ChIP-qPCR showed significant epigenetic remodeling at the enhancer and promoter regions of tumor suppressor gene NOV, one of the androgen-repressed genes that were upregulated upon PVT1 silencing. CONCLUSIONS Overall, we provide first evidence that PVT1 was involved in signaling a genome-wide androgen-dependent transcriptional repressive program of tumor suppressor protein-coding genes in prostate cancer cells. Identification of transcriptional inhibition of tumor suppressor genes by PVT1 highlights the pathway to the investigation of mechanisms that lie behind the oncogenic role of PVT1 in cancer. Video Abstract.
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Affiliation(s)
- Alexandre Videira
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
| | - Felipe C. Beckedorff
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
- Present Address: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Lucas F. daSilva
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
- Present Address: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
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