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Suba Z. DNA Damage Responses in Tumors Are Not Proliferative Stimuli, but Rather They Are DNA Repair Actions Requiring Supportive Medical Care. Cancers (Basel) 2024; 16:1573. [PMID: 38672654 PMCID: PMC11049279 DOI: 10.3390/cancers16081573] [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: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND In tumors, somatic mutagenesis presumably drives the DNA damage response (DDR) via altered regulatory pathways, increasing genomic instability and proliferative activity. These considerations led to the standard therapeutic strategy against cancer: the disruption of mutation-activated DNA repair pathways of tumors. PURPOSE Justifying that cancer cells are not enemies to be killed, but rather that they are ill human cells which have the remnants of physiologic regulatory pathways. RESULTS 1. Genomic instability and cancer development may be originated from a flaw in estrogen signaling rather than excessive estrogen signaling; 2. Healthy cells with genomic instability exhibit somatic mutations, helping DNA restitution; 3. Somatic mutations in tumor cells aim for the restoration of DNA damage, rather than further genomic derangement; 4. In tumors, estrogen signaling drives the pathways of DNA stabilization, leading to apoptotic death; 5. In peritumoral cellular infiltration, the genomic damage of the tumor induces inflammatory cytokine secretion and increased estrogen synthesis. In the inflammatory cells, an increased growth factor receptor (GFR) signaling confers the unliganded activation of estrogen receptors (ERs); 6. In breast cancer cells responsive to genotoxic therapy, constitutive mutations help the upregulation of estrogen signaling and consequential apoptosis. In breast tumors non-responsive to genotoxic therapy, the possibilities for ER activation via either liganded or unliganded pathways are exhausted, leading to farther genomic instability and unrestrained proliferation. CONCLUSIONS Understanding the real character and behavior of human tumors at the molecular level suggests that we should learn the genome repairing methods of tumors and follow them by supportive therapy, rather than provoking additional genomic damages.
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Affiliation(s)
- Zsuzsanna Suba
- Department of Molecular Pathology, National Institute of Oncology, Ráth György Str. 7-9, H-1122 Budapest, Hungary
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2
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Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management. Int J Mol Sci 2023; 24:ijms24021145. [PMID: 36674656 PMCID: PMC9863308 DOI: 10.3390/ijms24021145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
In the complex and articulated machinery of the human genome, less than 2% of the transcriptome encodes for proteins, while at least 75% is actively transcribed into non-coding RNAs (ncRNAs). Among the non-coding transcripts, those ≥200 nucleotides long (lncRNAs) are receiving growing attention for their involvement in human diseases, particularly cancer. Genomic studies have revealed the multiplicity of processes, including neoplastic transformation and tumor progression, in which lncRNAs are involved by regulating gene expression at epigenetic, transcriptional, and post-transcriptional levels by mechanism(s) that still need to be clarified. In breast cancer, several lncRNAs were identified and demonstrated to have either oncogenic or tumor-suppressive roles. The functional understanding of the mechanisms of lncRNA action in this disease could represent a potential for translational applications, as these molecules may serve as novel biomarkers of clinical use and potential therapeutic targets. This review highlights the relationship between lncRNAs and the principal hallmark of the luminal breast cancer phenotype, estrogen receptor α (ERα), providing an overview of new potential ways to inhibit estrogenic signaling via this nuclear receptor toward escaping resistance to endocrine therapy.
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DSCAM-AS1 Long Non-Coding RNA Exerts Oncogenic Functions in Endometrial Adenocarcinoma via Activation of a Tumor-Promoting Transcriptome Profile. Biomedicines 2022; 10:biomedicines10071727. [PMID: 35885035 PMCID: PMC9313190 DOI: 10.3390/biomedicines10071727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
Accumulating evidence suggests that lncRNA DSCAM-AS1 acts tumor-promoting in various cancer entities. In breast cancer, DSCAM-AS1 was shown to be the lncRNA being most responsive to induction by estrogen receptor α (ERα). In this study, we examined the function of DSCAM-AS1 in endometrial adenocarcinoma using in silico and different in vitro approaches. Initial analysis of open-source data revealed DSCAM-AS1 overexpression in endometrial cancer (EC) (p < 0.01) and a significant association with shorter overall survival of EC patients (HR = 1.78, p < 0.01). In EC, DSCAM-AS1 was associated with endometrial tumor promotor gene PRL and with expression of ERα and its target genes TFF1 and PGR. Silencing of this lncRNA by RNAi in two EC cell lines was more efficient in ERα-negative HEC-1B cells and reduced their growth and the expression of proliferation activators like NOTCH1, PTK2 and EGR1. DSCAM-AS1 knockdown triggered an anti-tumoral transcriptome response as revealed by Affymetrix microarray analysis, emerging from down-regulation of tumor-promoting genes and induction of tumor-suppressive networks. Finally, several genes regulated upon DSCAM-AS1 silencing in vitro were found to be inversely correlated with this lncRNA in EC tissues. This study clearly suggests an oncogenic function of DSCAM-AS1 in endometrial adenocarcinoma via activation of a tumor-promoting transcriptome profile.
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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5
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Jia X, Lei H, Jiang X, Yi Y, Luo X, Li J, Chen Y, Liu S, Yang C. Identification of Crucial lncRNAs for Luminal A Breast Cancer through RNA Sequencing. Int J Endocrinol 2022; 2022:6577942. [PMID: 35692369 PMCID: PMC9184229 DOI: 10.1155/2022/6577942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/16/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The growing body of evidence indicates aberrant expression of long noncoding RNAs (lncRNAs) in breast cancer. Nevertheless, a few studies have focused on identifying key lncRNAs for patients with luminal A breast cancer. In our study, we tried to find key lncRNAs and mRNAs in luminal A breast cancer. METHODS RNA sequencing was performed to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in luminal A breast cancer. The protein-protein interaction (PPI), DElncRNA-DEmRNA coexpression, DElncRNA-nearby DEmRNA interaction networks, and functional annotation were performed to uncover the function of DEmRNAs. Online databases were used to validate the RNA sequencing result. The diagnostic value of candidate mRNAs was evaluated by receiver operating characteristic (ROC) curve analysis. RESULTS A total number of 1451 DEmRNAs and 272 DElncRNAs were identified. Several hub proteins were identified in the PPI network, including TUBB3, HIST2H3C, MCM2, MYOC, NEK2, LIPE, FN1, FOXJ1, S100A7, and DLK1. In the DElncRNA-DEmRNA coexpression, some hub lncRNAs were identified, including AP001528.2, LINC00968, LINC02202, TRHDE-AS1, LINC01140, AL354707.1, AC097534.1, MIR222HG, and AL662844.4. The mRNA expression result of TFF1, COL10A1, LEP, PLIN1, PGM5-AS1, and TRHDE-AD1 in the GSE98793 was consistent with the RNA sequencing result. The protein expression results of TUBB3, MCM2, MYOC, FN1, S100A7, and TFF1 were consistent with the mRNA expression result COL10A1, LEP, PLIN1, PGM5-AS1, and TRHDE-AD1 were capable of discriminating luminal A breast cancer and normal controls. Four lncRNA-nearby and coexpressed mRNA pairs of HOXC-AS3-HOXC10, AC020907.2-FXYD1, AC026461.1-MT1X, and AC132217.1-IGF2 were identified. AMPK (involved LIPE and LEP) and PPAR (involved PLIN1) were two significantly enriched pathways in luminal A breast cancer. CONCLUSION This study could be helpful in unraveling the pathogenesis and providing novel therapeutic strategies for luminal A breast cancer.
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Affiliation(s)
- Xinjian Jia
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Hai Lei
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Xuemei Jiang
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Ying Yi
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Xue Luo
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Junyan Li
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Yu Chen
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Sha Liu
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
| | - Chengcheng Yang
- Department of Breast Surgery, Deyang People's Hospital, Deyang, Sichuan Province, China
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The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13246261. [PMID: 34944881 PMCID: PMC8699117 DOI: 10.3390/cancers13246261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.
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7
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Ebrahimzadeh K. A Review on the Carcinogenic Roles of DSCAM-AS1. Front Cell Dev Biol 2021; 9:758513. [PMID: 34708048 PMCID: PMC8542687 DOI: 10.3389/fcell.2021.758513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a group of transcripts with fundamental roles in the carcinogenesis. DSCAM Antisense RNA 1 (DSCAM−AS1) is an example of this group of transcripts which has been firstly identified in an attempt to find differentially expressed transcripts between breast tumor cells and benign breast samples. The pathogenic roles of DSCAM-AS1 have been vastly assessed in breast cancer, yet its roles are not restricted to this type of cancer. Independent studies in non-small cell lung cancer, colorectal cancer, osteosarcoma, hepatocellular carcinoma, melanoma and cervical cancer have validated participation of DSCAM-AS1 in the carcinogenic processes. miR-577, miR-122-5p, miR-204-5p, miR-136, miR−137, miR−382, miR−183, miR−99, miR-3173-5p, miR-874-3p, miR-874-3p, miR-150-5p, miR-2467-3p, miR-216b, miR-384, miR-186-5p, miR-338-3p, miR-877-5p and miR-101 are among miRNAs which interact with DSCAM-AS1. Moreover, this lncRNA has interactions with Wnt/β-catenin pathway. The current study aims at summarization of the results of studies which focused on the assessment of oncogenic role of DSCAM-AS1.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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Muluhngwi P, Klinge CM. Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells. Cancers (Basel) 2021; 13:3530. [PMID: 34298743 PMCID: PMC8307416 DOI: 10.3390/cancers13143530] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.
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Affiliation(s)
- Penn Muluhngwi
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
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He J, Ling L, Liu Z, Ren X, Wan L, Tu C, Li Z. Functional interplay between long non-coding RNAs and the Wnt signaling cascade in osteosarcoma. Cancer Cell Int 2021; 21:313. [PMID: 34130697 PMCID: PMC8207720 DOI: 10.1186/s12935-021-02013-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Osteosarcoma is a common and highly malignant bone tumor among children, adolescents and young adults. However, the underlying molecular mechanisms remain largely unexplored. LncRNAs are transcripts with no or limited protein-coding capacity in human genomes, and have been demonstrated to play crucial functions in initiation, progression, therapeutic resistance, recurrence and metastasis of tumor. Considerable studies revealed a dysregulated lncRNA expression pattern in osteosarcoma, which may act as oncogenes or suppressors to regulate osteosarcoma progression. Wnt signaling pathway is an important cascade in tumorigenesis by modulation of pleiotropic biological functions including cell proliferation, apoptosis, differentiation, stemness, genetic stability and chemoresistance. Hyperactivation or deficiency of key effectors in Wnt cascade is a common event in many osteosarcoma patients. Recently, increasing evidences have suggested that lncRNAs could interplay with component of Wnt pathway, and thereby contribute to osteosarcoma onset, progression and dissemination. In this review, we briefly summarize Wnt signaling-related lncRNAs in osteosarcoma progression, aiming to gain insights into their underlying crosstalk as well as clinical application in osteosarcoma therapeutic modalities.
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Affiliation(s)
- Jieyu He
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Lin Ling
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Zhongyue Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Lu Wan
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, No 139 Middle Renmin Road, Changsha, 410011, Hunan, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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Rudzinska M, Czarnecka-Chrebelska KH, Kuznetsova EB, Maryanchik SV, Parodi A, Korolev DO, Potoldykova N, Svetikova Y, Vinarov AZ, Nemtsova MV, Zamyatnin AA. Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness. Noncoding RNA 2021; 7:25. [PMID: 33920185 PMCID: PMC8167775 DOI: 10.3390/ncrna7020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can be specifically expressed in different tissues and cancers. By controlling the gene expression at the transcriptional and translational levels, lncRNAs have been reported to be involved in tumor growth and metastasis. Recent data demonstrated that multiple lncRNAs have a crucial role in renal cell carcinoma (RCC) progression-the most common malignant urogenital tumor. In the present study, we found a trend towards increased PROX1 antisense RNA 1 (PROX1-AS1) expression in RCC specimens compared to non-tumoral margins. Next, we found a positive correlation between PROX1-AS1 expression and the occurrence of distant and lymph node metastasis, higher tumor stage (pT1 vs. pT2 vs. pT3-T4) and high-grade (G1/G2 vs. G3/G4) clear RCC. Furthermore, global demethylation in RCC-derived cell lines (769-P and A498) and human embryonic kidney 293 (HEK293) cells induced a significant increase of PROX1-AS1 expression level, with the most remarkable change in HEK293 cells. In line with this evidence, bisulfite sequencing analysis confirmed the specific demethylation of bioinformatically selected CpG islands on the PROX1-AS1 promoter sequence in the HEK293 cell line but not in the tumor cells. Additionally, the human specimen analysis showed the hemimethylated state of CG dinucleotides in non-tumor kidney tissues, whereas the tumor samples presented the complete, partial, or no demethylation of CpG-islands. In conclusion, our study indicated that PROX1-AS1 could be associated with RCC progression, and further investigations may define its role as a new diagnostic marker and therapeutic target.
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Affiliation(s)
- Magdalena Rudzinska
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | | | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia
| | - Sofya V. Maryanchik
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | - Alessandro Parodi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | - Dmitry O. Korolev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Nataliya Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Yulia Svetikova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Andrey Z. Vinarov
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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Tarighi M, Khalaj-Kondori M, Hosseinzadeh A, Abtin M. Long non-coding RNA (lncRNA) DSCAM-AS1 is upregulated in breast cancer. Breast Dis 2021; 40:63-68. [PMID: 33554879 DOI: 10.3233/bd-201010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Accumulating evidence highlights that long noncoding RNA (lncRNA) DSCAM-AS1 play a key regulatory role in different stages of cancer development and progression. This study aimed to investigate whether the expression of DSCAM-AS1 is deregulated in breast cancer. MATERIALS AND METHODS The relative expression of DSCAM-AS1 was measured in fifty breast cancerous and matched adjacent non-neoplastic tissue samples using quantitative real-time polymerase chain reaction (qPCR) technique. The association between DSCAM-AS1 expression and patients' clinicopathological features was evaluated. Sensitivity and specificity of the DSCAM-AS1 expression for diagnosing breast cancer was obtained by the receiver operating characteristic (ROC) curve analysis. RESULTS Our results showed that the expression of DSCAM-AS1 was significantly up-regulated in breast cancerous tissues compared with the matched adjacent non-neoplastic tissues (P < 0.05). Furthermore, we observed a significant association between the DSCAM-AS1 expression and lymph node metastasis (P = 0.011) but no other clinicopathological characteristics (P > 0.05). ROC curve analysis resulted in an area under the curve (AUC) of 0.67 and showed that the DSCAM-AS1 expression level may discriminate cancerous and non-cancerous tissues with 68% sensitivity and 76% specificity. CONCLUSION This study provides further evidence that the expression of DSCAM-AS1 is deregulated in breast cancer and highlights its potential in breast cancer development.
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Affiliation(s)
- Mahsa Tarighi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Mohammad Khalaj-Kondori
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Asghar Hosseinzadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Abtin
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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12
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Moradi MT, Fallahi H, Rahimi Z. The clinical significance of circulating DSCAM-AS1 in patients with ER-positive breast cancer and construction of its competitive endogenous RNA network. Mol Biol Rep 2020; 47:7685-7697. [DOI: 10.1007/s11033-020-05841-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022]
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13
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Tahmouresi F, Razmara E, Pakravan K, Mossahebi-Mohammadi M, Rouhollah F, Montazeri M, Sarrafzadeh A, Fahimi H, Babashah S. Upregulation of the long noncoding RNAs DSCAM-AS1 and MANCR is a potential diagnostic marker for breast carcinoma. Biotechnol Appl Biochem 2020; 68:1250-1256. [PMID: 33012018 DOI: 10.1002/bab.2048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Breast cancer (BC) is one of the most common malignancies among women in the world. There is a global attempt to diagnose BC as early as possible. Long noncoding RNAs (lncRNAs) are emerging as novel targets and biomarkers for BC diagnosis and prognosis. Aberrant expression of lncRNAs is associated with BC development, making them a potential tumor marker for BC. To investigate this possibility, we determined the expression levels of Down syndrome cell adhesion molecule-antisense RNA-1 (DSCAM-AS1) and mitotically-associated long non-coding RNA (MANCR) lncRNAs in BC tissues. This case-control study included 50 paired tumor and adjacent nontumor tissues from female BC patients. The total RNA was isolated and the expression levels of MANCR and DSCAM-AS1 lncRNAs were assessed using quantitative real-time reverse transcription-PCR. Potential correlations between lncRNA levels and clinicopathological characteristics were also analyzed. DSCAM-AS1 and MANCR lncRNAs were significantly upregulated in BC tumor tissues compared with the adjacent nontumor tissues. We also found the significant upregulation of DSCAM-AS1 in advanced tumor-node-metastasis stage (TNM III) of BC tumor tissues. Furthermore, the expression of DSCAM-AS1 and MANCR in HER-2 positive patients was significantly higher than HER-2 negative affected individuals. Receiver operating characteristic curve analysis showed a satisfactory diagnostic efficacy (P value < 0.0001), which means that DSCAM-AS1 and MANCR lncRNAs can potentially serve as a biomarker. The present study might provide further approval for the clinical diagnostic significance of DSCAM-AS1 and MANCR lncRNAs that their high expressions were associated with aggressive clinical parameters of BC.
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Affiliation(s)
- Fatemeh Tahmouresi
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Katayoon Pakravan
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Mossahebi-Mohammadi
- School of Pharmaceutical Sciences and International Collaborative Center on Growth Factor Research, Wenzhou Medical University, Wenzhou, China
| | - Fatemeh Rouhollah
- Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Montazeri
- Department of Medical Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Hossein Fahimi
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Zhang Y, Huang YX, Wang DL, Yang B, Yan HY, Lin LH, Li Y, Chen J, Xie LM, Huang YS, Liao JY, Hu KS, He JH, Saw PE, Xu X, Yin D. LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network. Theranostics 2020; 10:10823-10837. [PMID: 32929382 PMCID: PMC7482804 DOI: 10.7150/thno.47830] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/15/2020] [Indexed: 12/21/2022] Open
Abstract
Rationale: The forkhead box A1 (FOXA1) is a crucial transcription factor in initiation and development of breast, lung and prostate cancer. Previous studies about the FOXA1 transcriptional network were mainly focused on protein-coding genes. Its regulatory network of long non-coding RNAs (lncRNAs) and their role in FOXA1 oncogenic activity remains unknown. Methods: The Cancer Genome Atlas (TCGA) data, RNA-seq and ChIP-seq data were used to analyze FOXA1 regulated lncRNAs. RT-qPCR was used to detect the expression of DSCAM-AS1, RT-qPCR and Western blotting were used to determine the expression of FOXA1, estrogen receptor α (ERα) and Y box binding protein 1 (YBX1). RNA pull-down and RIP-qPCR were employed to investigate the interaction between DSCAM-AS1 and YBX1. The effect of DSCAM-AS1 on malignant phenotypes was examined through in vitro and in vivo assays. Results: In this study, we conducted a global analysis of FOXA1 regulated lncRNAs. For detailed analysis, we chose lncRNA DSCAM-AS1, which is specifically expressed in lung adenocarcinoma, breast and prostate cancer. The expression level of DSCAM-AS1 is regulated by two super-enhancers (SEs) driven by FOXA1. High expression levels of DSCAM-AS1 was associated with poor prognosis. Knockout experiments showed DSCAM-AS1 was essential for the growth of xenograft tumors. Moreover, we demonstrated DSCAM-AS1 can regulate the expression of the master transcriptional factor FOXA1. In breast cancer, DSCAM-AS1 was also found to regulate ERα. Mechanistically, DSCAM-AS1 interacts with YBX1 and influences the recruitment of YBX1 in the promoter regions of FOXA1 and ERα. Conclusion: Our study demonstrated that lncRNA DSCAM-AS1 was transcriptionally activated by super-enhancers driven by FOXA1 and exhibited lineage-specific expression pattern. DSCAM-AS1 can promote cancer progression by interacting with YBX1 and regulating expression of FOXA1 and ERα.
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15
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Perspectives on the Role of Non-Coding RNAs in the Regulation of Expression and Function of the Estrogen Receptor. Cancers (Basel) 2020; 12:cancers12082162. [PMID: 32759784 PMCID: PMC7465269 DOI: 10.3390/cancers12082162] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptors (ERs) comprise several nuclear and membrane-bound receptors with different tissue-specific functions. ERα and ERβ are two nuclear members of this family, whereas G protein-coupled estrogen receptor (GPER), ER-X, and Gq-coupled membrane estrogen receptor (Gq-mER) are membrane-bound G protein-coupled proteins. ERα participates in the development and function of several body organs such as the reproductive system, brain, heart and musculoskeletal systems. ERβ has a highly tissue-specific expression pattern, particularly in the female reproductive system, and exerts tumor-suppressive roles in some tissues. Recent studies have revealed functional links between both nuclear and membrane-bound ERs and non-coding RNAs. Several oncogenic lncRNAs and miRNAs have been shown to exert their effects through the modulation of the expression of ERs. Moreover, treatment with estradiol has been shown to alter the malignant behavior of cancer cells through functional axes composed of non-coding RNAs and ERs. The interaction between ERs and non-coding RNAs has functional relevance in several human pathologies associated with estrogen regulation, such as cancers, intervertebral disc degeneration, coronary heart disease and diabetes. In the current review, we summarize scientific literature on the role of miRNAs and lncRNAs on ER-associated signaling and related disorders.
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16
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Elhasnaoui J, Miano V, Ferrero G, Doria E, Leon AE, Fabricio ASC, Annaratone L, Castellano I, Sapino A, De Bortoli M. DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. Cancers (Basel) 2020; 12:cancers12061453. [PMID: 32503257 PMCID: PMC7352480 DOI: 10.3390/cancers12061453] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022] Open
Abstract
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.
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Affiliation(s)
- Jamal Elhasnaoui
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Department of Computer Science, University of Turin, 10149 Turin, Italy
| | - Elena Doria
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Antonette E. Leon
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Aline S. C. Fabricio
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Isabella Castellano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Correspondence: ; Tel.: +39-0116-7050-58
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17
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Zaheed O, Samson J, Dean K. A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset. Noncoding RNA Res 2020; 5:48-59. [PMID: 32206740 PMCID: PMC7078458 DOI: 10.1016/j.ncrna.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
Breast cancer research has traditionally centred on genomic alterations, hormone receptor status and changes in cancer-related proteins to provide new avenues for targeted therapies. Due to advances in next generation sequencing technologies, there has been the emergence of long, non-coding RNAs (lncRNAs) as regulators of normal cellular events, with links to various disease states, including breast cancer. Here we describe our bioinformatic analyses of a previously published RNA sequencing (RNA-seq) dataset to identify lncRNAs with altered expression levels in a subset of breast cancer cell lines. Using a previously published RNA-seq dataset of 675 cancer cell lines, a subset of 18 cell lines was selected for our analyses that included 16 breast cancer lines, one ductal carcinoma in situ line and one normal-like breast epithelial cell line. Principal component analysis demonstrated correlation with well-established categorisation methods of breast cancer (i.e. luminal A/B, HER2 enriched and basal-like A/B). Through detailed comparison of differentially expressed lncRNAs in each breast cancer sub-type with normal-like breast epithelial cells, we identified 15 lncRNAs with consistently altered expression, including three uncharacterised lncRNAs. Utilising data from The Cancer Genome Atlas (TCGA) and The Genotype Tissue Expression (GETx) project via Gene Expression Profiling Interactive Analysis (GEPIA2), we assessed clinical relevance of several identified lncRNAs with invasive breast cancer. Lastly, we determined the relative expression level of six lncRNAs across a spectrum of breast cancer cell lines to experimentally confirm the findings of our bioinformatic analyses. Overall, we show that the use of existing RNA-seq datasets, if re-analysed with modern bioinformatic tools, can provide a valuable resource to identify lncRNAs that could have important biological roles in oncogenesis and tumour progression.
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Affiliation(s)
| | | | - Kellie Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62, Ireland
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18
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Long Noncoding RNAs Involved in the Endocrine Therapy Resistance of Breast Cancer. Cancers (Basel) 2020; 12:cancers12061424. [PMID: 32486413 PMCID: PMC7353012 DOI: 10.3390/cancers12061424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are defined as RNAs longer than 200 nucleotides that do not encode proteins. Recent studies have demonstrated that numerous lncRNAs are expressed in humans and play key roles in the development of various types of cancers. Intriguingly, some lncRNAs have been demonstrated to be involved in endocrine therapy resistance for breast cancer through their own mechanisms, suggesting that lncRNAs could be promising new biomarkers and therapeutic targets of breast cancer. Here, we summarize the functions and mechanisms of lncRNAs related to the endocrine therapy resistance of breast cancer.
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19
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Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21103711. [PMID: 32466143 PMCID: PMC7279485 DOI: 10.3390/ijms21103711] [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: 05/06/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.
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20
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Huang L, Liang G, Zhang Q, Zhao W. The Role of Long Noncoding RNAs in Antiestrogen Resistance in Breast Cancer: An Overview and Update. J Breast Cancer 2020; 23:129-140. [PMID: 32395373 PMCID: PMC7192751 DOI: 10.4048/jbc.2020.23.e10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
As a standard treatment, endocrine therapy has dramatically enhanced the prognosis of patients with estrogen receptor (ER)-positive breast cancer, which accounts for nearly 70% of all breast cancers. Antiestrogen drugs such as tamoxifen and aromatase inhibitors are the standard treatment options for ERα-positive breast cancer. However, acquired antiestrogen resistance is still the leading cause of disease recurrence and progression. Evidence has shown that long noncoding RNAs (lncRNAs) play an essential role in the development of antiestrogen resistance in ER-positive breast cancer and can serve as biomarkers or potential therapeutic targets. This review highlights the role of lncRNAs in the development of antiestrogen resistance in breast cancer.
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Affiliation(s)
- Lan Huang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Guohua Liang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Qingyuan Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China
- Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Wenhui Zhao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
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21
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Mathias C, Zambalde EP, Rask P, Gradia DF, de Oliveira JC. Long non-coding RNAs differential expression in breast cancer subtypes: What do we know? Clin Genet 2019; 95:558-568. [PMID: 30614523 DOI: 10.1111/cge.13502] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022]
Abstract
Breast Cancer (BC) is the most commonly diagnosed cancer and is the leading cause of cancer deaths in women. BC is a heterogeneous disease with different clinical and genetic features. According to immunohistochemical markers, BC is subdivided into four main subtypes: luminal A, luminal B, ERBB2 positive and triple negative. Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides and deregulated lncRNAs are associated with human diseases, including BC. In order to improve BC molecular classification, non-coding RNAs (ncRNAs), including lncRNAs, have been used. In this review, we focus on lncRNAs with differential expression in BC subtypes and how these RNAs may act to contribute to BC heterogeneity. We also emphasize the potential of these lncRNAs as biomarkers.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Erika P Zambalde
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Philip Rask
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
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22
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Khorshidi H, Azari I, Oskooei VK, Taheri M, Ghafouri-Fard S. DSCAM-AS1 up-regulation in invasive ductal carcinoma of breast and assessment of its potential as a diagnostic biomarker. Breast Dis 2019; 38:25-30. [PMID: 30594914 DOI: 10.3233/bd-180351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND The long non-coding RNA (lncRNA) DSCAM-AS1 has been demonstrated to participate in the pathogenesis of breast cancer and tamoxifen resistance. OBJECTIVE To evaluate expression profile of DSCAM-AS1 in invasive ductal carcinoma of breast and its suitability as a biomarker for diagnosis of breast cancer. METHODS We evaluated expression of DSCAM-AS1 in 108 breast tissues including tumoral and adjacent non-cancerous tissues (ANCTs) by means of quantitative real time PCR. RESULTS DSCAM-AS1 was up-regulated in tumoral tissues compared with ANCTs (Fold change = 2.86, P = 0.011). Its expression was significantly higher in patients aged less than 55 compared with older patients (P = 0.02). However, its expression levels had not a good performance as a diagnostic biomarker for breast cancer. CONCLUSIONS The significant up-regulation of DSCAM-AS1 in tumoral tissues compared with ANCTs provides further evidences for participation of this lncRNA in the pathogenesis of breast cancer.
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Affiliation(s)
- Hamidreza Khorshidi
- Department of Surgery, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Iman Azari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi Oskooei
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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23
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Liang WH, Li N, Yuan ZQ, Qian XL, Wang ZH. DSCAM-AS1 promotes tumor growth of breast cancer by reducing miR-204-5p and up-regulating RRM2. Mol Carcinog 2018; 58:461-473. [PMID: 30457164 DOI: 10.1002/mc.22941] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/17/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
Breast cancer (BC) is a common malignancy worldwide. More than 3 700 000 women die of BC every year. DSCAM-AS1 was overexpressed several kinds of cancer and miR-204-5p was lowly expressed, which indicated that miR-204-5p had anti-tumor activity and DSCAM-AS1 had pro-tumor activity. We intended to analyze DSCAM-AS1, miR-204-5p, and ribonucleotide reductase M2 (RRM2). Microarray analysis and quantitative Real Time fluorescence Polymerase Chain Reaction (qRT-PCR) were employed to determine DSCAM-AS1 and miR-204-5p expression. Luciferase reporter assay was applied to examine the target relationship between DSCAM-AS1, miR-204-5p, and RRM2. Cell Counting Kit-8 (CCK-8 assay), transwell assay, and flow cytometry were used to detect cell proliferation, invasion, and apoptosis. The expression of DSCAM-AS1, miR-204-5p, and RRM2 were confirmed by Western blot. We also conducted in vivo assay to verify the effect of DSCAM-AS1. DSCAM-AS1 was up-regulated, while miR-204-5p was down-regulated in BC tissues and cells. DSCAM-AS1 directly targeted miR-204-5p. DSCAM-AS1 promoted the proliferation and invasion of BC cells by reducing miR-204-5p and inhibiting miR-204-5p expression. DSCAM-AS1 expression was related to the expression of RRM2, and miR-204-5p could reverse the function of DSCAM-AS1. RRM2 was up-regulated in BC cells, and miR-204-5p inhibited RRM2 expression by targeting RRM2. Overexpression of RRM2 stimulated proliferation and cell invasion and impeded apoptosis. In vivo experiments showed that knockdown of DSCAM-AS1 decreased the tumorigenesis of BC cells, increased the expression of miR-204-5p. DSCAM-AS1 promoted proliferation and impaired apoptosis of BC cells by reducing miR-204-5p and enhancing RRM2 expression. DSCAM-AS1/miR-204-5p/RRM2 may serve as novel therapeutic targets for BC.
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Affiliation(s)
- Wen-Hui Liang
- The Affiliated Center Hospital, Xinxiang Medical University, Xinxiang, Henan, China
| | - Na Li
- Department of Pathology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhi-Qing Yuan
- Department of Pathology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xin-Lai Qian
- Department of Pathology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhi-Hui Wang
- Department of Pathology, Xinxiang Medical University, Xinxiang, Henan, China
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24
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Sun W, Li AQ, Zhou P, Jiang YZ, Jin X, Liu YR, Guo YJ, Yang WT, Shao ZM, Xu XE. DSCAM-AS1 regulates the G 1 /S cell cycle transition and is an independent prognostic factor of poor survival in luminal breast cancer patients treated with endocrine therapy. Cancer Med 2018; 7:6137-6146. [PMID: 30430768 PMCID: PMC6308059 DOI: 10.1002/cam4.1603] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/12/2023] Open
Abstract
DSCAM-AS1 is one of the few intensively studied lncRNAs with high specific expression in luminal breast cancer. It is directly regulated by estrogen receptor α (ERα) and plays vital roles in tumor proliferation, invasion, and tamoxifen resistance. However, the detailed function of DSCAM-AS1 in tumor progression and its clinical significance remain unclear. We reveal that DSCAM-AS1 regulates cell proliferation and colony formation by inducing the G1/S transition. RNA-seq analysis demonstrated that DSCAM-AS1 participates in crucial biological processes, including DNA replication, the G1/S phase transition, sister chromatid cohesion, chromosome segregation, protein localization to the chromosome and DNA recombination. Most importantly, in the retrospectively registered clinical analysis, high expression of DSCAM-AS1 is a poor prognostic factor in patients with luminal breast cancer treated with endocrine therapy. In conclusion, DSCAM-AS1 is a promising clinical therapeutic target that may prolong survival of luminal breast cancer patients treated with endocrine therapy.
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Affiliation(s)
- Wei Sun
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - An-Qi Li
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ping Zhou
- Department of Breast Surgery, The Third Hospital of Nanchang, Nanchang, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Rong Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Jie Guo
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Tao Yang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiao-En Xu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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25
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Miglio U, Berrino E, Panero M, Ferrero G, Coscujuela Tarrero L, Miano V, Dell'Aglio C, Sarotto I, Annaratone L, Marchiò C, Comoglio PM, De Bortoli M, Pasini B, Venesio T, Sapino A. The expression of LINE1-MET chimeric transcript identifies a subgroup of aggressive breast cancers. Int J Cancer 2018; 143:2838-2848. [PMID: 30144023 DOI: 10.1002/ijc.31831] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/17/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
Demethylation of the long interspersed nuclear element (LINE-1; L1) antisense promoter can result in transcription of neighboring sequences as for the L1-MET transcript produced by the L1 placed in the second intron of MET. To define the role of L1-MET, we investigated the sequence and the transcription of L1-MET in vitro models and heterogeneous breast cancers, previously reported to show other L1-derived transcripts. L1-MET expressing cell lines were initially identified in silico and investigated for L1-MET promoter methylation, cDNA sequence and cell fraction mRNA. The transcriptional level of L1-MET and MET were then evaluated in breast specimens, including 9 cancer cell lines, 41 carcinomas of different subtypes, and 11 normal tissues. In addition to a L1-MET transcript ending at MET exon 21, six novel L1-MET splice variants were identified. Normal breast tissues were negative for the L1-MET expression, whereas the triple-negative breast cancer (TNBC) and the high-grade carcinomas were enriched with the L1-MET mRNA (p = 0.005 and p = 0.018, respectively). In cancer cells and tissues the L1-MET expression was associated with its promoter hypomethylation (ρ = -0.8 and -0.9, respectively). No correlation was found between L1-MET and MET mRNA although L1-MET expressing tumors with higher L1-MET/MET ratio were negative for the MET protein expression (p = 0.006). Besides providing the first identification and detailed description of L1-MET in breast cancer, we clearly demonstrate that higher levels of this transcript specifically recognize a subset of more aggressive carcinomas, mainly TNBC. We suggest the possible evaluation of L1-MET in the challenging diagnosis of early TNBCs.
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Affiliation(s)
- Umberto Miglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mara Panero
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | | | - Valentina Miano
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Carmine Dell'Aglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo M Comoglio
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tiziana Venesio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
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26
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De Bortoli M, Miano V, Coscujuela Tarrero L. The new world of RNA biomarkers and explorers’ prudence rules. Int J Biol Markers 2018; 33:239-243. [DOI: 10.1177/1724600818764071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Michele De Bortoli
- Center for Molecular Systems Biology and Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Valentina Miano
- Center for Molecular Systems Biology and Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Lucia Coscujuela Tarrero
- Center for Molecular Systems Biology and Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
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27
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Amodio N, Raimondi L, Juli G, Stamato MA, Caracciolo D, Tagliaferri P, Tassone P. MALAT1: a druggable long non-coding RNA for targeted anti-cancer approaches. J Hematol Oncol 2018; 11:63. [PMID: 29739426 PMCID: PMC5941496 DOI: 10.1186/s13045-018-0606-4] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/26/2018] [Indexed: 02/07/2023] Open
Abstract
The deeper understanding of non-coding RNAs has recently changed the dogma of molecular biology assuming protein-coding genes as unique functional biological effectors, while non-coding genes as junk material of doubtful significance. In the last decade, an exciting boom of experimental research has brought to light the pivotal biological functions of long non-coding RNAs (lncRNAs), representing more than the half of the whole non-coding transcriptome, along with their dysregulation in many diseases, including cancer.In this review, we summarize the emerging insights on lncRNA expression and functional role in cancer, focusing on the evolutionary conserved and abundantly expressed metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) that currently represents the best characterized lncRNA. Altogether, literature data indicate aberrant expression and dysregulated activity of MALAT1 in human malignancies and envision MALAT1 targeting as a novel treatment strategy against cancer.
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Affiliation(s)
- Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy.
| | - Lavinia Raimondi
- IRCSS Rizzoli Orthopedic Institute, Bologna, Italy
- Innovative Technology Platforms for Tissue Engineering, Theranostic and Oncology, Rizzoli Orthopedic Institute, Palermo, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy
| | - Maria Angelica Stamato
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Viale Europa, 88100, Catanzaro, Italy.
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28
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Richard JLC, Eichhorn PJA. Deciphering the roles of lncRNAs in breast development and disease. Oncotarget 2018; 9:20179-20212. [PMID: 29732012 PMCID: PMC5929455 DOI: 10.18632/oncotarget.24591] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.
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Affiliation(s)
- John Lalith Charles Richard
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- Current Address: Genome Institute of Singapore, Agency for Science Technology and Research, 138672, Singapore
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- School of Pharmacy, Curtin University, Perth, 6845, Australia
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29
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Hu G, Niu F, Humburg BA, Liao K, Bendi S, Callen S, Fox HS, Buch S. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget 2018; 9:18648-18663. [PMID: 29719633 PMCID: PMC5915100 DOI: 10.18632/oncotarget.24307] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.
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Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Niu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bree A. Humburg
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sunil Bendi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon Callen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S. Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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30
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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31
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Clark BJ, Prough RA, Klinge CM. Mechanisms of Action of Dehydroepiandrosterone. VITAMINS AND HORMONES 2018; 108:29-73. [PMID: 30029731 DOI: 10.1016/bs.vh.2018.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Dehydroepiandrosterone (3β-hydroxy-5-androsten-17-one, DHEA) and its sulfated metabolite DHEA-S are the most abundant steroids in circulation and decline with age. Rodent studies have shown that DHEA has a wide variety of effects on liver, kidney, adipose, reproductive tissues, and central nervous system/neuronal function. The mechanisms by which DHEA and DHEA-S impart their physiological effects may be direct actions on plasma membrane receptors, including a DHEA-specific, G-protein-coupled receptor in endothelial cells; various neuroreceptors, e.g., aminobutyric-acid-type A, N-methyl-d-aspartate (NMDA), and sigma-1 (S1R) receptors; by binding steroid receptors: androgen and estrogen receptors (ARs, ERα, or ERβ); or by their metabolism to more potent sex steroid hormones, e.g., testosterone, dihydrotestosterone, and estradiol, which bind with higher affinity to ARs and ERs. DHEA inhibits voltage-gated T-type calcium channels. DHEA activates peroxisome proliferator-activated receptor (PPARα) and CAR by a mechanism apparently involving PP2A, a protein phosphatase dephosphorylating PPARα and CAR to activate their transcriptional activity. We review our recent study showing DHEA activated GPER1 (G-protein-coupled estrogen receptor 1) in HepG2 cells to stimulate miR-21 transcription. This chapter reviews some of the physiological, biochemical, and molecular mechanisms of DHEA and DHEA-S activity.
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Affiliation(s)
- Barbara J Clark
- Department of Biochemistry and Molecular Genetics, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY, United States
| | - Russell A Prough
- Department of Biochemistry and Molecular Genetics, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY, United States
| | - Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY, United States.
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32
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Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer. Oncotarget 2018; 7:68851-68863. [PMID: 27634900 PMCID: PMC5356595 DOI: 10.18632/oncotarget.11998] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/24/2016] [Indexed: 01/12/2023] Open
Abstract
Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.
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33
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Coscujuela Tarrero L, Ferrero G, Miano V, De Intinis C, Ricci L, Arigoni M, Riccardo F, Annaratone L, Castellano I, Calogero RA, Beccuti M, Cordero F, De Bortoli M. Luminal breast cancer-specific circular RNAs uncovered by a novel tool for data analysis. Oncotarget 2018; 9:14580-14596. [PMID: 29581865 PMCID: PMC5865691 DOI: 10.18632/oncotarget.24522] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/12/2018] [Indexed: 12/31/2022] Open
Abstract
Circular RNAs are highly stable molecules present in all eukaryotes generated by distinct transcript processing. We have exploited poly(A-) RNA-Seq data generated in our lab in MCF-7 breast cancer cells to define a compilation of exonic circRNAs more comprehensive than previously existing lists. Development of a novel computational tool, named CircHunter, allowed us to more accurately characterize circRNAs and to quantitatively evaluate their expression in publicly available RNA-Seq data from breast cancer cell lines and tumor tissues. We observed and confirmed, by ChIP analysis, that exons involved in circularization events display significantly higher levels of the histone post-transcriptional modification H3K36me3 than non-circularizing exons. This result has potential impact on circRNA biogenesis since H3K36me3 has been involved in alternative splicing mechanisms. By analyzing an Ago-HITS-CLIP dataset we also found that circularizing exons overlapped with an unexpectedly higher number of Ago binding sites than non-circularizing exons. Finally, we observed that a subset of MCF-7 circRNAs are specific to tumor versus normal tissue, while others can distinguish Luminal from other tumor subtypes, thus suggesting that circRNAs can be exploited as novel biomarkers and drug targets for breast cancer.
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Affiliation(s)
- Lucia Coscujuela Tarrero
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Carlo De Intinis
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Laura Ricci
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federica Riccardo
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Raffaele A Calogero
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Marco Beccuti
- Department of Computer Science, University of Turin, Turin, Italy
| | - Francesca Cordero
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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34
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Miano V, Ferrero G, Rosti V, Manitta E, Elhasnaoui J, Basile G, De Bortoli M. Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells. Int J Mol Sci 2018; 19:E593. [PMID: 29462945 PMCID: PMC5855815 DOI: 10.3390/ijms19020593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022] Open
Abstract
Estrogen receptor-α (ERα) is a ligand-inducible protein which mediates estrogenic hormones signaling and defines the luminal BC phenotype. Recently, we demonstrated that even in absence of ligands ERα (apoERα) binds chromatin sites where it regulates transcription of several protein-coding and lncRNA genes. Noteworthy, apoERα-regulated lncRNAs marginally overlap estrogen-induced transcripts, thus representing a new signature of luminal BC genes. By the analysis of H3K27ac enrichment in hormone-deprived MCF-7 cells, we defined a set of Super Enhancers (SEs) occupied by apoERα, including one mapped in proximity of the DSCAM-AS1 lncRNA gene. This represents a paradigm of apoERα activity since its expression is largely unaffected by estrogenic treatment, despite the fact that E2 increases ERα binding on DSCAM-AS1 promoter. We validated the enrichment of apoERα, p300, GATA3, FoxM1 and CTCF at both DSCAM-AS1 TSS and at its associated SE by ChIP-qPCR. Furthermore, by analyzing MCF-7 ChIA-PET data and by 3C assays, we confirmed long range chromatin interaction between the SE and the DSCAM-AS1 TSS. Interestingly, CTCF and p300 binding showed an enrichment in hormone-depleted medium and in the presence of ERα, elucidating the dynamics of the estrogen-independent regulation of DSCAM-AS1 expression. The analysis of this lncRNA provides a paradigm of transcriptional regulation of a luminal specific apoERα regulated lncRNA.
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Affiliation(s)
- Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy.
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy.
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
- Department of Computer Science, University of Turin, 10149 Turin, Italy.
| | - Valentina Rosti
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
| | - Eleonora Manitta
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
| | - Jamal Elhasnaoui
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy.
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
| | - Giulia Basile
- Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy.
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy.
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy.
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35
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Ma Z, Xin Z, Hu W, Jiang S, Yang Z, Yan X, Li X, Yang Y, Chen F. Forkhead box O proteins: Crucial regulators of cancer EMT. Semin Cancer Biol 2018; 50:21-31. [PMID: 29427645 DOI: 10.1016/j.semcancer.2018.02.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 12/02/2017] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is an acknowledged cellular transition process in which epithelial cells acquire mesenchymal-like properties that endow cancer cells with increased migratory and invasive behavior. Forkhead box O (FOXO) proteins have been shown to orchestrate multiple EMT-associated pathways and EMT-related transcription factors (EMT-TFs), thereby modulating the EMT process. The focus of the current review is to evaluate the latest research progress regarding the roles of FOXO proteins in cancer EMT. First, a brief overview of the EMT process in cancer and a general background on the FOXO family are provided. Next, we present the interactions between FOXO proteins and multiple EMT-associated pathways during malignancy development. Finally, we propose several novel potential directions for future research. Collectively, the information compiled herein should serve as a comprehensive repository of information on this topic and should aid in the design of additional studies and the future development of FOXO proteins as therapeutic targets.
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Affiliation(s)
- Zhiqiang Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an 710069 China; Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, 1 Xinsi Road, Xi'an 710038, China
| | - Zhenlong Xin
- Department of Occupational and Environmental Health and The Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China
| | - Wei Hu
- Department of Immunology, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China
| | - Shuai Jiang
- Department of Aerospace Medicine, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China
| | - Zhi Yang
- Department of Biomedical Engineering, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, 1 Xinsi Road, Xi'an 710038, China
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, 1 Xinsi Road, Xi'an 710038, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an 710069 China; Department of Biomedical Engineering, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China.
| | - Fulin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, 229 Taibai North Road, Xi'an 710069 China.
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36
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Tracy KM, Tye CE, Ghule PN, Malaby HLH, Stumpff J, Stein JL, Stein GS, Lian JB. Mitotically-Associated lncRNA (MANCR) Affects Genomic Stability and Cell Division in Aggressive Breast Cancer. Mol Cancer Res 2018; 16:587-598. [PMID: 29378907 DOI: 10.1158/1541-7786.mcr-17-0548] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/05/2017] [Accepted: 01/08/2018] [Indexed: 12/31/2022]
Abstract
Aggressive breast cancer is difficult to treat as it is unresponsive to many hormone-based therapies; therefore, it is imperative to identify novel, targetable regulators of progression. Long non-coding RNAs (lncRNA) are important regulators in breast cancer and have great potential as therapeutic targets; however, little is known about how the majority of lncRNAs function within breast cancer. This study characterizes a novel lncRNA, MANCR (mitotically-associated long noncoding RNA; LINC00704), which is upregulated in breast cancer patient specimens and cells. Depletion of MANCR in triple-negative breast cancer cells significantly decreases cell proliferation and viability, with concomitant increases in DNA damage. Transcriptome analysis, based on RNA sequencing, following MANCR knockdown reveals significant differences in the expression of >2,000 transcripts, and gene set enrichment analysis identifies changes in multiple categories related to cell-cycle regulation. Furthermore, MANCR expression is highest in mitotic cells by both RT-qPCR and RNA in situ hybridization. Consistent with a role in cell-cycle regulation, MANCR-depleted cells have a lower mitotic index and higher incidences of defective cytokinesis and cell death. Taken together, these data reveal a role for the novel lncRNA, MANCR, in genomic stability of aggressive breast cancer, and identify it as a potential therapeutic target.Implications: The novel lncRNA, MANCR (LINC00704), is upregulated in breast cancer and is functionally linked with cell proliferation, viability, and genomic stability. Mol Cancer Res; 16(4); 587-98. ©2018 AACR.
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Affiliation(s)
- Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Heidi L H Malaby
- Department of Molecular Physiology and Biophysics and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont.
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37
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Latgé G, Poulet C, Bours V, Josse C, Jerusalem G. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers. Int J Mol Sci 2018; 19:ijms19010123. [PMID: 29301303 PMCID: PMC5796072 DOI: 10.3390/ijms19010123] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.
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Affiliation(s)
- Guillaume Latgé
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Christophe Poulet
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Center of Genetics, University Hospital (CHU), 4500 Liège, Belgium.
| | - Claire Josse
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Guy Jerusalem
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
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Long non-coding RNA00544 serves as a potential novel predictive and prognostic marker for HR+ HER2- subtype breast cancer. Sci Rep 2017; 7:12382. [PMID: 28959047 PMCID: PMC5620366 DOI: 10.1038/s41598-017-11066-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022] Open
Abstract
Luminal breast cancers (BC) account for majority of breast cancer. Due to its heterogeneity and the development of treatment resistance, luminal BC patients can vary substantially. Long noncoding RNAs (lncRNAs), as we known, is involved in breast cancer progression. Here, we aim to identify the lncRNAs which are involved in the particular type luminal BC progression. By Gene Chips analysis, we found a novel lncRNA00544, which was highly expressed in the metastatic axillary nodes compared with corresponding luminal BC tissues (fold change = 2.26, P = 0.043). This result was confirmed in luminal BC cell lines (p = 0.0113) and 49 paired breast cancer samples compared with in corresponding controls (p = 0.011). Furthermore, Kaplan-Meier survival curves of 373 breast cancer patients indicated that disease-free survival was significantly poor in breast cancer patients with high lncRNA00544 expression (p < 0.001). Univariate and multivariate Cox regression analyses showed that lncRNA00544 was a significant independent prognostic biomarker in luminal BC patients. Further analysis showed that the prognosis of high lncRNA00544 expression in breast cancer patients was actually related to HR + HER2- subtype. Together, our studies indicate that lncRNA00544 may represent a novel predictive and prognostic indicator in luminal BC patients.
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Zhang Y, Wang DL, Yan HY, Liao JY, He JH, Hu KS, Deng WX, Wang YJ, Xing HT, Koeffler HP, Yin D. Genome-wide study of ER-regulated lncRNAs shows AP000439.3 may function as a key regulator of cell cycle in breast cancer. Oncol Rep 2017; 38:3227-3237. [PMID: 29048636 DOI: 10.3892/or.2017.5975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/12/2017] [Indexed: 11/06/2022] Open
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40
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Zhao T, Wu L, Li X, Dai H, Zhang Z. Large intergenic non-coding RNA-ROR as a potential biomarker for the diagnosis and dynamic monitoring of breast cancer. Cancer Biomark 2017; 20:165-173. [PMID: 28869448 DOI: 10.3233/cbm-170064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tianhe Zhao
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Lichun Wu
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
- Division of Clinical Laboratory, Sichuan Cancer Hospital, Chengdu, Sichuan, China
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xinyang Li
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Huangmei Dai
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
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Ferrero G, Miano V, Beccuti M, Balbo G, De Bortoli M, Cordero F. Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Sci Rep 2017; 7:8564. [PMID: 28819152 PMCID: PMC5561104 DOI: 10.1038/s41598-017-08754-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells. We went through the definition of reference cistromes for different experimental contexts, the integration of data relative to co-regulators and the overlay of chromatin states as defined by epigenetic marks in MCF-7 cells. With our strategy, we identified novel features of estrogen-independent ERα activity, including FoxM1 interaction, eRNAs transcription and a peculiar ontology of connected genes.
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Affiliation(s)
- Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, 10043, Orbassano, Turin, Italy.,Dept. of Computer Science, University of Turin, 10149, Turin, Italy.,Dept. of Biological and Clinical Sciences, University of Turin, 10043, Orbassano, Turin, Italy
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, 10043, Orbassano, Turin, Italy.,Dept. of Biological and Clinical Sciences, University of Turin, 10043, Orbassano, Turin, Italy
| | - Marco Beccuti
- Dept. of Computer Science, University of Turin, 10149, Turin, Italy
| | - Gianfranco Balbo
- Center for Molecular Systems Biology, University of Turin, 10043, Orbassano, Turin, Italy.,Dept. of Computer Science, University of Turin, 10149, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, 10043, Orbassano, Turin, Italy. .,Dept. of Biological and Clinical Sciences, University of Turin, 10043, Orbassano, Turin, Italy.
| | - Francesca Cordero
- Center for Molecular Systems Biology, University of Turin, 10043, Orbassano, Turin, Italy.,Dept. of Computer Science, University of Turin, 10149, Turin, Italy
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Tracy KM, Tye CE, Page NA, Fritz AJ, Stein JL, Lian JB, Stein GS. Selective expression of long non-coding RNAs in a breast cancer cell progression model. J Cell Physiol 2017; 233:1291-1299. [PMID: 28488769 DOI: 10.1002/jcp.25997] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are acknowledged as regulators of cancer biology and pathology. Our goal was to perform a stringent profiling of breast cancer cell lines that represent disease progression. We used the MCF-10 series, which includes the normal-like MCF-10A, HRAS-transformed MCF-10AT1 (pre-malignant), and MCF-10CA1a (malignant) cells, to perform transcriptome wide sequencing. From these data, we have identified 346 lncRNAs with dysregulated expression across the progression series. By comparing lncRNAs from these datasets to those from an additional set of cell lines that represent different disease stages and subtypes, MCF-7 (early stage, luminal), and MDA-MB-231 (late stage, basal), 61 lncRNAs that are associated with breast cancer progression were identified. Querying breast cancer patient data from The Cancer Genome Atlas, we selected a lncRNA, IGF-like family member 2 antisense RNA 1 (IGFL2-AS1), of potential clinical relevance for functional characterization. Among the 61 lncRNAs, IGFL2-AS1 was the most significantly decreased. Our results indicate that this lncRNA plays a role in downregulating its nearest neighbor, IGFL1, and affects migration of breast cancer cells. Furthermore, the lncRNAs we identified provide a valuable resource to mechanistically and clinically understand the contribution of lncRNAs in breast cancer progression.
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Affiliation(s)
- Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Natalie A Page
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
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43
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Chung IH, Lu PH, Lin YH, Tsai MM, Lin YW, Yeh CT, Lin KH. The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma. Sci Rep 2017; 7:295. [PMID: 28331184 PMCID: PMC5428265 DOI: 10.1038/s41598-017-00382-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 02/22/2017] [Indexed: 12/28/2022] Open
Abstract
Anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma (NHL). Currently, only studies on the chimeric oncogene NPM-ALK have reported a link to ALCL progression. However, the specific molecular mechanisms underlying the invasion of ALCL are still unclear. Here, we sought to investigate differentially expressed, long non-coding RNAs (lncRNAs) in ALCL and their potential biological function. Our microarray analyses revealed that LINC01013, a novel non-coding RNA gene, was highly expressed in clinical specimens of ALCL and was significantly upregulated in invasive ALCL cell lines. Knockdown of LINC01013 suppressed tumor cell invasion; conversely, its overexpression enhanced tumor cell invasion. LINC01013-induced invasion was mediated by activation of the epithelial-to-mesenchymal transition (EMT)-associated proteins, snail and fibronectin. Specifically, LINC01013 induced snail, resulting in activation of fibronectin and enhanced ALCL cell invasion. Collectively, these findings support a potential role for LINC01013 in cancer cell invasion through the snail-fibronectin activation cascade and suggest that LINC01013 could potentially be utilized as a metastasis marker in ALCL.
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Affiliation(s)
- I-Hsiao Chung
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Pei-Hsuan Lu
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.).,Department of Dermatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.)
| | - Yang-Hsiang Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Ming-Ming Tsai
- Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.).,Department of General Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan (R.O.C.)
| | - Yun-Wen Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.)
| | - Kwang-Huei Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.). .,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.). .,Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.).
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44
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Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. CURRENT PATHOBIOLOGY REPORTS 2017; 5:23-34. [PMID: 28616363 DOI: 10.1007/s40139-017-0122-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The goal of this review was to compare and contrast the results and implications from several recent transcriptomic studies that analyzed the expression of lncRNAs in breast cancer. How many lncRNAs are dysregulated in breast cancer? Do dysregulated lncRNAs contribute to breast cancer etiology? Are lncRNAs viable biomarkers in breast cancer? RECENT FINDINGS Transcriptomic profiling of breast cancer tissues, mostly from The Cancer Genome Atlas, identified thousands of long noncoding RNAs that are expressed and dysregulated in breast cancer. The expression of lncRNAs alone can divide patients into molecular subtypes. Subsequent functional studies demonstrated that several of these lncRNAs have important roles in breast cancer cell biology. SUMMARY Thousands of lncRNAs are dysregulated in breast cancer that can be developed as biomarkers for prognostic or therapeutic purposes. The reviewed reports provide a roadmap to guide functional studies to discover lncRNAs with critical biological functions relating to breast cancer development and progression.
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45
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The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat Commun 2016; 7:12791. [PMID: 27666543 PMCID: PMC5052669 DOI: 10.1038/ncomms12791] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022] Open
Abstract
Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples. We show that lncRNA-based profiling categorizes breast tumours by their known molecular subtypes in breast cancer. We identify a cohort of breast cancer-associated and oestrogen-regulated lncRNAs, and investigate the role of the top prioritized oestrogen receptor (ER)-regulated lncRNA, DSCAM-AS1. We demonstrate that DSCAM-AS1 mediates tumour progression and tamoxifen resistance and identify hnRNPL as an interacting protein involved in the mechanism of DSCAM-AS1 action. By highlighting the role of DSCAM-AS1 in breast cancer biology and treatment resistance, this study provides insight into the potential clinical implications of lncRNAs in breast cancer. LncRNAs have been associated with cancer. Here, the authors carry out a systematic review of lncRNAs in breast cancer and show that DSCAM-AS1 is highly expressed in oestrogen receptor positive tumours and enhances cancer through an interaction with hnRNPL; and is also associated with tamoxifen resistance.
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46
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Cerk S, Schwarzenbacher D, Adiprasito JB, Stotz M, Hutterer GC, Gerger A, Ling H, Calin GA, Pichler M. Current Status of Long Non-Coding RNAs in Human Breast Cancer. Int J Mol Sci 2016; 17:ijms17091485. [PMID: 27608009 PMCID: PMC5037763 DOI: 10.3390/ijms17091485] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 02/07/2023] Open
Abstract
Breast cancer represents a major health burden in Europe and North America, as recently published data report breast cancer as the second leading cause of cancer related death in women worldwide. Breast cancer is regarded as a highly heterogeneous disease in terms of clinical course and biological behavior and can be divided into several molecular subtypes, with different prognosis and treatment responses. The discovery of numerous non-coding RNAs has dramatically changed our understanding of cell biology, especially the pathophysiology of cancer. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts >200 nucleotides in length. Several studies have demonstrated their role as key regulators of gene expression, cell biology and carcinogenesis. Deregulated expression levels of lncRNAs have been observed in various types of cancers including breast cancer. lncRNAs are involved in cancer initiation, progression, and metastases. In this review, we summarize the recent literature to highlight the current status of this class of long non-coding lncRNAs in breast cancer.
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Affiliation(s)
- Stefanie Cerk
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
- Research Unit of Non-coding RNA and Genome Editing in Cancer, Medical University of Graz, Graz 8036, Austria.
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
- Research Unit of Non-coding RNA and Genome Editing in Cancer, Medical University of Graz, Graz 8036, Austria.
| | - Jan Basri Adiprasito
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
- Research Unit of Non-coding RNA and Genome Editing in Cancer, Medical University of Graz, Graz 8036, Austria.
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
- Research Unit of Non-coding RNA and Genome Editing in Cancer, Medical University of Graz, Graz 8036, Austria.
| | - Georg C Hutterer
- Department of Urology, Medical University of Graz, Graz 8036, Austria.
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz 8026, Austria.
- Research Unit of Non-coding RNA and Genome Editing in Cancer, Medical University of Graz, Graz 8036, Austria.
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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Van Grembergen O, Bizet M, de Bony EJ, Calonne E, Putmans P, Brohée S, Olsen C, Guo M, Bontempi G, Sotiriou C, Defrance M, Fuks F. Portraying breast cancers with long noncoding RNAs. SCIENCE ADVANCES 2016; 2:e1600220. [PMID: 27617288 PMCID: PMC5010371 DOI: 10.1126/sciadv.1600220] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 08/05/2016] [Indexed: 05/24/2023]
Abstract
Evidence is emerging that long noncoding RNAs (lncRNAs) may play a role in cancer development, but this role is not yet clear. We performed a genome-wide transcriptional survey to explore the lncRNA landscape across 995 breast tissue samples. We identified 215 lncRNAs whose genes are aberrantly expressed in breast tumors, as compared to normal samples. Unsupervised hierarchical clustering of breast tumors on the basis of their lncRNAs revealed four breast cancer subgroups that correlate tightly with PAM50-defined mRNA-based subtypes. Using multivariate analysis, we identified no less than 210 lncRNAs prognostic of clinical outcome. By analyzing the coexpression of lncRNA genes and protein-coding genes, we inferred potential functions of the 215 dysregulated lncRNAs. We then associated subtype-specific lncRNAs with key molecular processes involved in cancer. A correlation was observed, on the one hand, between luminal A-specific lncRNAs and the activation of phosphatidylinositol 3-kinase, fibroblast growth factor, and transforming growth factor-β pathways and, on the other hand, between basal-like-specific lncRNAs and the activation of epidermal growth factor receptor (EGFR)-dependent pathways and of the epithelial-to-mesenchymal transition. Finally, we showed that a specific lncRNA, which we called CYTOR, plays a role in breast cancer. We confirmed its predicted functions, showing that it regulates genes involved in the EGFR/mammalian target of rapamycin pathway and is required for cell proliferation, cell migration, and cytoskeleton organization. Overall, our work provides the most comprehensive analyses for lncRNA in breast cancers. Our findings suggest a wide range of biological functions associated with lncRNAs in breast cancer and provide a foundation for functional investigations that could lead to new therapeutic approaches.
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Affiliation(s)
- Olivier Van Grembergen
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Machine Learning Group, Computer Science Department, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics Brussels, Université Libre de Bruxelles–Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Eric J. de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Sylvain Brohée
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Catharina Olsen
- Machine Learning Group, Computer Science Department, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Gianluca Bontempi
- Machine Learning Group, Computer Science Department, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics Brussels, Université Libre de Bruxelles–Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics Brussels, Université Libre de Bruxelles–Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB–Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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Mao X, Qiao Z, Fan C, Guo A, Yu X, Jin F. Expression pattern and methylation of estrogen receptor α in breast intraductal proliferative lesions. Oncol Rep 2016; 36:1868-74. [PMID: 27498697 PMCID: PMC5022874 DOI: 10.3892/or.2016.4988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/13/2016] [Indexed: 01/12/2023] Open
Abstract
Intraductal proliferative lesions of the breast including usual ductal hyperplasia (UDH), atypical ductal hyperplasia (ADH) and ductal carcinoma in situ (DCIS) are associated with increased risk, albeit of greatly different magnitudes, for the subsequent development of invasive carcinoma. Estrogen receptor α (ERα) has been widely accepted as a prognostic marker and a predictor for endocrine therapy response of breast cancer. To investigate the ERα expression and methylation in breast intraductal proliferative lesions, we analyzed ERα expression in breast intraductal proliferative lesions including pure UDH (N=98), ADH without DCIS (N=160), DCIS without invasive breast cancer (N=149) by immunohistochemistry. Furthermore, the methylation status of ERα by methylation-specific PCR (MSP) was defined in 217 cases of breast intraductal proliferative lesions. Immunohistochemistry showed that 98/98 (100%) of the UDH cases were positive for ERα expression. ERα protein expression in ADH (132/160) (92.5%) was higher than in DCIS (101/149) (67.8%). But the ERα expression pattern was different with histological diversity of breast intraductal proliferative lesions. The average percent cells staining positive for ERα was 35.33% in UDH, 87.75% in ADH and 71.45% in DCIS. ERα methylation in 32/60 (53.3%) UDH, 11/77 (10.2%) ADH and 32/80 (40.0%) DCIS. Our results demonstrated a strong negative correlation between the percent of cells staining positive for ERα and ERα methylation (r=−0.831, p<0.001). Taken together, our results underlined that ERα expression or methylation may be involved in the breast carcinogenesis and advancement, thus it is not parallel to breast cancer risk in breast intraductal proliferative lesions. No obvious watershed between ERα-positive and -negative breast carcinogenesis was established. Estrogen receptor (ER) methylation or expression is a reversible signal in breast carcinogenesis which affected biological behavior of cells.
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Affiliation(s)
- Xiaoyun Mao
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Zhen Qiao
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Chuifeng Fan
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ayao Guo
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Xinmiao Yu
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Feng Jin
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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