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Stoneman HR, Price A, Trout NS, Lamont R, Tifour S, Pozdeyev N, Crooks K, Lin M, Rafaels N, Gignoux CR, Marker KM, Hendricks AE. Characterizing substructure via mixture modeling in large-scale genetic summary statistics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577805. [PMID: 38766180 PMCID: PMC11100604 DOI: 10.1101/2024.01.29.577805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic summary data are broadly accessible and highly useful including for risk prediction, causal inference, fine mapping, and incorporation of external controls. However, collapsing individual-level data into groups masks intra- and inter-sample heterogeneity, leading to confounding, reduced power, and bias. Ultimately, unaccounted substructure limits summary data usability, especially for understudied or admixed populations. Here, we present Summix2, a comprehensive set of methods and software based on a computationally efficient mixture model to estimate and adjust for substructure in genetic summary data. In extensive simulations and application to public data, Summix2 characterizes finer-scale population structure, identifies ascertainment bias, and identifies potential regions of selection due to local substructure deviation. Summix2 increases the robust use of diverse publicly available summary data resulting in improved and more equitable research.
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Affiliation(s)
- Hayley R Stoneman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Adelle Price
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikole Scribner Trout
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Riley Lamont
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Souha Tifour
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikita Pozdeyev
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Meng Lin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher R Gignoux
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katie M Marker
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Audrey E Hendricks
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
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2
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Sanchez-Lopez JM, Juarez-Mancera MA, Bustamante B, Ruiz-Silvestre A, Espinosa M, Mendoza-Almanza G, Ceballos-Cancino G, Melendez-Zajgla J, Maldonado V, Lizarraga F. Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses. RNA Biol 2024; 21:1-11. [PMID: 38832821 PMCID: PMC11152094 DOI: 10.1080/15476286.2024.2355393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
LncRNA is a group of transcripts with a length exceeding 200 nucleotides that contribute to tumour development. Our research group found that LINC00052 expression was repressed during the formation of breast cancer (BC) multicellular spheroids. Intriguingly, LINC00052 precise role in BC remains uncertain. We explored LINC00052 expression in BC patients` RNA samples (TCGA) in silico, as well as in an in-house patient cohort, and inferred its cellular and molecular mechanisms. In vitro studies evaluated LINC00052 relevance in BC cells viability, cell cycle and DNA damage. Results. Bioinformatic RNAseq analysis of BC patients showed that LINC00052 is overexpressed in samples from all BC molecular subtypes. A similar LINC00052 expression pattern was observed in an in-house patient cohort. In addition, higher LINC00052 levels are related to better BC patient´s overall survival. Remarkably, MCF-7 and ZR-75-1 cells treated with estradiol showed increased LINC00052 expression compared to control, while these changes were not observed in MDA-MB-231 cells. In parallel, bioinformatic analyses indicated that LINC00052 influences DNA damage and cell cycle. MCF-7 cells with low LINC00052 levels exhibited increased cellular protection against DNA damage and diminished growth capacity. Furthermore, in cisplatin-resistant MCF-7 cells, LINC00052 expression was downregulated. Conclusion. This work shows that LINC00052 expression is associated with better BC patient survival. Remarkably, LINC00052 expression can be regulated by Estradiol. Additionally, assays suggest that LINC00052 could modulate MCF-7 cells growth and DNA damage repair. Overall, this study highlights the need for further research to unravel LINC00052 molecular mechanisms and potential clinical applications in BC.
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Affiliation(s)
- Jose Manuel Sanchez-Lopez
- Laboratorio de Epigenetica, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | | | - Benjamin Bustamante
- Laboratorio de Genomica Funcional del Cancer, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Araceli Ruiz-Silvestre
- Laboratorio de Epigenetica, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Magali Espinosa
- Laboratorio de Genomica Funcional del Cancer, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Gretel Mendoza-Almanza
- Laboratorio de Epigenetica, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Gisela Ceballos-Cancino
- Laboratorio de Genomica Funcional del Cancer, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Jorge Melendez-Zajgla
- Laboratorio de Genomica Funcional del Cancer, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Vilma Maldonado
- Laboratorio de Epigenetica, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
| | - Floria Lizarraga
- Laboratorio de Epigenetica, Instituto Nacional de Medicina Genomica (INMEGEN), Ciudad de México, Mexico
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3
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Patel K, Rao DM, Sundersingh S, Velusami S, Rajkumar T, Nair B, Pandey A, Chatterjee A, Mani S, Gowda H. MicroRNA Expression Profile in Early-Stage Breast Cancers. Microrna 2024; 13:71-81. [PMID: 37873952 DOI: 10.2174/0122115366256479231003064842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Breast cancer is one of the leading causes of cancer deaths in women. Early diagnosis offers the best hope for a cure. Ductal carcinoma in situ is considered a precursor of invasive ductal carcinoma of the breast. In this study, we carried out microRNA sequencing from 7 ductal carcinoma in situ (DCIS), 6 infiltrating ductal carcinomas (IDC Stage IIA) with paired normal, and 5 unpaired normal breast tissue samples. METHODS We have deployed miRge for microRNA analysis, DESeq for differential expression analysis, and Cytoscape for competing endogenous RNA network investigation. RESULTS Here, we identified 76 miRNAs that were differentially expressed in DCIS and IDC. Additionally, we provide preliminary evidence of miR-365b-3p and miR-7-1-3p being overexpressed, and miR-6507-5p, miR-487b-3p, and miR-654-3p being downregulated in DCIS relative to normal breast tissue. We also identified a miRNA miR-766-3p that was overexpressed in earlystage IDCs. The overexpression of miR-301a-3p in DCIS and IDC was confirmed in 32 independent breast cancer tissue samples. CONCLUSION Higher expression of miR-301a-3p is associated with poor overall survival in The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) dataset, indicating that it may be associated with DCIS at high risk of progressing to IDC and warrants deeper investigation.
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MESH Headings
- Humans
- Female
- MicroRNAs/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/mortality
- Gene Expression Regulation, Neoplastic/genetics
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Middle Aged
- Neoplasm Staging
- Gene Expression Profiling
- Biomarkers, Tumor/genetics
- Transcriptome/genetics
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Affiliation(s)
- Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
| | - Deva Magendhra Rao
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai 600036, India
| | | | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066 India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai 600036, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
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4
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Najafi S, Khatami SH, Khorsand M, Jamali Z, Shabaninejad Z, Moazamfard M, Majidpoor J, Aghaei Zarch SM, Movahedpour A. Long non-coding RNAs (lncRNAs); roles in tumorigenesis and potentials as biomarkers in cancer diagnosis. Exp Cell Res 2022; 418:113294. [PMID: 35870535 DOI: 10.1016/j.yexcr.2022.113294] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 12/15/2022]
Abstract
New research has indicated that long non-coding RNAs (lncRNAs) play critical roles in a broad range of biological processes, including the pathogenesis of many complex human diseases, including cancer. The detailed regulation mechanisms of many lncRNAs in cancer initiation and progression have yet to be discovered, even though a few of lncRNAs' functions in cancer have been characterized. In the present study, we summarize recent advances in the mechanisms and functions of lncRNAs in cancer. We focused on the roles of newly-identified lncRNAs as oncogenes and tumor suppressors, as well as the potential pathways these molecules could play. The paper also discusses their potential uses as biomarkers for the diagnosis and prognosis of cancer.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Khorsand
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Jamali
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Seyed Mohsen Aghaei Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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5
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Hu X, Zhang Q, Xing W, Wang W. Role of microRNA/lncRNA Intertwined With the Wnt/β-Catenin Axis in Regulating the Pathogenesis of Triple-Negative Breast Cancer. Front Pharmacol 2022; 13:814971. [PMID: 35814205 PMCID: PMC9263262 DOI: 10.3389/fphar.2022.814971] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 05/17/2022] [Indexed: 12/12/2022] Open
Abstract
Objective (s): In this mini-review, we aimed to discuss the Wnt/β-catenin signaling pathway modulation in triple-negative breast cancer, particularly the contribution of lncRNAs and miRNAs in its regulation and their possible entwining role in breast cancer pathogenesis, proliferation, migration, or malignancy.Background: Malignant tumor formation is very high for breast cancer in women and is a leading cause of death all over the globe. Among breast cancer subtypes, triple-negative breast cancer is rife in premenopausal women, most invasive, and prone to metastasis. Complex pathways are involved in this cancer’s pathogenesis, advancement, and malignancy, including the Wnt/β-catenin signaling pathway. This pathway is conserved among vertebrates and is necessary for sustaining cell homeostasis. It is regulated by several elements such as transcription factors, enhancers, non-coding RNAs (lncRNAs and miRNAs), etc.Methods: We evaluated lncRNAs and miRNAs differentially expressed in triple-negative breast cancer (TNBC) from the cDNA microarray data set literature survey. Using in silico analyses combined with a review of the current literature, we anticipated identifying lncRNAs and miRNAs that might modulate the Wnt/β-catenin signaling pathway.Result: The miRNAs and lncRNAs specific to triple-negative breast cancer have been identified based on literature and database searches. Tumorigenesis, metastasis, and EMT were all given special attention. Apart from cross-talk being essential for TNBC tumorigenesis and treatment outcomes, our results indicated eight upregulated and seven downregulated miRNAs and 19 upregulated and three downregulated lncRNAs that can be used as predictive or diagnostic markers. This consolidated information could be useful in the clinic and provide a combined literature resource for TNBC researchers working on the Wnt/β-catenin miRNA/lncRNA axis.Conclusion: In conclusion, because the Wnt pathway and miRNAs/lncRNAs can modulate TNBC, their intertwinement results in a cascade of complex reactions that affect TNBC and related processes. Their function in TNBC pathogenesis has been highlighted in molecular processes underlying the disease progression.
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Affiliation(s)
- Xue Hu
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Wanying Xing
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wan Wang
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Wan Wang,
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6
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Wang G, Dong Y, Liu H, Ji N, Cao J, Liu A, Tang X, Ren Y. Long noncoding RNA (lncRNA) metallothionein 1 J, pseudogene (MT1JP) is downregulated in triple-negative breast cancer and upregulates microRNA-138 (miR-138) to downregulate hypoxia-inducible factor-1α (HIF-1α). Bioengineered 2022; 13:13718-13727. [PMID: 35703312 PMCID: PMC9276039 DOI: 10.1080/21655979.2022.2077906] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly invasive subtype of breast cancer. This study explored the molecular mechanism and influences of metallothionein 1 J, pseudogene (MT1JP), microRNA-138 (miR-138), and hypoxia-inducible factor-1α (HIF-1α) on TNBC cell proliferation and migration. We confirmed TNBC cases by immunohistochemistry (IHC) staining. The expression of MT1JP in two types of tissue collected from 78 TNBC patients was detected by performing real-time quantitative fluorescence PCR (RT-qPCR). To further evaluate the relationship among MT1JP, miR-138 and HIF-1α, expression vectors of MT1JP and HIF-1α, as well as miR-138 mimic and inhibitor, were delivered into BT-549 cells. We observed that MT1JP was downregulated in TNBC. MT1JP was positively correlated with miR-138 but negatively correlated with HIF-1α in TNBC tissues. In TNBC cells, upregulation of miR-138 and downregulation of HIF-1α were observed after overexpression of MT1JP. In addition, overexpression of miR-138 resulted in downregulation of HIF-1α but did not affect the expression of MT1JP. Decreased proliferation rate of TNBC cells was observed after overexpression of MT1JP and miR-138. HIF-1α increased cell proliferation and migration. HIF-1α also suppressed the role of MT1JP and miR-138 in TNBC cell proliferation and migration. In conclusion, our findings demonstrated that MT1JP inhibited TNBC by regulating the miR-138/HIF-1α axis, indicating that MT1JP might serve as a biomarker or target for TNBC treatment.
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Affiliation(s)
- Gangyue Wang
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yi Dong
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Heng Liu
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Nang Ji
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Jilei Cao
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Aihui Liu
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xin Tang
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yu Ren
- Department of Breast, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
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7
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Selem NA, Youness RA, Gad MZ. What is beyond LncRNAs in breast cancer: A special focus on colon cancer-associated Transcript-1 (CCAT-1). Noncoding RNA Res 2021; 6:174-186. [PMID: 34938928 PMCID: PMC8666458 DOI: 10.1016/j.ncrna.2021.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) play a vital role in the process of malignant transformation. In breast cancer (BC), lncRNAs field is currently under intensive investigations. Yet, the role of lncRNAs as promising diagnostic and/or prognostic biomarkers and as therapeutic target/tool among BC patients still needs a special focus from the biomedical scientists. In BC, triple negative breast cancer patients (TNBC) are the unlucky group as they are always represented with the worst prognosis and the highest mortality rates. For that reason, a special focus on TNBC and associated lncRNAs was addressed in this review. Colon cancer-associated transcript 1 (CCAT-1) is a newly discovered oncogenic lncRNA that has been emerged as a vital biomarker for diagnosis, prognosis and therapeutic interventions in multiple malignancies and showed differential expression among TNBC patients. In this review, the authors shed the light onto the general role of lncRNAs in BC and the specific functional activities, molecular mechanisms, competing endogenous ncRNA role of CCAT-1 in TNBC.
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Affiliation(s)
- Noha A. Selem
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Rana A. Youness
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, New Administrative Capital, 11586, Cairo, Egypt
| | - Mohamed Z. Gad
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
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8
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Pinkney HR, Black MA, Diermeier SD. Single-Cell RNA-Seq Reveals Heterogeneous lncRNA Expression in Xenografted Triple-Negative Breast Cancer Cells. BIOLOGY 2021; 10:987. [PMID: 34681087 PMCID: PMC8533545 DOI: 10.3390/biology10100987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/03/2022]
Abstract
Breast cancer is the most commonly diagnosed cancer in the world, with triple-negative breast cancer (TNBC) making up 12% of these diagnoses. TNBC tumours are highly heterogeneous in both inter-tumour and intra-tumour gene expression profiles, where they form subclonal populations of varying levels of aggressiveness. These aspects make it difficult to study and treat TNBC, requiring further research into tumour heterogeneity as well as potential therapeutic targets and biomarkers. Recently, it was discovered that the majority of the transcribed genome comprises non-coding RNAs, in particular long non-coding RNAs (lncRNAs). LncRNAs are transcripts of >200 nucleotides in length that do not encode a protein. They have been characterised as regulatory molecules and their expression can be associated with a malignant phenotype. We set out to explore TNBC tumour heterogeneity in vivo at a single cell level to investigate whether lncRNA expression varies across different cells within the tumour, even if cells are coming from the same cell line, and whether lncRNA expression is sufficient to define cellular subpopulations. We applied single-cell expression profiling due to its ability to capture expression signals of lncRNAs expressed in small subpopulations of cells. Overall, we observed most lncRNAs to be expressed at low, but detectable levels in TNBC xenografts, with a median of 25 lncRNAs detected per cell. LncRNA expression alone was insufficient to define a subpopulation of cells, and lncRNAs showed highly heterogeneous expression patterns, including ubiquitous expression, subpopulation-specific expression, and a hybrid pattern of lncRNAs expressed in several, but not all subpopulations. These findings reinforce that transcriptionally defined tumour cell subpopulations can be identified in cell-line derived xenografts, and uses single-cell RNA-seq (scRNA-seq) to detect and characterise lncRNA expression across these subpopulations in xenografted tumours. Future studies will aim to investigate the spatial distribution of lncRNAs within xenografts and patient tissues, and study the potential of subclone-specific lncRNAs as new therapeutic targets and/or biomarkers.
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Affiliation(s)
- Holly R. Pinkney
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand; (H.R.P.); (M.A.B.)
| | - Michael A. Black
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand; (H.R.P.); (M.A.B.)
| | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand; (H.R.P.); (M.A.B.)
- Amaroq Therapeutics Ltd., Dunedin 9016, New Zealand
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9
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Masoud Eslami M, Soufizomorrod M, Ahmadvand M. High expression of long noncoding RNA NORAD is associated with poor clinical outcomes in non-M3 acute myeloid leukemia patients. Hematol Oncol Stem Cell Ther 2021:S1658-3876(21)00065-0. [PMID: 34419481 DOI: 10.1016/j.hemonc.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/18/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE/BACKGROUND Dysregulation of long noncoding RNA NORAD has been identified in human solid tumors. However, the expression profile of NORAD and its clinical implications in acute myeloid leukemia (AML) is unclear. The current study aimed to explore the NORAD expression status and its clinical significance in non-M3 AML patients. METHODS NORAD expression was evaluated in 60 de novo non-M3 AML patients and 49 healthy individuals using quantitative reverse transcription-polymerase chain reaction method. The correlation between NORAD transcription levels and clinicopathologic characteristics was statistically studied. RESULTS Compared with the healthy controls, NORAD was consistently higher in non-M3 AML patients (p = .01). Furthermore, initial NORAD upregulation occurred more frequently in patients with unfavorable cytogenetic risk (p = .02). The non-M3 AML patients were divided into NORAD high-expressing (NORADhigh) and NORAD low-expressing (NORADlow) groups based on the median NORAD expression level. Univariate analyses revealed that patients with high expression levels of NORAD had relatively poor overall survival (p = .03) and relapse-free survival (RFS) (p = .01). Additionally, multivariate analysis highlighted that NORAD upregulation was an independent risk factor for RFS. CONCLUSION Our observations indicate the fact that high expression of NORAD could be an unfavorable risk factor in non-M3 AML patients, and NORAD might be a novel therapeutic candidate for future treatments targeting AML.
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Affiliation(s)
- Mohammad Masoud Eslami
- Department of Hematology, School of Medicine, Tarbiat Modares University (TMU), Tehran, Iran
| | - Mina Soufizomorrod
- Department of Hematology Applied Cell Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Ahmadvand
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
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10
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Multifaceted roles of long non-coding RNAs in triple-negative breast cancer: biology and clinical applications. Biochem Soc Trans 2021; 48:2791-2810. [PMID: 33258920 DOI: 10.1042/bst20200666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer subtype that lacks targeted therapy due to the absence of estrogen, progesterone, and HER2 receptors. Moreover, TNBC was shown to have a poor prognosis, since it involves aggressive phenotypes that confer significant hindrance to therapeutic treatments. Recent state-of-the-art sequencing technologies have shed light on several long non-coding RNAs (lncRNAs), previously thought to have no biological function and were considered as genomic junk. LncRNAs are involved in various physiological as well as pathological conditions, and play a key role in drug resistance, gene expression, and epigenetic regulation. This review mainly focuses on exploring the multifunctional roles of candidate lncRNAs, and their strong association with TNBC development. We also summarise various emerging research findings that establish novel paradigms of lncRNAs function as oncogenes and/or tumor suppressors in TNBC development, suggesting their role as prospective therapeutic targets.
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11
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Wang X, Song B, Zang M, Ji H, Yang H, Jiang S, Yang X. LOC100996425 acts as a promoter in prostate cancer by mediating hepatocyte nuclear factor 4A and the AMPK/mTOR pathway. J Cell Mol Med 2021; 25:8174-8186. [PMID: 34309216 PMCID: PMC8419185 DOI: 10.1111/jcmm.16657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 04/23/2021] [Accepted: 05/01/2021] [Indexed: 12/11/2022] Open
Abstract
The involvement of long non-coding RNAs (lncRNAs), differentially expressed genes and signals in prostate cancer (PCa) continues to be a subject of investigation. This study determined effects of LOC100996425 on human PCa by targeting hepatocyte nuclear factor 4A (HNF4A) via the AMPK/mTOR pathway. PCa and adjacent normal tissues were obtained to characterize expression pattern of LOC100996425, HNF4A and the AMPK/mTOR pathway-related genes. Then, the target gene of LOC100996425 was determined with lncRNA target prediction website and further verification was obtained through luciferase assay and ribonucleoprotein immunoprecipitation. After that, PCa cells were introduced with LOC100996425, HNF4A, siLOC100996425 or siHNF4A to explore the specific significance of LOC100996425 and HNF4A in PCa. The mechanism associated with AMPK/mTOR pathway was investigated using AMPK inhibitor or activator. LOC100996425 was up-regulated, while HNF4A was down-regulated in the PCa tissues. HNF4A was a target gene of LOC100996425. PCa cells transfected with either siLOC100996425 or HNF4A displayed reduced rates of PCa cell proliferation and migration while elevating cell apoptosis. HNF4A overexpression reversed the promotive effect of LOC100996425 overexpression on PCa. The activation of AMPK pathway involved in the cancer progression mediated by LOC100996425. Down-regulation of LOC100996425 retards progression of PCa through HNF4A-mediated AMPK/mTOR pathway.
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Affiliation(s)
- Xiuyan Wang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Bin Song
- Department of Neurosurgery, The Second Hospital of Jilin University, Changchun, China
| | - Mingcui Zang
- Department of Hepatobiliary and Pancreatic Surgery I, The First Hospital of Jilin University, Changchun, China
| | - He Ji
- Department of Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - He Yang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Shuang Jiang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Xiao Yang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
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12
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Thakur KK, Kumar A, Banik K, Verma E, Khatoon E, Harsha C, Sethi G, Gupta SC, Kunnumakkara AB. Long noncoding RNAs in triple-negative breast cancer: A new frontier in the regulation of tumorigenesis. J Cell Physiol 2021; 236:7938-7965. [PMID: 34105151 DOI: 10.1002/jcp.30463] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
In recent years, triple-negative breast cancer (TNBC) has emerged as the most aggressive subtype of breast cancer and is usually associated with increased mortality worldwide. The severity of TNBC is primarily observed in younger women, with cases ranging from approximately 12%-24% of all breast cancer cases. The existing hormonal therapies offer limited clinical solutions in completely circumventing the TNBC, with chemoresistance and tumor recurrences being the common hurdles in the path of TNBC treatment. Accumulating evidence has correlated the dysregulation of long noncoding RNAs (lncRNAs) with increased cell proliferation, invasion, migration, tumor growth, chemoresistance, and decreased apoptosis in TNBC. Various clinical studies have revealed that aberrant expression of lncRNAs in TNBC tissues is associated with poor prognosis, lower overall survival, and disease-free survival. Due to these specific characteristics, lncRNAs have emerged as novel diagnostic and prognostic biomarkers for TNBC treatment. However, the underlying mechanism through which lncRNAs perform their actions remains unclear, and extensive research is being carried out to reveal it. Therefore, understanding of mechanisms regulating the modulation of lncRNAs will be a substantial breakthrough in effective treatment therapies for TNBC. This review highlights the association of several lncRNAs in TNBC progression and treatment, along with their possible functions and mechanisms.
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Affiliation(s)
- Krishan K Thakur
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Aviral Kumar
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Kishore Banik
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Elika Verma
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Elina Khatoon
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Choudhary Harsha
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Subash C Gupta
- Department of Biochemistry, Laboratory for Translational Cancer Research, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Ajaikumar B Kunnumakkara
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
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13
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Sanchez-Lopez JM, Mandujano-Tinoco EA, Garcia-Venzor A, Lozada-Rodriguez LF, Zampedri C, Uribe-Carvajal S, Melendez-Zajgla J, Maldonado V, Lizarraga F. Integrative analysis of transcriptional profile reveals LINC00052 as a suppressor of breast cancer cell migration. Cancer Biomark 2021; 30:365-379. [PMID: 33361583 DOI: 10.3233/cbm-200337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Long-non-coding RNAs, a class of transcripts with lengths > 200 nt, play key roles in tumour progression. Previous reports revealed that LINC00052 (long intergenic non-coding RNA 00052) was strongly downregulated during breast cancer multicellular spheroids formation and suggested a role in cell migration and oxidative metabolism. OBJECTIVE To examine the function of LINC00052 in MCF-7 breast cancer cells. METHODS Loss-of-function studies were performed to evaluate LINC00052 role on MCF-7 breast cancer cells. Microarray expression assays were performed to determine genes and cellular functions modified after LINC00052 knockdown. Next, the impact of LINC00052 depletion on MCF-7 cell respiration and migration was evaluated. RESULTS 1,081 genes were differentially expressed upon LINC00052 inhibition. Gene set enrichment analysis, Gene Ontology and Key Pathway Advisor analysis showed that signalling networks related to cell migration and oxidative phosphorylation were enriched. However, whereas LINC00052 knockdown in MCF-7 cells revealed marginal difference in oxygen consumption rates when compared with control cells, LINC00052 inhibition enhanced cell migration in vitro and in vivo, as observed using a Zebrafish embryo xenotransplant model. CONCLUSION Our data show that LINC00052 modulates MCF-7 cell migration. Genome-wide microarray experiments suggest that cancer cell migration is affected by LINC00052 through cytoskeleton modulation and Notch/β-catenin/NF-κB signalling pathways.
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Affiliation(s)
- Jose Manuel Sanchez-Lopez
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Postgraduate Program in Biological Sciences, Faculty of Medicine, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edna Ayerim Mandujano-Tinoco
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación Luís Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Alfredo Garcia-Venzor
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Cecilia Zampedri
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Salvador Uribe-Carvajal
- Department of Molecular Genetics, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Functional Genomics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vilma Maldonado
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Floria Lizarraga
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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14
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Wang SM, Pang J, Zhang KJ, Zhou ZY, Chen FY. lncRNA MIR503HG inhibits cell proliferation and promotes apoptosis in TNBC cells via the miR-224-5p/HOXA9 axis. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:62-73. [PMID: 33869743 PMCID: PMC8027537 DOI: 10.1016/j.omto.2021.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/14/2021] [Indexed: 12/19/2022]
Abstract
Triple-negative breast cancer (TNBC) is a highly invasive subtype of breast cancer. This study investigated the molecular mechanism and influences of MIR503HG, miR-224-5p, and homeobox A9 (HOXA9) on TNBC cell growth and migration. Dual-luciferase reporter gene and RNA immunoprecipitation were performed to examine the regulation of MIR503HG, miR-224-5p, and HOXA9. Cell proliferation, apoptosis, migration, and invasion were evaluated by colony formation, flow cytometry, and Transwell assays. Finally, nude mice were employed to investigate the influence of MIR503HG on TNBC tumor growth. HOXA9 protein levels were detected by immunohistochemical staining. MIR503HG and HOXA9 expression were reduced in TNBC, while miR-224-5p was increased. Overexpression of MIR503HG or HOXA9 reduced the cell migration ability and proliferation and promoted apoptosis, and knockdown of MIR503HG or overexpression of miR-224-5p exhibited the opposite effects. Furthermore, MIR503HG promoted HOXA9 expression by inhibiting miR-224-5p. Overexpression of miR-224-5p reversed the effects of MIR503HG overexpression on TNBC cells, while overexpression of HOXA9 reversed the effect of MIR503HG knockdown. Additionally, an in vivo study proved that MIR503HG inhibited TNBC tumor growth via the miR-224-5p/HOXA9 axis. MIR503HG inhibited cell proliferation and promoted the apoptosis of TNBC cells via the miR-224-5p/HOXA9 axis, which may function as a novel target for the treatment of TNBC.
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Affiliation(s)
- Shou-Man Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.,Clinical Research Center for Breast Cancer in Hunan Province, Changsha 410008, Hunan Province, P.R. China
| | - Jian Pang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.,Clinical Research Center for Breast Cancer in Hunan Province, Changsha 410008, Hunan Province, P.R. China
| | - Ke-Jing Zhang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.,Clinical Research Center for Breast Cancer in Hunan Province, Changsha 410008, Hunan Province, P.R. China
| | - Zhi-Yang Zhou
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.,Clinical Research Center for Breast Cancer in Hunan Province, Changsha 410008, Hunan Province, P.R. China
| | - Fei-Yu Chen
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.,Clinical Research Center for Breast Cancer in Hunan Province, Changsha 410008, Hunan Province, P.R. China
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15
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Xiong D, Wang D, Chen Y. Role of the long non-coding RNA LINC00052 in tumors. Oncol Lett 2021; 21:316. [PMID: 33692848 PMCID: PMC7933760 DOI: 10.3892/ol.2021.12577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Long intergenic non-protein coding RNA 52 (LINC00052) is a non-coding RNA with >200 nucleotides in length, which exerts important effects on several physiological and pathological processes of the human body. Recent studies have demonstrated that LINC00052 plays key roles in the tumorigenesis, progression and metastasis of multiple types of human cancer, including hepatocellular carcinoma, breast cancer, colorectal cancer, cervical carcinoma and gastric cancer. However, the associations between LINC00052 and these tumors remain unclear. The present review summarizes the biological functions of LINC00052 during the pathogenic process of certain tumors, and discusses its potential therapeutic targets.
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Affiliation(s)
- Dongmei Xiong
- Early Childhood Health Research Innovation Team, Nursing School of Chongqing Medical and Pharmaceutical College, Chongqing 401331, P.R. China
| | - Dan Wang
- Clinical Laboratory, The People's Hospital of Rongchang, Chongqing 402460, P.R. China
| | - Yanmeng Chen
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
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16
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The role of EMT-related lncRNA in the process of triple-negative breast cancer metastasis. Biosci Rep 2021; 41:227597. [PMID: 33443534 PMCID: PMC7859322 DOI: 10.1042/bsr20203121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most malignant and fatal subtype of breast cancer, which has characterized by negativity expression of ER, PR, and HER2. Metastasis is the main factor affecting the prognosis of TNBC, and the process of metastasis is related to abnormal activation of epithelial–mesenchymal transition (EMT). Recent studies have shown that long non-coding RNA (LncRNA) plays an important role in regulating the metastasis and invasion of TNBC. Therefore, based on the metastasis-related EMT signaling pathway, great efforts have confirmed that LncRNA is involved in the molecular mechanism of TNBC metastasis, which will provide new strategies to improve the treatment and prognosis of TNBC. In this review, we summarized many signal pathways related to EMT involved in the transfer process. The advances from the most recent studies of lncRNAs in the EMT-related signal pathways of TNBC metastasis. We also discussed the clinical research, application, and challenges of LncRNA in TNBC.
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17
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The potential of long noncoding RNAs for precision medicine in human cancer. Cancer Lett 2020; 501:12-19. [PMID: 33359450 DOI: 10.1016/j.canlet.2020.11.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/13/2020] [Accepted: 11/26/2020] [Indexed: 12/20/2022]
Abstract
Precision medicine promises to better classify patients by individual clinical and biological biomarkers, which may provide an accurate assessment of disease risk, diagnosis, prognosis and treatment response. Cancer frequently displays substantial inter-tumor and intra-tumor heterogeneity and hence oncology is well suited for application of precision approaches. Recent studies have demonstrated that dysregulated lncRNAs play pivotal roles in tumor heterogeneity. In this review, attention is focused on the potential applications of lncRNAs as biomarker candidates for cancer risk evaluation, detection, surveillance and prognosis. LncRNAs are often stable in clinical samples and easily detected. The functional implications and therapeutic potential of targeting lncRNAs in human cancer are further discussed. Finally, existing deficiencies and future perspectives in translating fundamental lncRNA knowledge into clinical practice are highlighted.
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18
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Zhang W, Guan X, Tang J. The long non-coding RNA landscape in triple-negative breast cancer. Cell Prolif 2020; 54:e12966. [PMID: 33314471 PMCID: PMC7848969 DOI: 10.1111/cpr.12966] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Triple‐negative breast cancer (TNBC) is a type of breast cancer that has a higher risk of distant recurrence and metastasis, leading to a relatively aggressive biological behaviour and poor outcome. So far, the clinical management of TNBC is challenging because of its heterogeneity and paucity of specific targeted therapy. Recently, various studies have identified a lot of differently expressed long non‐coding RNAs (lncRNAs) in TNBC. Those lncRNAs have been reported to play important roles in the multistep process of TNBC tumorigenesis. Here, we review the biological characteristics of lncRNAs, and present the current state of knowledge concerning the expression, function and regulation of lncRNAs in TNBC. Accumulating studies explored the potential lncRNAs‐based therapeutics in TNBC, including the techniques of genetic modification using antisense oligonucleotides, locked nucleic acid and RNA nanotechnology. In current review, we also discuss the future prospects of studies about lncRNAs in TNBC and development of lncRNA‐based strategies for clinical TNBC patients.
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Affiliation(s)
- Wenwen Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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19
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Wang Y, Wu S, Zhu X, Zhang L, Deng J, Li F, Guo B, Zhang S, Wu R, Zhang Z, Wang K, Lu J, Zhou Y. LncRNA-encoded polypeptide ASRPS inhibits triple-negative breast cancer angiogenesis. J Exp Med 2020; 217:132618. [PMID: 31816634 PMCID: PMC7062514 DOI: 10.1084/jem.20190950] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/27/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022] Open
Abstract
In this study, Wang et al. demonstrate that lncRNA-encoded polypeptide ASRPS is down-regulated in TNBC. ASRPS regulates angiogenesis and may serve as a novel prognostic marker and therapeutic target for TNBC. Triple-negative breast cancer (TNBC) is a subtype of breast cancer (BC) with the most aggressive phenotype and poor overall survival. Using bioinformatics tools, we identified LINC00908 encoding a 60–aa polypeptide and differentially expressed in TNBC tissues. We named this endogenously expressed polypeptide ASRPS (a small regulatory peptide of STAT3). ASRPS expression was down-regulated in TNBCs and associated with poor overall survival. We showed that LINC00908 was directly regulated by ERα, which was responsible for the differential down-regulation of LINC00908 in TNBCs. ASRPS directly bound to STAT3 through the coiled coil domain (CCD) and down-regulated STAT3 phosphorylation, which led to reduced expression of VEGF. In human endothelial cells, a mouse xenograft breast cancer model, and a mouse spontaneous BC model, ASRPS expression reduced angiogenesis. In a mouse xenograft breast cancer model, down-regulation of ASRPS promoted tumor growth, and ASRPS acted as an antitumor peptide. We presented strong evidence that LINC00908-encoded polypeptide ASRPS represented a TNBC-specific target for treatment.
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Affiliation(s)
- Yirong Wang
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Siqi Wu
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Xun Zhu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Liyuan Zhang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jieqiong Deng
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Fang Li
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Binbin Guo
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Shenghua Zhang
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Rui Wu
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Zheng Zhang
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Kexin Wang
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, The School of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, China
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20
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Abba MC, Canzoneri R, Gurruchaga A, Lee J, Tatineni P, Kil H, Lacunza E, Aldaz CM. LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression. Int J Mol Sci 2020; 21:ijms21197407. [PMID: 33049922 PMCID: PMC7582527 DOI: 10.3390/ijms21197407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022] Open
Abstract
Long intergenic non-protein coding RNA 885 (LINC00885) was identified as significantly upregulated in breast ductal carcinoma in situ (DCIS). The aim of this study was to characterize the phenotypic effects and signaling pathways modulated by LINC00885 in non-invasive and invasive breast cancer models. We determined that LINC00885 induces premalignant phenotypic changes by increasing cell proliferation, motility, migration and altering 3D growth in normal and DCIS breast cell lines. Transcriptomic studies (RNA-seq) identified the main signaling pathways modulated by LINC00885, which include bioprocesses related to TP53 signaling pathway and proliferative signatures such as activation of EREG, EGFR and FOXM1 pathways. LINC00885 silencing in breast cancer lines overexpressing this lncRNA leads to downregulation of proliferation related transcripts such as EREG, CMYC, CCND1 and to significant decrease in cell migration and motility. TCGA-BRCA data analyses show an association between high LINC00885 expression and worse overall survival in patients with primary invasive breast carcinomas (p = 0.024), suggesting that the pro-tumorigenic effects of LINC00885 overexpression persist post-invasion. We conclude that LINC00885 behaves as a positive regulator of cell growth both in normal and DCIS breast cells possibly operating as a ceRNA and representing a novel oncogenic lncRNA associated with early stage breast cancer progression.
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Affiliation(s)
- Martin C. Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
- Correspondence: (M.C.A.); (C.M.A.)
| | - Romina Canzoneri
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - Agustina Gurruchaga
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - Jaeho Lee
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Pradeep Tatineni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Hyunsuk Kil
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
| | - Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata CP1900, Argentina; (R.C.); (A.G.); (E.L.)
| | - C. Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; (J.L.); (P.T.); (H.K.)
- Correspondence: (M.C.A.); (C.M.A.)
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21
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Long non-coding RNA LINC00511/miR-150/MMP13 axis promotes breast cancer proliferation, migration and invasion. Biochim Biophys Acta Mol Basis Dis 2020; 1867:165957. [PMID: 33031905 DOI: 10.1016/j.bbadis.2020.165957] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
Breast cancer is the most common cancer affecting women and one of the leading causes of cancer-related deaths worldwide. In existing studies, some long non-coding RNAs (lncRNAs) are considered to have important regulatory roles in the development of cancers. However, the pathogenic significance of LINC00511 in breast cancer is unclear. In this study, LINC00511 was significantly up-regulated in breast cancer, and its expression level was correlated to poor prognosis of patients with breast cancer. To further study the role of LINC00511 in breast cancer, we knocked down the expression of LINC00511 using siRNAs. Cells transfected with siRNA-2 proliferated, and its metastasis was suppressed. RNA-seq analysis revealed 182 potential targets for LINC00511. The in-silico analysis revealed that differently expressed genes were closely related to signaling mediated by p38-alpha and p38-beta. Subcellular localization showed that LINC00511 was mainly located in the cytoplasm, and knocking down the LINC00511 gene could down-regulate the expression of MMP13. Using bioinformatics analysis combined with dual-luciferase report assay, we finally determined that miR-150 was the direct target of LINC00511. The dual-luciferase report assays also showed that MMP13 was the target of miR-150. LINC00511 knockdown significantly reduced MMP13 protein levels, and miR-150 gene knockdown significantly rescued the down-regulation of MMP13 caused by LINC00511 gene silencing. Moreover, silencing MMP13 and overexpression of miR-150 could reduce the proliferation of breast cancer cells. In conclusion, our data show that LINC00511 is a breast cancer promoter, and the LINC00511/miR-150/MMP13 axis may be a new therapeutic strategy for breast cancer patients.
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22
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Zhao E, Lan Y, Quan F, Zhu X, A S, Wan L, Xu J, Hu J. Identification of a Six-lncRNA Signature With Prognostic Value for Breast Cancer Patients. Front Genet 2020; 11:673. [PMID: 32849766 PMCID: PMC7396575 DOI: 10.3389/fgene.2020.00673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BRCA) is the most common cancer and a major cause of death in women. Long non-coding RNAs (lncRNAs) are emerging as key regulators and have been implicated in carcinogenesis and prognosis. In this study, we aimed to develop a lncRNA signature of BRCA patients to improve risk stratification. In the training cohort (GSE21653, n = 232), 17 lncRNAs were identified by univariate Cox proportional hazards regression, which were significantly associated with patients’ survival. The least absolute shrinkage and selection operator-penalized Cox proportional hazards regression analysis was used to identify a six-lncRNA signature. According to the median of the signature risk score, patients were divided into a high-risk group and a low-risk group with significant disease-free survival differences in the training cohort. A similar phenomenon was observed in validation cohorts (GSE42568, n = 101; GSE20711, n = 87). The six-lncRNA signature remained as independent prognostic factors after adjusting for clinical factors in these two cohorts. Furthermore, this signature significantly predicted the survival of grade III patients and estrogen receptor-positive patients. Furthermore, in another cohort (GSE19615, n = 115), the low-risk patients that were treated with tamoxifen therapy had longer disease-free survival than those who underwent no therapy. Overall, the six-lncRNA signature can be a potential prognostic tool used to predict disease-free survival of patients and to predict the benefits of tamoxifen treatment in BRCA, which will be helpful in guiding individualized treatments for BRCA patients.
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Affiliation(s)
- Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaojing Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Suru A
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Linyun Wan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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23
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Amelio I, Bernassola F, Candi E. Emerging roles of long non-coding RNAs in breast cancer biology and management. Semin Cancer Biol 2020; 72:36-45. [PMID: 32619506 DOI: 10.1016/j.semcancer.2020.06.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 01/01/2023]
Abstract
Breast cancer is the most common cancer in women with the highest mortality among this gender. Despite treatment strategies including surgery, hormone therapy and targeted therapy have recently advanced, innovative biomarkers are needed for the early detection, treatment and prognosis. An increasing number of non-coding RNAs (ncRNAs) have shown great potential as crucial players in different stages of the breast cancer tumorigenesis, influencing cell death, metabolism, epithelial-mesenchymal transition (EMT), metastasis and drug resistance. Long non-coding RNAs (lncRNAs), specifically, are a class of RNA transcripts with a length greater than 200 nucleotides, which have also been shown to exerts oncogenic or tumour suppressive roles in the pathogenesis of breast cancer. LncRNAs are implicated in different molecular mechanisms by regulating gene expressions and functions at transcriptional, translational, and post-translational levels. Here, we aim to briefly discuss the latest existing body of knowledge regarding the key functions and the molecular mechanisms of some of the most relevant lncRNAs in the pathogenesis, treatment and prognosis of breast cancer.
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Affiliation(s)
- I Amelio
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, Italy; School of Life Sciences, University of Nottingham, Nottingham, UK
| | - F Bernassola
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, Italy
| | - E Candi
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, Italy; Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy.
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24
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Yuan C, Luo X, Duan S, Guo L. Long noncoding RNA LINC00115 promotes breast cancer metastasis by inhibiting miR-7. FEBS Open Bio 2020; 10:1230-1237. [PMID: 32175684 PMCID: PMC7327907 DOI: 10.1002/2211-5463.12842] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/06/2020] [Accepted: 03/12/2020] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the second leading cause of cancer-related deaths in women. The long noncoding RNA LINC00115 has been reported to be involved in the poor outcome of patients with breast cancer, but the biological function and underlying mechanism remain unclear. Here, we report that LINC00115 expression is increased in triple-negative breast cancer tissue compared with matched normal tissue, and LINC00115 knockdown suppresses breast cancer cell migration and invasion. Furthermore, we show that LINC00115 directly targets miR-7 and inhibits its expression. LINC00115 also reduces the expression of KLF4, which is a direct target of miR-7 and is involved in breast cancer metastasis. Together, our findings suggest that LINC00115 promotes breast cancer metastasis through modulating the expression of miR-7 and KLF4.
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Affiliation(s)
- Chunlei Yuan
- Department of Breastthe Second Affiliated Hospital of Nanchang UniversityChina
| | - Xuliang Luo
- Department of Breastthe Second Affiliated Hospital of Nanchang UniversityChina
| | - Sijia Duan
- Department of Breastthe Second Affiliated Hospital of Nanchang UniversityChina
| | - Liangyun Guo
- Department of Ultrasoundthe Second Affiliated Hospital of Nanchang UniversityChina
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25
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Wu Y, Bi QJ, Han R, Zhang Y. Long noncoding RNA KCNQ1OT1 is correlated with human breast cancer cell development through inverse regulation of hsa-miR-107. Biochem Cell Biol 2020; 98:338-344. [PMID: 32379482 DOI: 10.1139/bcb-2019-0271] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this work, we investigated the expression pattern and regulatory function of long noncoding RNA (lncRNA) KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in breast cancer. We found that KCNQ1OT1 was significantly upregulated in breast cancer cell lines. In lentiviral-transduced BT-549 and HCC1599 cells, KCNQ1OT1 knockdown impaired cancer cell functions, including in vitro proliferation and migration, and in vivo transplant growth. The possible sponging target of KCNQ1OT1, human microRNA-107 (hsa-miR-107), was confirmed to be bound by KCNQ1OT1, and was upregulated in breast cancer cells with KCNQ1OT1 downregulation. Further, hsa-miR-107 knockdown in KCNQ1OT1-downregulated cancer cells reversed its impairing effects on cancer cell proliferation and migration in vitro. Thus, loss of KCNQ1OT1 is associated with functional impairment in breast cancer cells, likely through inverse regulation of its sponging target, hsa-miR-107.
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Affiliation(s)
- Yanyan Wu
- Mammary gland thyroid Surgery, Affiliated Hospital of Jining Medical University, Jining, 272000, Shandong, China
| | - Qing-Jun Bi
- Department of Oncology, Fourth People’s Hospital of Zibo, Zibo, 255067, Shandong, China
| | - Rui Han
- Department of Oncology, Fourth People’s Hospital of Zibo, Zibo, 255067, Shandong, China
| | - Yajie Zhang
- Mammary gland thyroid Surgery, Affiliated Hospital of Jining Medical University, Jining, 272000, Shandong, China
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26
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Zhang X, Yang H. Research Progress on Long Non-coding RNAs and Drug Resistance of Breast Cancer. Clin Breast Cancer 2020; 20:275-282. [PMID: 32414649 DOI: 10.1016/j.clbc.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 01/02/2023]
Abstract
Breast cancer, as the foremost cause of women's death in the world, is highly metastatic and mutable. Resistance to drugs for chemotherapies, endocrine therapies, and targeted therapies is an important factor that impacts the prognosis of breast cancer. Long non-coding ribonucleic acids (LncRNAs) are crucial regulators of intracellular gene expressions. Some researchers have suggested that expression level of several types of LncRNAs were closely related to the prognosis of patients with breast cancer. LncRNAs significantly impact biological processes such as drug transport, detoxication, apoptosis, epithelial to mesenchymal transition (EMT), and autophagy by regulating intracellular signaling pathways such as multi-drug resistance gene 1 (MDR1), nuclear factor erythroid 2-related factor 2 (NRF2), phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR), transforming growth factor-β (TGF-β), BRCA1/2, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). This paper will summarize research progress on correlations between LncRNA and drug resistance of breast cancer. It will particularly expound molecular mechanisms through which LncRNAs regulate drug resistance of breast cancer. It will further discuss the feasibility as molecular markers for forecasting drug resistance of breast cancer and may be becoming new targets for treating breast cancer in the future.
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Affiliation(s)
- Xiping Zhang
- Department of Breast Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, China
| | - Hongjian Yang
- Department of Breast Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, China.
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27
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Mei J, Hao L, Wang H, Xu R, Liu Y, Zhu Y, Liu C. Systematic characterization of non-coding RNAs in triple-negative breast cancer. Cell Prolif 2020; 53:e12801. [PMID: 32249490 PMCID: PMC7260065 DOI: 10.1111/cpr.12801] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
Triple‐negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer with negativity for oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (HER2). Non‐coding RNAs (ncRNAs) make up most of the transcriptome and are widely present in eukaryotic cells. In recent years, emerging evidence suggests that ncRNAs, mainly microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), play prominent roles in the tumorigenesis and development of TNBC, but the functions of most ncRNAs have not been fully described. In this review, we systematically elucidate the general characteristics and biogenesis of miRNAs, lncRNAs and circRNAs, discuss the emerging functions of these ncRNAs in TNBC and present future perspectives in clinical practice.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Leiyu Hao
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Huiyu Wang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Rui Xu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yan Liu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chaoying Liu
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
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28
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Brown JM, Wasson MCD, Marcato P. The Missing Lnc: The Potential of Targeting Triple-Negative Breast Cancer and Cancer Stem Cells by Inhibiting Long Non-Coding RNAs. Cells 2020; 9:cells9030763. [PMID: 32244924 PMCID: PMC7140662 DOI: 10.3390/cells9030763] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Treatment decisions for breast cancer are based on staging and hormone receptor expression and include chemotherapies and endocrine therapy. While effective in many cases, some breast cancers are resistant to therapy, metastasize and recur, leading to eventual death. Higher percentages of tumor-initiating cancer stem cells (CSCs) may contribute to the increased aggressiveness, chemoresistance, and worse outcomes among breast cancer. This may be particularly true in triple-negative breast cancers (TNBCs) which have higher percentages of CSCs and are associated with worse outcomes. In recent years, increasing numbers of long non-coding RNAs (lncRNAs) have been identified as playing an important role in breast cancer progression and some of these have been specifically associated within the CSC populations of breast cancers. LncRNAs are non-protein-coding transcripts greater than 200 nucleotides which can have critical functions in gene expression regulation. The preclinical evidence regarding lncRNA antagonists for the treatment of cancer is promising and therefore, presents a potential novel approach for treating breast cancer and targeting therapy-resistant CSCs within these tumors. Herein, we summarize the lncRNAs that have been identified as functionally relevant in breast CSCs. Furthermore, our review of the literature and analysis of patient datasets has revealed that many of these breast CSC-associated lncRNAs are also enriched in TNBC. Together, this suggests that these lncRNAs may be playing a particularly important role in TNBC. Thus, certain breast cancer-promoting/CSC-associated lncRNAs could be targeted in the treatment of TNBCs and the CSCs within these tumors should be susceptible to anti-lncRNA therapy.
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Affiliation(s)
- Justin M Brown
- Departments of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (J.M.B.); (M.-C.D.W.)
| | - Marie-Claire D Wasson
- Departments of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (J.M.B.); (M.-C.D.W.)
| | - Paola Marcato
- Departments of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (J.M.B.); (M.-C.D.W.)
- Departments of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Correspondence: ; Tel.: +1-902-494-4239; Fax: +1-902-494-2519
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29
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Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton SE, Bhargava R, Lal A, Prasanth SG, Prasanth KV. LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells. RNA (NEW YORK, N.Y.) 2020; 26:175-185. [PMID: 31690584 PMCID: PMC6961546 DOI: 10.1261/rna.073254.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 05/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.
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Affiliation(s)
- Aamira Tariq
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Sarah E Holton
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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30
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Zhang S, Song X. Long non-coding RNA SNHG1 promotes cell proliferation and invasion of hepatocellular carcinoma by acting as a molecular sponge to modulate miR-195. Arch Med Sci 2020; 16:386-394. [PMID: 32190150 PMCID: PMC7069425 DOI: 10.5114/aoms.2019.81311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/09/2018] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Although long non-coding RNA SNHG1 (lncRNA SNHG1) action on cell proliferation and invasion of hepatocellular carcinoma (HCC) cells has been reported, the effects of lncRNA SNHG1 on migration of HCC cells and the mechanisms are still unclear. The present study aimed to investigate the influence of lncRNA SNHG1 on metastasis in HCC cells and the possible mechanisms underlying this phenotype. MATERIAL AND METHODS Expression of lncRNA SNHG1 and miR-195 was determined using qRT-PCR in both HCC cell lines Huh7 and HepG2. Si-RNA was used to silence SNHG1 and miR-195 inhibitor was used to inhibit expression of miR-195. Luciferase reporter assay was conducted to confirm whether miR-195 was the direct binding target of SNHG1. RESULTS lncRNA SNHG1 was significantly up-regulated and miR-195 was significantly down-regulated in HCC cell lines. When transfected with si-SNHG1, migration and invasion of HCC cells, as well as expression of astrocyte elevated gene 1 (AEG-1) protein, were significantly inhibited compared with the control cells. Results of dual luciferase reporter assay showed that lncRNA SNHG1 acted as an endogenous sponge of miR-195. On the other hand, the expression of miR-195 in tumor tissue was much lower than that of miR-195 in the corresponding normal tissue. Furthermore, the correlation analysis showed a strong negative relationship between lncRNA SNHG1 and miR-195 expression in HCC tissues. CONCLUSIONS SNHG1 may promote cell invasion and migration in HCC cells by sponging miR-195. These results can provide deeper understanding of SNHG1 in hepatocellular cancer and give new potential targets for treatment of HCC.
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Affiliation(s)
- Shuai Zhang
- Department of Radiation Oncology, Hainan General Hospital, Haikou, China
| | - Xiaoding Song
- Clinical Laboratory, Hainan General Hospital, Haikou, China
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31
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Long Non-Coding RNA: Dual Effects on Breast Cancer Metastasis and Clinical Applications. Cancers (Basel) 2019; 11:cancers11111802. [PMID: 31744046 PMCID: PMC6896003 DOI: 10.3390/cancers11111802] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
As a highly heterogeneous malignancy, breast cancer (BC) has become the most significant threat to female health. Distant metastasis and therapy resistance of BC are responsible for most of the cases of mortality and recurrence. Distant metastasis relies on an array of processes, such as cell proliferation, epithelial-to-mesenchymal transition (EMT), mesenchymal-to-epithelial transition (MET), and angiogenesis. Long non-coding RNA (lncRNA) refers to a class of non-coding RNA with a length of over 200 nucleotides. Currently, a rising number of studies have managed to investigate the association between BC and lncRNA. In this study, we summarized how lncRNA has dual effects in BC metastasis by regulating invasion, migration, and distant metastasis of BC cells. We also emphasize that lncRNA has crucial regulatory effects in the stemness and angiogenesis of BC. Clinically, some lncRNAs can regulate chemotherapy sensitivity in BC patients and may function as novel biomarkers to diagnose or predict prognosis for BC patients. The exact impact on clinical relevance deserves further study. This review can be an approach to understanding the dual effects of lncRNAs in BC, thereby linking lncRNAs to quasi-personalized treatment in the future.
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32
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Luo JZ, Qin L, Zhang LJ. Expression and function of long non-coding RNA LINC01420 in thyroid cancer. Oncol Lett 2019; 19:399-405. [PMID: 31897152 PMCID: PMC6924109 DOI: 10.3892/ol.2019.11076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
The Human Genome Project revealed that >90% of the human genome was found to transcribe non-coding RNAs, including micro RNAs and long non-coding RNAs (lncRNAs). lncRNAs have been identified to play a crucial role in cancer progression. Thyroid cancer (TC) is a common type of endocrine cancer; however, the functional roles of lncRNAs in TC have yet to be fully elucidated. The present study investigated whether LINC01420 was upregulated in TC tissues, compared with normal thyroid tissues, and the results suggested that LINC01420 may play a regulatory role in TC. Bioinformatics analysis demonstrated that LINC01420 was associated with translation, rRNA processing, mRNA splicing, regulation of transcription, DNA repair and double-strand break repair. Furthermore, the exact role of LINC01420 in TC was explored by performing a loss-of-function assay, which revealed that the knockdown of LINC01420 inhibited TC cell proliferation and cell cycle progression. The findings of the present study provide a novel insight into the molecular mechanisms underlying TC development. Moreover, they suggest that LINC01420 may serve as a potential therapeutic target for the treatment of TC, and that increased LINC01420 expression levels show potential as a prognostic marker for the disease.
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Affiliation(s)
- Jin-Zhu Luo
- Department of Clinical Laboratory, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Lu Qin
- Department of Thyroid Vascular Surgery, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Ling-Jie Zhang
- Department of Anesthesiology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei 430015, P.R. China
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33
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Huang Y, Ge H, Zheng M, Cui Y, Fu Z, Wu X, Xia Y, Chen L, Wang Z, Wang S, Xie H. Serum tRNA-derived fragments (tRFs) as potential candidates for diagnosis of nontriple negative breast cancer. J Cell Physiol 2019; 235:2809-2824. [PMID: 31535382 DOI: 10.1002/jcp.29185] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
Breast cancer has become the most common cancer in women, and nontriple negative breast cancer (non-TNBC) accounts for 80-90% of all invasive breast cancers. Early detection, diagnosis, and treatment are considered key to a successful cure. Conventionally, breast imaging and needle core biopsy are used for detection and monitoring. However, small variations in volume might be ignored in imaging, and traditional biopsies are spatially and temporally limited, leading to a significant delay in cancer detection and thus prompting renewed focus on early and accurate diagnosis. In this article, we investigated whether there is an accurate molecule in peripheral blood that can help diagnose breast cancer. Similar to microRNAs, tRNA-derived fragments (tRFs) have been reported to be involved in many pathological processes in breast cancer, but whether they can serve as candidate biomarkers for breast cancer remains unclear. Using high-throughput sequencing technology, we identified 4,021 differentially expressed tRFs in normal and breast cancer cell lines, and eight tRFs were selected to establish a signature as a predictive biomarker of non-TNBC. Furthermore, quantitative reverse-transcriptase polymerase chain reaction was performed to verify the expression of the signature and analyze the correlation between dysregulated tRFs and breast cancer. The results indicated that tDR-7816, tDR-5334, and tDR-4733 might be promising biomarkers. Through further bioinformatics analysis, we predicted that tDR-7816 influences the xenobiotic metabolic processes that support the oncogenesis of breast cancer. In summary, our results provide a rationale for using circulating tDR-7816 expression as a novel potential biomarker for the diagnosis of patients with early non-TNBC.
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Affiliation(s)
- Yue Huang
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Han Ge
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Mingjie Zheng
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yangyang Cui
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China.,Department of Obstetrics and Gynecology, Northwestern University, Illinois
| | - Xiaowei Wu
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yiqin Xia
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Lie Chen
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenghui Wang
- Department of Thyroid and Breast Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
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Chen J, Lan J, Ye Z, Duan S, Hu Y, Zou Y, Zhou J. Long noncoding RNA LRRC75A-AS1 inhibits cell proliferation and migration in colorectal carcinoma. Exp Biol Med (Maywood) 2019; 244:1137-1143. [PMID: 31505952 DOI: 10.1177/1535370219874339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With the continuous improvement of technology in the molecular field, more and more evidence indicated that long noncoding RNAs (lncRNAs) are widely expressed in a broad spectrum of human tumors, playing an important role in the development and progression of tumors. Most studies reported that lncRNAs might serve as reliable biomarkers and effective clinical therapeutic target. Leucine-rich repeat containing 75 A-antisense RNA1 (LRRC75A-AS1) was reported to be relevant to many types of cancers and indicated to do influence on colorectal carcinoma (CRC). This research firstly examined the role of LRRC75A-AS1 in CRC and analyzed its association with the biological behaviors of CRC cells. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) brought to light that LRRC75A-AS1 was remarkably expressed at low levels in CRC tissues. We also found that LRRC75A-AS1 was localized in the cytoplasm. In addition, LRRC75A-AS1 knockdown also notably promoted CRC cell proliferation, metastasis, invasion, and colony formation. To summarize, these experimental results showed that LRRC75A-AS1 might serve as an anti-oncogene for CRC tumorigenesis and advancement, and it may become a novel molecular marker for clinical diagnosis. Impact statement It is reported that colorectal cancer has seriously threatened human health. The incidence of colorectal cancer in China is increasing year by year. At present, the treatment of cancer is gradually developing towards individualized treatment whose core is targeted therapy, and molecular pathology is the basis of targeted therapy. Previous studies have shown that in addition to protein-coding genes that regulate tumor invasion and metastasis, there are also some non-coding genes involved in tumor encroachment and spread. Our study found that long noncoding RNA LRRC75A-AS1 is closely related to CRC and is related to its proliferation and migration. And it may become a novel molecular marker for clinical diagnosis and treatment.
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Affiliation(s)
- Jianxiong Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiawen Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhiwei Ye
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shiyu Duan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou 510515, China
| | - Yukun Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou 510515, China
| | - Ying Zou
- Department of Traditional Chinese Medicine, Scientific Research Platform, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Jun Zhou
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou 510515, China
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35
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Muñoz-Galindo L, Melendez-Zajgla J, Pacheco-Fernández T, Rodriguez-Sosa M, Mandujano-Tinoco EA, Vazquez-Santillan K, Castro-Oropeza R, Lizarraga F, Sanchez-Lopez JM, Maldonado V. Changes in the transcriptome profile of breast cancer cells grown as spheroids. Biochem Biophys Res Commun 2019; 516:1258-1264. [PMID: 31301772 DOI: 10.1016/j.bbrc.2019.06.155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Multicellular tumor spheroids mimic the functional organization of tumors in vivo, providing biological readouts that predict the behavior of cancer cells more accurately. The current study aimed to evaluate the transcriptome (mRNAs and long non-coding RNAs) of multicellular tumor spheroids from breast cancer cells. METHODS MCF-7 cell spheroids were used; the transcriptome was analyzed using RNAseq and RNA microarrays; the secretion of macrophage migration inhibitor (MIF), a cytokine exported by the cholesterol efflux regulatory protein, was measured by ELISA. Linc00052 was inhibited using short-hairpin RNAs (shRNAs). RESULTS We found several differentially regulated mRNAs and lncRNAs in MCF-7 cell spheroids. We also found significant enrichment of the Wnt/B-catenin death receptor and the cholesterol metabolic processes. Interestingly, we also found an increased concentration of MIF. Further, at 12 and 20 days of 3D culture we found 221 and 1146 dysregulated lncRNAs, respectively; including linc00052 (long intergenic non-protein coding RNA 52), which has been involved in breast cancer. Linc00052 knock-down experiments suggest that it could be a key regulator of cholesterol pathways in breast cancer. CONCLUSIONS Our data shows that tumor spheroids can induce changes in the transcriptome of the cultured cells, including both mRNAs and ncRNA. One of the major changes included the deregulation of cholesterol pathways, of which linc00052 is apparently a key regulator.
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Affiliation(s)
- Laura Muñoz-Galindo
- Laboratorio de Epigenética, CDMX, México; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM). CDMX, Mexico
| | - Jorge Melendez-Zajgla
- Genómica Functional. Instituto Nacional de Medicina Genómica (INMEGEN). CDMX, Mexico
| | - Thalia Pacheco-Fernández
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Estado de Mexico, Mexico
| | - Miriam Rodriguez-Sosa
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Estado de Mexico, Mexico
| | - Edna Ayerim Mandujano-Tinoco
- Laboratorio de Epigenética, CDMX, México; Laboratorio de Tejido Conjuntivo. Instituto Nacional de Rehabilitación (INR) "Luis Guillermo Ibarra Ibarra". CDMX, Mexico
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36
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Profile analysis reveals transfer RNA fragments involved in mesangial cells proliferation. Biochem Biophys Res Commun 2019; 514:1101-1107. [PMID: 31097225 DOI: 10.1016/j.bbrc.2019.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 01/21/2023]
Abstract
Mesangial cell (MCs) proliferation is an essential component of glomerulonephritis. To find some bio-markers of mesangial cell proliferation, we investigate the relationship between transfer RNA fragments (tRFs) and proliferating mesangial cells. The model of proliferating mesangial cells was built by using transforming growth factor-1(TGF-β1) treated mesangial cells. Then we analyzed the expression of tRFs in normal mesangial cells and mesangial cells treated by TGF-β1 through high-throughput sequencing technique. qRT-PCR was conducted to validate the differently expressed tRFs in normal mesangial cells and mesangial cells treated by TGF-β1. tDR-000064 and tDR-000103 were notably down-regulated in mesangial cells treated by TGF-β1 compared with normal mesangial cells. Then we confirmed that tDR-000064 and tDR-000103 were correlated with proliferation of mesangial cells through receiver operating characteristic curve analysis. Furthermore, Gene ontology (GO) and pathway analysis demonstrated that the two dys-regulated tRFs were mostly involved in mesangial cells and TGF-β1 receptor-mediated signaling pathway. Our research provides a comprehensive analysis of tRFs in proliferating mesangial cells. (Figure 1A).
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37
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Xu Q, Yin H, Ao H, Leng X, Liu M, Liu Y, Ma J, Wang X. An 11-lncRNA expression could be potential prognostic biomarkers in head and neck squamous cell carcinoma. J Cell Biochem 2019; 120:18094-18103. [PMID: 31144382 DOI: 10.1002/jcb.29113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/24/2022]
Abstract
The aim of our study is to construct the competing endogenous RNA (ceRNA) network of head and neck squamous cell carcinoma (HNSCC) and identify key long noncoding RNAs (lncRNAs) to predict prognosis. The genes whose expression were differentially in HNSCC and normal tissues were explored by the Cancer Genome Atlas database. The ceRNA network was constructed by the Cytoscape software. The lncRNAs which could estimate the overall survival were explored from Cox proportional hazards regression. There are 1997, 589, and 82 mRNAs, lncRNAs, and miRNAs whose expression were statistically significant different, respectively. Then, the network between miRNA and mRNA or miRNA and lncRNA was constructed by miRcode, miRDB, TargetScan, and miRanda. Five mRNAs, 10 lncRNAs, and 3 miRNAs were associated with overall survival. Then, 11-lncRNAs were found to be prognostic factors. Therefore, our research analyzed the potential signature of novel 11-lncRNA as candidate prognostic biomarker from the ceRNA network for patients with HNSCC.
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Affiliation(s)
- Qingyong Xu
- The Department of Radiotherapy Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Hang Yin
- The Department of Radiotherapy Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Haijiao Ao
- The Department of Radiotherapy Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xue Leng
- The Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Mingdong Liu
- The Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yang Liu
- The Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Jianqun Ma
- The Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xiaoyuan Wang
- The Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
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38
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Yu G, Xiong D, Liu Z, Li Y, Chen K, Tang H. Long noncoding RNA LINC00052 inhibits colorectal cancer metastasis by sponging microRNA-574-5p to modulate CALCOCO1 expression. J Cell Biochem 2019; 120:17258-17272. [PMID: 31104316 DOI: 10.1002/jcb.28988] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Abstract
The dysregulation of long-chain noncoding ribonucleic acid (lncRNA) is a common phenomenon in many human cancers. Some studies on the biological function of long intergenic non-protein-coding RNA 52 (LINC00052) in cancer indicate that this gene can act as either oncogene or tumor suppressor in some kinds of cancers, such as breast cancer, gastric cancer, liver cancer, and lung cancer. However, the biological function of LINC00052 in colorectal cancer (CRC) has not been studied. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and Western blot (WB) techniques were applied to detect the expression levels of LINC00052, miR-574-5p, and calcium-binding and coiled-coil domain 1 (CALCOCO1) in CRC cells and tissues. We authenticated the biological function of LINC00052 and miR-574-5p in CRC, and find some target genes for LINC00052 and miR-574-5p via bioinformatics methods. Dual-luciferase reporter gene assay was performed to identify the interaction between LINC00052 and miR-574-5p or CALCOCO1 and miR-574-5p. The results demonstrated that LINC00052 was downregulated in CRC tissues compared with their adjacent tissues. And LINC00052 could suppress CRC cells metastasis both in vivo and in vitro. Beyond that, miR-574-5p was upregulated in CRC tissues, and as an oncogene, it accelerated CRC cell migration and invasion. More importantly, the results of our research demonstrated that LINC00052 could regulate the expression of CALCOCO1 via sponging miR-574-5p in CRC. Overall, our study illuminated the lncRNA-miRNA functional networks in CRC, and these results might provide a new research direction for the diagnosis and treatment of CRC.
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Affiliation(s)
- Gangfeng Yu
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dongmei Xiong
- Nursing Department, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Zhengshu Liu
- Department of Physical Examination, he First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongguo Li
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Ke Chen
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hua Tang
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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39
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Collina F, Aquino G, Brogna M, Cipolletta S, Buonfanti G, De Laurentiis M, Di Bonito M, Cantile M, Botti G. LncRNA HOTAIR up-regulation is strongly related with lymph nodes metastasis and LAR subtype of Triple Negative Breast Cancer. J Cancer 2019; 10:2018-2024. [PMID: 31205562 PMCID: PMC6548158 DOI: 10.7150/jca.29670] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/05/2019] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancers (TNBCs) represent a heterogeneous disease characterized by several molecular subtypes with different prognoses and responses to therapy. For a correct clinical management of TNBC patients the knowledge of the gene regulation mechanisms related to tumor progression and drug response has become fundamental. LncRNAs regulate gene expression through various processes, including chromatin modification, transcription and post-transcription and they are emerging as important cancer biomarkers being involved in tumor pathogenesis, metastatic progression and drug resistance. In this study we aimed to analyze the expression of the lncRNA HOTAIR, mainly involved in breast cancer disease, in a large case series of TNBC patients. We used ISH methods by a RNA probe to better define its staining in tumor tissues and its relation with clinical-pathological parameters and outcomes of patients. Our results show that high HOTAIR expression in tumor tissues is strongly correlated with lymph nodes metastasis (LNM) (p=0.039), as reported also for other tumor types, and has a direct strong association with Androgen Receptor (AR) expression (p= 0.019). These data confirm the prognostic role of HOTAIR in TNBC, and, its involvement in the regulation of AR pathway, suggests the possibility to establish new therapeutic strategies for AR+TNBC patients.
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Affiliation(s)
- Francesca Collina
- Pathology Unit, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
| | - Gabriella Aquino
- Pathology Unit, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
| | - Marianna Brogna
- Università degli Studi di Napoli "Federico II", Naples, Italy
| | | | | | - Michelino De Laurentiis
- Department of Breast Surgery and Cancer Prevention, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
| | - Maurizio Di Bonito
- Pathology Unit, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
| | - Monica Cantile
- Pathology Unit, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
| | - Gerardo Botti
- Department of Breast Surgery and Cancer Prevention, ISTITUTO NAZIONALE TUMORI-IRCCS-FONDAZIONE G.PASCALE, Naples, ITALY
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40
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Khaled N, Bidet Y. New Insights into the Implication of Epigenetic Alterations in the EMT of Triple Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11040559. [PMID: 31003528 PMCID: PMC6521131 DOI: 10.3390/cancers11040559] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/22/2019] [Accepted: 04/11/2019] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most common cancer and leading cause of cancer death among women worldwide, encompassing a wide heterogeneity of subtypes with different clinical features. During the last two decades, the use of targeted therapies has emerged in clinical research in order to increase treatment efficiency, improve prognosis and reduce recurrence. However, the triple negative breast cancer (TNBC) subtype remains a clinical challenge, with poor prognosis since no therapeutic targets have been identified. This aggressive breast cancer entity lacks expression of oestrogen receptor (ER) and progesterone receptor (PR), and it does not overexpress human epidermal growth factor receptor 2 (HER2). The major reason for TNBC poor prognosis is early therapeutic escape from conventional treatments, leading to aggressive metastatic relapse. Metastases occur after an epithelial-mesenchymal transition EMT of epithelial cells, allowing them to break free from the primary tumour site and to colonize distant organs. Cancer-associated EMT consists not only of acquired migration and invasion ability, but involves complex and comprehensive reprogramming, including changes in metabolism, expression levels and epigenetic. Recently, many studies have considered epigenetic alterations as the primary initiator of cancer development and metastasis. This review builds a picture of the epigenetic modifications implicated in the EMT of breast cancer. It focuses on TNBC and allows comparisons with other subtypes. It emphasizes the role of the main epigenetic modifications lncRNAs, miRNAs, histone and DNA- modifications in tumour invasion and appearance of metastases. These epigenetic alterations can be considered biomarkers representing potential diagnostic and prognostic factors in order to define a global metastatic signature for TNBC.
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Affiliation(s)
| | - Yannick Bidet
- Laboratoire d'Oncologie Moléculaire, Centre Jean PERRIN et IMoST, UMR 1240, Inserm/Université Clermont Auvergne 58 rue Montalembert, 63000 Clermont-Ferrand, France.
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41
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Jeong G, Kwon DH, Shin S, Choe N, Ryu J, Lim YH, Kim J, Park WJ, Kook H, Kim YK. Long noncoding RNAs in vascular smooth muscle cells regulate vascular calcification. Sci Rep 2019; 9:5848. [PMID: 30971745 PMCID: PMC6458154 DOI: 10.1038/s41598-019-42283-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/27/2019] [Indexed: 01/10/2023] Open
Abstract
Vascular calcification is characterized by the accumulation of hydroxyapatite crystals, which is a result of aberrant mineral metabolism. Although many clinical studies have reported its adverse effects on cardiovascular morbidity, the molecular mechanism of vascular calcification, especially the involvement of long noncoding RNAs (lncRNAs), is not yet reported. From the transcriptomic analysis, we discovered hundreds of lncRNAs differentially expressed in rat vascular smooth muscle cells (VSMCs) treated with inorganic phosphate, which mimics vascular calcification. We focused on Lrrc75a-as1 and elucidated its transcript structure and confirmed its cytoplasmic localization. Our results showed that calcium deposition was elevated after knockdown of Lrrc75a-as1, while its overexpression inhibited calcium accumulation in A10 cells. In addition, Lrrc75a-as1 attenuated VSMCs calcification by decreasing the expression of osteoblast-related factors. These findings suggest that Lrrc75a-as1 acts as a negative regulator of vascular calcification, and may serve as a possible therapeutic target in vascular calcification.
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Affiliation(s)
- Geon Jeong
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biochemistry, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.,Center for Creative Biomedical Scientists, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Duk-Hwa Kwon
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Sera Shin
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Nakwon Choe
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Juhee Ryu
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biochemistry, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.,Center for Creative Biomedical Scientists, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.,Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Yeong-Hwan Lim
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Department of Biochemistry, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.,Center for Creative Biomedical Scientists, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea
| | - Jaetaek Kim
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Republic of Korea
| | - Woo Jin Park
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.,College of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyun Kook
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea. .,Center for Creative Biomedical Scientists, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea. .,Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.
| | - Young-Kook Kim
- Basic Research Laboratory for Cardiac Remodeling Research Laboratory, Chonnam National University Medical School, Jeollanam-do, Republic of Korea. .,Department of Biochemistry, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea. .,Center for Creative Biomedical Scientists, Chonnam National University Medical School, Hwasun, Jeollanam-do, 58128, Republic of Korea.
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42
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Chatterjee M, Sengupta S. Emerging roles of long non-coding RNAs in cancer. J Biosci 2019; 44:22. [PMID: 30837373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cancer is a physiological condition that has both the endogenous and exogenous influences on its progression. It originates from unusual cell growth, where the cells undergo massive genetic alterations, bypass the signaling machinery and compromise its genetic cohesion. Literature has well narrated the DNA damage studies including driver mutations that interfere with the treatment strategies. However, with evolving medical excellence, recent day studies are trying to unveil the contribution of RNAs in the progression of tumor malignancies. A number of non-coding RNAs have been identified as an active component in cancer genomics. This article aims to review the role of long non-coding RNAs in the spectra of cancers and its prognostic value as the biomarkers in molecular targeting with clinical utility and therapeutic beneficence.
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Affiliation(s)
- Manjima Chatterjee
- School of BioSciences and Technology, VIT University, Vellore 632 014, India
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43
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Youness RA, Gad MZ. Long non-coding RNAs: Functional regulatory players in breast cancer. Noncoding RNA Res 2019; 4:36-44. [PMID: 30891536 PMCID: PMC6404363 DOI: 10.1016/j.ncrna.2019.01.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/24/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Historically, the long-held protein-centered bias has denoted 98% of the human genome as 'Junk' DNA. However, the current work has shifted the perception of such 'junk' transcriptional products to functional regulatory molecules. The recent surveillance of the human transcriptome has highlighted the pivotal role of such non-coding RNA (ncRNA) molecules in diverse physiological and pathological conditions. Long non-coding RNA (lncRNA) is a recent class of ncRNA molecules that is still in its infancy stage. The main focus of this review is to unravel the importance of lncRNAs in the most prevalent malignancy among females which is Breast Cancer (BC). A specific focus on lncRNAs as prognostic markers among BC patients showing molecular subtype heterogeneity was also tackled in this review. Finally, the functional and the mechanistic roles of such booming ncRNA molecules in shaping the fate of the BC progression have been highlighted.
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Affiliation(s)
- Rana Ahmed Youness
- Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, New Cairo City, Main Entrance Al Tagamoa Al Khames, 11835, Cairo, Egypt
| | - Mohamed Zakaria Gad
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, New Cairo City, Main Entrance Al Tagamoa Al Khames, 11835, Cairo, Egypt
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44
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Zheng Y, Xu Q, Liu M, Hu H, Xie Y, Zuo Z, Ren J. lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays. Cancer Res 2019; 79:2076-2083. [PMID: 30786995 DOI: 10.1158/0008-5472.can-18-2169] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/05/2018] [Accepted: 02/15/2019] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) have emerged as promising biomarkers in cancer diagnosis, treatment, and prognosis. Recent studies suggest that a large number of coding gene expression microarray probes could be reannotated as lncRNAs. Microarray, once the most cutting-edge high-throughput gene expression technology, has been used for thousands of cancer studies and has brought invaluable resources for studying the functions of lncRNA in cancer development. However, a comprehensive lncRNA resource based on microarray data is still lacking. Here, we present lnCAR (lncRNAs from cancer arrays), a comprehensive open resource for providing expression profiles and prognostic landscape of lncRNAs derived from reannotation of public microarray data. Currently, lnCAR contains 52,300 samples for differential expression analysis and 12,883 samples for survival analysis from 10 cancer types. lnCAR allows users to interactively explore any annotated or novel lncRNAs. We believe lnCAR will serve as a valuable resource for the community focused on lncRNA research in cancer. SIGNIFICANCE: lnCAR, a new interactive tool of reannotated public cancer-related microarray data, provides expression profiles and prognostic landscapes of lncRNAs across thousands of samples and multiple cancer types.
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Affiliation(s)
- Yueyuan Zheng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingxian Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Mengni Liu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huanjing Hu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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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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Wu Y, Zhang J, Wang M, Yang L, Wang Y, Hu T, Liu A, Cheng Q, Fu Z, Zhang P, Cao L. Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects. J Cell Physiol 2019; 234:13544-13556. [PMID: 30635921 DOI: 10.1002/jcp.28033] [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: 05/26/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.
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Affiliation(s)
- Yun Wu
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Mei Wang
- Department of Pathology, Nanjing Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Yang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yongmei Wang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tao Hu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - An Liu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Qing Cheng
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Ziyi Fu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pingyang Zhang
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Cao
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
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Li RH, Chen M, Liu J, Shao CC, Guo CP, Wei XL, Li YC, Huang WH, Zhang GJ. Long noncoding RNA ATB promotes the epithelial-mesenchymal transition by upregulating the miR-200c/Twist1 axe and predicts poor prognosis in breast cancer. Cell Death Dis 2018; 9:1171. [PMID: 30518916 PMCID: PMC6281614 DOI: 10.1038/s41419-018-1210-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 02/05/2023]
Abstract
Recent studies indicate that the long noncoding RNA ATB (lncATB) can induce the epithelial−mesenchymal transition (EMT) in cancer cells, but the specific cellular targets of lncATB require further investigation. In the present study, the upregulation of lncATB in breast cancer cells was validated in a TGF-β-induced EMT model. Gain- and loss-of-function studies demonstrated that lncATB enhanced cell migration, invasion and clonogenicity in vitro and in vivo. LncATB promoted the EMT by acting as a sponge for the miR-200 family and restoring Twist1 expression. Subsequently, the clinical significance of lncATB was investigated in a cohort of breast cancer patients (N = 131). Higher lncATB expression was correlated with increased nodal metastasis (P = 0.036) and advanced clinical stage (P = 0.011) as well as shorter disease-free survival (P = 0.043) and overall survival (P = 0.046). These findings define Twist1 as a major target of lncATB in the induction of the EMT and highlight lncATB as a biomarker in breast cancer patients.
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Affiliation(s)
- Rong-Hui Li
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Min Chen
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China.,The Cancer Center, Xiang'an Hospital of Xiamen University, 2000 East Xiang'an Rd., Xiang'an, Xiamen, China
| | - Jing Liu
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Chang-Chun Shao
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Cui-Ping Guo
- The Breast Center, The Cancer Hospital of SUMC, 515041, Shantou, Guangdong, China
| | - Xiao-Long Wei
- Department of Pathology, The Cancer Hospital of SUMC, Shantou, Guangdong, China
| | - Yao-Chen Li
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Wen-He Huang
- The Breast Center, The Cancer Hospital of SUMC, 515041, Shantou, Guangdong, China
| | - Guo-Jun Zhang
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China. .,The Cancer Center, Xiang'an Hospital of Xiamen University, 2000 East Xiang'an Rd., Xiang'an, Xiamen, China.
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Zhang Y, Zhang H, Kang H, Huo W, Zhou Y, Zhang Y. Knockdown of long non-coding RNA HOST2 inhibits the proliferation of triple negative breast cancer via regulation of the let-7b/CDK6 axis. Int J Mol Med 2018; 43:1049-1057. [PMID: 30483747 DOI: 10.3892/ijmm.2018.3995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/06/2018] [Indexed: 11/05/2022] Open
Abstract
The upregulation of long non‑coding RNA (lncRNA) human ovarian cancer‑specific transcript 2 (HOST2) has been identified in breast cancer. The present study aimed to investigate whether lncRNA HOST2 regulated the proliferation of triple negative breast cancer (TNBC) cells, and the underlying molecular mechanism. In total, 30 patients with primary TNBC, who were treated at Wuhai People's Hospital (Wuhai, China), were recruited for the present study. Reverse transcription‑quantitative polymerase chain reaction analysis was used for the examination of gene expression levels. A Cell Counting kit‑8 (CCK‑8) assay was used for the detection of cell proliferation. Phases of the cell cycle were evaluated by flow cytometry. Western blot analysis was performed to detect protein expression levels. A dual luciferase activity assay was performed to examine the interaction between microRNA (miRNA) and the 3' untranslated region (UTR) of target mRNA. The results revealed increased expression levels of HOST2 in tumor tissues from patients with TNBC. A positive correlation was identified between the expression of HOST2 and cyclin‑dependent kinase 6 (CDK6) in tumor tissues. The silencing of HOST2 induced cell proliferation inhibition and cell cycle redistribution in MDA‑MB‑231 and MDA‑MB‑468 TNBC cells. In these two cell lines, HOST2 silencing caused a decrease in the phosphorylation of RB1 and CDK6, which was observed at the mRNA and protein levels. However, the silencing of CDK6 did not alter the expression of HOST2. It was hypothesized and confirmed that let‑7b, a previously reported target miRNA of HOST2, was able to directly bind to the 3'UTR of CDK6 and repress its expression. The expression of let‑7b was negatively correlated with the expression of HOST2 and CDK6 in tumor tissues. Overall, the data suggested that lncRNA HOST2 acts as an oncogene in TNBC via the upregulation of CDK6.
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Affiliation(s)
- Yuedong Zhang
- Department of Oncology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
| | - Hongwei Zhang
- Department of Oncology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
| | - Huiqing Kang
- Department of Pathology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
| | - Wenjie Huo
- Department of Oncology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
| | - Yu Zhou
- Department of Oncology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
| | - Yuchao Zhang
- Department of Oncology, Wuhai People's Hospital, Wuhai, Inner Mongolia Autonomous Region 016000, P.R. China
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Panoutsopoulou K, Avgeris M, Scorilas A. miRNA and long non-coding RNA: molecular function and clinical value in breast and ovarian cancers. Expert Rev Mol Diagn 2018; 18:963-979. [DOI: 10.1080/14737159.2018.1538794] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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