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Hussain MS, Majami AA, Ali H, Gupta G, Almalki WH, Alzarea SI, Kazmi I, Syed RU, Khalifa NE, Bin Break MK, Khan R, Altwaijry N, Sharma R. The complex role of MEG3: An emerging long non-coding RNA in breast cancer. Pathol Res Pract 2023; 251:154850. [PMID: 37839358 DOI: 10.1016/j.prp.2023.154850] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
MEG3, a significant long non-coding RNA (lncRNA), substantially functions in diverse biological processes, particularly breast cancer (BC) development. Within the imprinting DLK-MEG3 region on human chromosomal region 14q32.3, MEG3 spans 35 kb and encompasses ten exons. It exerts regulatory effects through intricate interactions with miRNAs, proteins, and epigenetic modifications. MEG3's multifaceted function in BC is evident in gene expression modulation, osteogenic tissue differentiation, and involvement in bone-related conditions. Its role as a tumor suppressor is highlighted by its influence on miR-182 and miRNA-29 expression in BC. Additionally, MEG3 is implicated in acute myocardial infarction and endothelial cell function, emphasising cell-specific regulatory mechanisms. MEG3's impact on gene activity encompasses transcriptional and post-translational adjustments, including DNA methylation, histone modifications, and interactions with transcription factors. MEG3 dysregulation is linked to unfavourable outcomes and drug resistance. Notably, higher MEG3 expression is associated with enhanced survival in BC patients. Overcoming challenges such as unravelling context-specific interactions, understanding epigenetic control, and translating findings into clinical applications is imperative. Prospective endeavours involve elucidating underlying mechanisms, exploring epigenetic alterations, and advancing MEG3-based diagnostic and therapeutic approaches. A comprehensive investigation into broader signaling networks and rigorous clinical trials are pivotal. Rigorous validation through functional and molecular analyses will shed light on MEG3's intricate contribution to BC progression.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan.
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, 302017, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, 11115, Sudan
| | - Mohammed Khaled Bin Break
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Ruqaiyah Khan
- Department of Basic Health Sciences, Deanship of Preparatory Year for the Health Colleges, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint, Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Rahul Sharma
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
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2
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Baljon KJ, Ramaiah P, Saleh EAM, Al-Dolaimy F, Al-Dami FH, Gandla K, Alkhafaji AT, Abbas AHR, Alsaalamy AH, Bisht YS. LncRNA PVT1: as a therapeutic target for breast cancer. Pathol Res Pract 2023; 248:154675. [PMID: 37531833 DOI: 10.1016/j.prp.2023.154675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
A significant number of women are identified with breast cancer (BC) every year, making it among the most prevalent malignancies and one of the leading causes of mortality globally. Despite significant progress in understanding BC pathogenesis and treatment options, there is still a need to identify new therapeutic targets and develop more effective treatments. LncRNAs have been discovered as biomarkers and a promising target for various cancers, including BC. PVT1 is a particular one of these lncRNAs, and research has indicated that it has a significant impact on the appearance and progression of BC.PVT1 is an attractive therapeutic target for BC due to its role in promoting cancer cell growth, metastasis and invasion. In addition to its potential as a treatment strategy, PVT1 may also have diagnostic value in BC. In this article, we will discuss targeting PVT1 as a treatment strategy for BC.
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Affiliation(s)
| | | | - Ebraheem Abdu Musad Saleh
- Department of Chemistry,College of Arts and Science, Prince Sattam Bin Abdulaziz University, Wadi Al-Dawasir 11991, Saudi Arabia.
| | | | - Farqad Hassan Al-Dami
- Department of Medical Laboratory Techniques, Altoosi University College, Najaf, Iraq
| | - Kumaraswamy Gandla
- Department of Pharmaceutical Analysis, Chaitanya Deemed to be University, Hanamkonda, India.
| | | | - Ahmed Hussien R Abbas
- College of technical engineering, the Islamic University, Najaf, Iraq; College of technical engineering, the Islamic University of Al Diwaniyah, Iraq; College of technical engineering, the Islamic University of Babylon, Iraq
| | - Ali Hashiem Alsaalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Yashwant Singh Bisht
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun 248007, India
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3
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Sanders LM, Chandra R, Zebarjadi N, Beale HC, Lyle AG, Rodriguez A, Kephart ET, Pfeil J, Cheney A, Learned K, Currie R, Gitlin L, Vengerov D, Haussler D, Salama SR, Vaske OM. Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors. Commun Biol 2022; 5:1367. [PMID: 36513728 PMCID: PMC9747808 DOI: 10.1038/s42003-022-04075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and to identify biomarkers of response to therapeutic agents. Advances in genomic sequencing have made possible large-scale genomic characterizations of collections of cancer cell lines and primary tumors, such as the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA). These studies allow for the first time a comprehensive evaluation of the comparability of cancer cell lines and primary tumors on the genomic and proteomic level. Here we employ bulk mRNA and micro-RNA sequencing data from thousands of samples in CCLE and TCGA, and proteomic data from partner studies in the MD Anderson Cell Line Project (MCLP) and The Cancer Proteome Atlas (TCPA), to characterize the extent to which cancer cell lines recapitulate tumors. We identify dysregulation of a long non-coding RNA and microRNA regulatory network in cancer cell lines, associated with differential expression between cell lines and primary tumors in four key cancer driver pathways: KRAS signaling, NFKB signaling, IL2/STAT5 signaling and TP53 signaling. Our results emphasize the necessity for careful interpretation of cancer cell line experiments, particularly with respect to therapeutic treatments targeting these important cancer pathways.
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Affiliation(s)
- Lauren M. Sanders
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Rahul Chandra
- grid.34477.330000000122986657Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA USA
| | - Navid Zebarjadi
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Holly C. Beale
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - A. Geoffrey Lyle
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Analiz Rodriguez
- grid.241054.60000 0004 4687 1637Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Ellen Towle Kephart
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Jacob Pfeil
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Allison Cheney
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Katrina Learned
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Rob Currie
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Leonid Gitlin
- grid.266102.10000 0001 2297 6811Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California USA
| | - David Vengerov
- grid.419799.b0000 0004 4662 4679Oracle Labs, Oracle Corporation, Pleasanton, CA USA
| | - David Haussler
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Sofie R. Salama
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA USA
| | - Olena M. Vaske
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
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4
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Wang Q, Feng J, Tang L. Non-Coding RNA Related to MAPK Signaling Pathway in Liver Cancer. Int J Mol Sci 2022; 23:ijms231911908. [PMID: 36233210 PMCID: PMC9570382 DOI: 10.3390/ijms231911908] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The advancement in high-throughput sequencing analysis and the evaluation of chromatin state maps have revealed that eukaryotic cells produce many non-coding transcripts/RNAs. Further, a strong association was observed between some non-coding RNAs and cancer development. The mitogen-activated protein kinases (MAPK) belong to the serine–threonine kinase family and are the primary signaling pathways involved in cell proliferation from the cell surface to the nucleus. They play an important role in various human diseases. A few non-coding RNAs associated with the MAPK signaling pathway play a significant role in the development of several malignancies, including liver cancer. In this review, we summarize the molecular mechanisms and interactions of microRNA, lncRNA, and other non-coding RNAs in the development of liver cancer that are associated with the MAPK signaling pathway. Further, we briefly discuss the therapeutic strategies for liver cancer related to ncRNA and the MAPK signaling pathway.
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Affiliation(s)
- Qiuxia Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Laboratory of Anesthesiology, Southwest Medical University, Luzhou 646000, China
- Correspondence: (J.F.); (L.T.); Tel.: +86-1399-605-1730 (L.T.)
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Correspondence: (J.F.); (L.T.); Tel.: +86-1399-605-1730 (L.T.)
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5
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Jorgensen MM, de la Puente P. Leukemia Inhibitory Factor: An Important Cytokine in Pathologies and Cancer. Biomolecules 2022; 12:biom12020217. [PMID: 35204717 PMCID: PMC8961628 DOI: 10.3390/biom12020217] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Leukemia Inhibitory Factor (LIF) is a member of the IL-6 cytokine family and is expressed in almost every tissue type within the body. Although LIF was named for its ability to induce differentiation of myeloid leukemia cells, studies of LIF in additional diseases and solid tumor types have shown that it has the potential to contribute to many other pathologies. Exploring the roles of LIF in normal physiology and non-cancer pathologies can give important insights into how it may be dysregulated within cancers, and the possible effects of this dysregulation. Within various cancer types, LIF expression has been linked to hallmarks of cancer, such as proliferation, metastasis, and chemoresistance, as well as overall patient survival. The mechanisms behind these effects of LIF are not well understood and can differ between different tissue types. In fact, research has shown that while LIF may promote malignancy progression in some solid tumors, it can have anti-neoplastic effects in others. This review will summarize current knowledge of how LIF expression impacts cellular function and dysfunction to help reveal new adjuvant treatment options for cancer patients, while also revealing potential adverse effects of treatments targeting LIF signaling.
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Affiliation(s)
- Megan M Jorgensen
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, SD 57104, USA
- MD/PhD Program, University of South Dakota Sanford School of Medicine, Sioux Falls, SD 57105, USA
| | - Pilar de la Puente
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, SD 57104, USA
- Department of Surgery, University of South Dakota Sanford School of Medicine, Sioux Falls, SD 57105, USA
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6
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Long Noncoding RNA LIFR-AS1: A New Player in Human Cancers. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1590815. [PMID: 35071590 PMCID: PMC8776453 DOI: 10.1155/2022/1590815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/16/2021] [Accepted: 12/24/2021] [Indexed: 12/23/2022]
Abstract
Emerging evidence has indicated that aberrantly expressed long noncoding RNAs (lncRNAs) play a vital role in various biological processes associated with tumorigenesis. Leukemia inhibitory factor receptor antisense RNA1 (LIFR-AS1) is a recently identified lncRNA transcribed in an antisense manner from the LIFR gene located on human chromosome 5p13.1. LIFR-AS1 regulates tumor proliferation, migration, invasion, apoptosis, and drug resistance through different mechanisms. Its expression level is related to the clinicopathological characteristics of tumors and plays a key role in tumor occurrence and development. In this review, we summarize the role of LIFR-AS1 in the development and progression of different cancers and highlight the potential for LIFR-AS1 to serve as a biomarker and therapeutic target for a variety of human cancers.
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7
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Chen JQ, Tao YP, Hong YG, Li HF, Huang ZP, Xu XF, Zheng H, Hu LK. M 6A-mediated up-regulation of LncRNA LIFR-AS1 enhances the progression of pancreatic cancer via miRNA-150-5p/ VEGFA/Akt signaling. Cell Cycle 2021; 20:2507-2518. [PMID: 34658294 DOI: 10.1080/15384101.2021.1991122] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A) modification, the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing. There is extensive evidence indicating that long non-coding RNAs (lncRNAs) serve as key regulators of oncogenesis and tumor progression in humans. Through prior study has assessed that LIFR-AS1 plays a key role in various kinds of malignant tumors. However, the exact role of m6A induced LIFR-AS1 in pancreatic cancer (PC) and its potential molecular mechanisms remain largely unknown. In this study, we determined that PC cell lines and tumors exhibit increased LIFR-AS1 expression that correlates with larger tumor size, lymph node metastasis, and more advanced TNM stage. Functionally, loss-of-function studies indicated that LIFR-AS1 knockdown decreased the proliferation, migration, and invasion of PC cells in vitro. Mechanistically, we found that METTL3 induced m6A hyper-methylation on the 3' UTR of LIFR-AS1 to enhance its mRNA stability and LIFR-AS1 could directly interact with miR-150-5p, thereby indirectly up-regulating VEGFA expressions within cells. Through rescue experiments, we were able to confirm that the unfavorable impact of LIFR-AS1 knockdown on VEGFA /PI3K/Akt Signaling could be reversed via the inhibition of miR-150-5p expression. Together, these findings indicate that a noval m6A-LIFR-AS1 axis promotes PC progression at least in part via regulation of the miR-150-5p/VEGFA axis, indicating that this regulatory axis may be a viable clinical target for the treatment of PC.
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Affiliation(s)
- Jian-Qing Chen
- Department of Digestive Internal, Yangpu Shidong Hospital, Anhui Medical University, Shanghai, China
| | - Yuan-Ping Tao
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Yong-Gang Hong
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Hui-Fen Li
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-Ping Huang
- Department of Hepatobiliary Surgery, General Hospital of Southern Theatre Command, Guangzhou, China
| | - Xuan-Fu Xu
- Department of Digestive Internal, Yangpu Shidong Hospital, Anhui Medical University, Shanghai, China
| | - Hao Zheng
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.,Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Liang-Kai Hu
- Department of Digestive Internal, Yangpu Shidong Hospital, Anhui Medical University, Shanghai, China
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8
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Dastmalchi N, Safaralizadeh R, Latifi-Navid S, Banan Khojasteh SM, Mahmud Hussen B, Teimourian S. An updated review of the role of lncRNAs and their contribution in various molecular subtypes of breast cancer. Expert Rev Mol Diagn 2021; 21:1025-1036. [PMID: 34334086 DOI: 10.1080/14737159.2021.1962707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Breast cancer (BC) is the most significant threat to women's life. To demonstrate its molecular mechanisms, which results in BC progression, it is crucial to develop approaches to enhance prognosis and survival in BC cases.Areas covered: In the current study, we aimed to highlight the updated data on the oncogenic and tumor suppressive roles of lncRNAs in the progression of various subtypes of BC by specifically putting importance on the functional characteristics, modulatory agents, therapeutic potential, future perspectives and challenges of lncRNAs in BC. We reviewed recent studies published between 2019 and 2020.Expert opinion: The latest investigations have demonstrated that the long non-coding RNAs (lncRNAs) participate in different BC molecular subtypes via different molecular mechanisms; however, the exact functional information of the lncRNAs has yet to be elucidated. The studied lncRNAs could be more applicable as therapeutic targets in BC treatment after pre-clinical and clinical studies.
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Affiliation(s)
- Narges Dastmalchi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | | | - Bashdar Mahmud Hussen
- Pharmacognosy Department, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Shahram Teimourian
- Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran
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9
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Li S, Wang C, Lu Y, Li W. Long non-coding RNA LIFR-AS1 regulates the proliferation, migration and invasion of human thyroid cancer cells. 3 Biotech 2021; 11:187. [PMID: 33927978 PMCID: PMC7985231 DOI: 10.1007/s13205-021-02739-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/12/2021] [Indexed: 10/21/2022] Open
Abstract
The long non-coding RNA (lncRNA) LIFR-AS1 has been shown to be involved in the development of several human cancers. This study was designed to determine the expression profile and role of lncRNA-LIFR-AS1 in human thyroid cancer. The results showed significant (p < 0.05) upregulation of LncRNA-LIFR-AS1 in thyroid cancer tissues and cells. However, silencing of LncRNA-LIFR-AS1 inhibited the viability and proliferation of human thyroid cancer cells inducing G2/M cell cycle arrest. The G2/M phase cells increased from 8.56% in negative control (NC) to around 35.03% in si-LIFR-AS1. This was also found to be concomitant with the downregulation of cyclin B1 and CDK1 expressions. The thyroid cancer cells exhibited remarkably lower invasion and migration under transcriptional knockdown of lncRNA-LIFR-AS1 which was also associated with downregulation of MMP-2 and MMP-9 expression. Importantly, transcriptional silencing of lncRNA-LIFR-AS1 inhibited thyroid cancer tumorigenesis, in vivo. Collectively, the results suggest the tumor-promoting role of lncRNA-LIFR-AS1 in thyroid cancer and highlight its potential as therapeutic target.
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Affiliation(s)
- Sha Li
- Department of Endocrinology, TangShan GongRen Hospital, No. 27 of Wenhua Road, TangShan, 063000 Hebei China
| | - Chen Wang
- Department of Endocrinology, TangShan GongRen Hospital, No. 27 of Wenhua Road, TangShan, 063000 Hebei China
| | - Yifang Lu
- Department of Endocrinology, TangShan GongRen Hospital, No. 27 of Wenhua Road, TangShan, 063000 Hebei China
| | - Weijuan Li
- Department of Endocrinology, TangShan GongRen Hospital, No. 27 of Wenhua Road, TangShan, 063000 Hebei China
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10
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Zhang H, Yu Y, Wang J, Han Y, Ren T, Huang Y, Chen C, Huang Q, Wang W, Niu J, Lou J, Guo W. Macrophages-derived exosomal lncRNA LIFR-AS1 promotes osteosarcoma cell progression via miR-29a/NFIA axis. Cancer Cell Int 2021; 21:192. [PMID: 33794884 PMCID: PMC8017664 DOI: 10.1186/s12935-021-01893-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Osteosarcoma (OS) is the most common primary malignant bone tumor in young people. Tumor-associated macrophages (TAMs) have been reported to play an important role in the development of osteosarcoma. However, the detailed molecular mechanisms remain largely unknown and need to be elucidated. Recently, exosomes have been reported as the crucial mediator between tumor cells and the tumor microenvironment. And a lot of lncRNAs have been reported to act as either oncogenes or tumor suppressors in osteosarcoma. In this research, we aim to explore the role of macrophages-derived exosomal lncRNA in osteosarcoma development and further elucidated the potential molecular mechanisms involved. Methods TAMs were differentiated from human mononuclear cells THP-1, and a high-throughput microarray assay was used to analyze the dysregulated lncRNAs and miRNAs in osteosarcoma cells co-cultured with macrophages-derived exosomes. Western blot, qRT-PCR assays, and Dual-luciferase reporter assay were used to verify the interaction among LIFR-AS1, miR-29a, and NFIA. Cck-8, EdU, colony formation assay, wound-healing, and transwell assay were performed to explore the characterize the proliferation and metastasis ability of OS cells. And qPCR, Western blots, immunohistochemistry, and cell immunofluorescence were used to detect the expression of relative genes or proteins. Results In this study, we found that THP-1-induced macrophage-derived exosomes could facilitate osteosarcoma cell progression both in vitro and in vivo. Then, the results of the high-throughput microarray assay showed that LIFR-AS1 was highly expressed and miR-29a was lowly expressed. Furthermore, LIFR-AS1 was identified as a miR-29a sponge, and NFIA was validated as a direct target of miR-29a. Functional assays demonstrated that knockdown of exosomal LIFR-AS1 could attenuate the promotion effects of macrophages-derived exosomes on osteosarcoma cell progression and miR-29a inhibition could reserve the effect of LIFR-AS1-knockdown exosomes. Correspondingly, NFIA-knockdown could partially reverse the tumor inhibition effect of miR-29a on osteosarcoma cells. Conclusions Taken together, macrophages-derived exosomal lncRNA LIFR-AS1 can promote osteosarcoma cell proliferation, invasion, and restrain cell apoptosis via miR-29a/NFIA axis, which can act as a potential novel therapeutic target for osteosarcoma therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01893-0.
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Affiliation(s)
- Hongliang Zhang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Yiyang Yu
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Jun Wang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Yu Han
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Tingting Ren
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Yi Huang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Chenglong Chen
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Qingshan Huang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Wei Wang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Jianfang Niu
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Jingbing Lou
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China.,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China
| | - Wei Guo
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Beijing, 100044, People's Republic of China. .,Beijing Key Laboratory of Musculoskeletal Tumor, Beijing, People's Republic of China.
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11
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Zhao J, Li X, Fu L, Zhang N, Yang J, Cai J. lncRNA LIFR‑AS1 inhibits gastric carcinoma cell proliferation, migration and invasion by sponging miR‑4698. Mol Med Rep 2020; 23:153. [PMID: 33355363 PMCID: PMC7789130 DOI: 10.3892/mmr.2020.11792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
The vital functions of long non-coding (lnc)RNAs have been verified in gastric carcinoma (GC). However, as a novel cancer-related lncRNA, the influence of leukemia inhibitory factor receptor antisense RNA 1 (LIFR-AS1) in GC cell biological behaviors remains unreported. The present study explored the biological effects of lncRNA LIFR-AS1 on GC progression. Reverse transcription-quantitative PCR was performed to examine lncRNA LIFR-AS1 expression in GC tissues and cells. Cell Counting Kit-8, 5-ethynyl-2′-deoxyuridine incorporation, cell wound healing and Transwell invasion assays were used to assess the functions of lncRNA LIFR-AS1 in GC cell proliferation, migration and invasion. Additionally, associations among lncRNA LIFR-AS1, microRNA (miR)-4698 and microtubule-associated tumor suppressor 1 (MTUS1) were investigated via bioinformatics software and a luciferase reporter system. In addition, western blotting was used to examine the expression of MEK and ERK. Decreased lncRNA LIFR-AS1 expression was observed in GC tissues and cells. Upregulated lncRNA LIFR-AS1 inhibited GC cell proliferation, migration and invasion. Upregulated miR-4698 and downregulated MTUS1 were identified in GC tissues and cells. The inhibitory interaction between lncRNA LIFR-AS1 and miR-4698 was confirmed. Additionally, MTUS1 was predicted as a target gene of miR-4698 positively regulated by lncRNA LIFR-AS1. The MEK/ERK pathway was inhibited by lncRNA LIFR-AS1 via regulating MTUS1. These findings revealed the inhibitory functions of lncRNA LIFR-AS1 in GC cell proliferation, migration and invasion. The process was mediated via miR-4698, MTUS1 and the MEK/ERK pathway.
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Affiliation(s)
- Jiangqiao Zhao
- Department of Surgery, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Xiaoning Li
- Department of General Surgery, Baoding First Central Hospital, Baoding, Hebei 071000, P.R. China
| | - Liping Fu
- Department of General Surgery, Cangzhou People's Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Na Zhang
- Department of Radiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Jiaping Yang
- Department of General Surgery, Cangzhou People's Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Jianhui Cai
- Department of Surgery, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
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12
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Baek S, Ho YY, Ma Y. Using sufficient direction factor model to analyze latent activities associated with breast cancer survival. Biometrics 2020; 76:1340-1350. [PMID: 31860141 PMCID: PMC7305041 DOI: 10.1111/biom.13208] [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: 03/23/2018] [Revised: 09/20/2019] [Accepted: 12/16/2019] [Indexed: 11/27/2022]
Abstract
High-dimensional gene expression data often exhibit intricate correlation patterns as the result of coordinated genetic regulation. In practice, however, it is difficult to directly measure these coordinated underlying activities. Analysis of breast cancer survival data with gene expressions motivates us to use a two-stage latent factor approach to estimate these unobserved coordinated biological processes. Compared to existing approaches, our proposed procedure has several unique characteristics. In the first stage, an important distinction is that our procedure incorporates prior biological knowledge about gene-pathway membership into the analysis and explicitly model the effects of genetic pathways on the latent factors. Second, to characterize the molecular heterogeneity of breast cancer, our approach provides estimates specific to each cancer subtype. Finally, our proposed framework incorporates sparsity condition due to the fact that genetic networks are often sparse. In the second stage, we investigate the relationship between latent factor activity levels and survival time with censoring using a general dimension reduction model in the survival analysis context. Combining the factor model and sufficient direction model provides an efficient way of analyzing high-dimensional data and reveals some interesting relations in the breast cancer gene expression data.
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Affiliation(s)
- Seungchul Baek
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, Maryland, U.S.A
| | - Yen-Yi Ho
- Department of Statistics, University of South Carolina, Columbia, South Carolina, U.S.A
| | - Yanyuan Ma
- Department of Statistics, Penn State University, University Park, Pennsylvania, U.S.A
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13
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Balomenos P, Dragomir A, Tsakalidis AK, Bezerianos A. Identification of differentially expressed subpathways via a bilevel consensus scoring of network topology and gene expression. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2020:5316-5319. [PMID: 33019184 DOI: 10.1109/embc44109.2020.9176556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Identifying differentially expressed subpathways connected to the emergence of a disease that can be considered as candidates for pharmacological intervention, with minimal off-target effects, is a daunting task. In this direction, we present a bilevel subpathway analysis method to identify differentially expressed subpathways that are connected with an experimental condition, while taking into account potential crosstalks between subpathways which arise due to their connectivity in a combined multi-pathway network. The efficacy of the method is demonstrated on a hematopoietic stem cell aging dataset, with findings corroborated using recent literature.
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14
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Zhang T, Hu H, Yan G, Wu T, Liu S, Chen W, Ning Y, Lu Z. Long Non-Coding RNA and Breast Cancer. Technol Cancer Res Treat 2020; 18:1533033819843889. [PMID: 30983509 PMCID: PMC6466467 DOI: 10.1177/1533033819843889] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Breast cancer, one of the most common diseases among women, is regarded as a
heterogeneous and complicated disease that remains a major public health concern.
Recently, owing to the development of next-generation sequencing technologies, long
non-coding RNAs have received extensive attention. Numerous studies reveal that long
non-coding RNAs are playing important roles in tumor development. Although the biological
function and molecular mechanisms of long non-coding RNAs remain enigmatic, recent
researchers have demonstrated that an array of long non-coding RNAs express abnormally in
cancers, including breast cancer. Herein, we summarized the latest literature about long
non-coding RNAs in breast cancer, with a particular focus on the multiple molecular roles
of regulatory long non-coding RNAs that regulate cell proliferation, invasion, metastasis,
and apoptosis.
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Affiliation(s)
- Tianzhu Zhang
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Hu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ge Yan
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Tangwei Wu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiyi Liu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiqun Chen
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Ning
- 2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhongxin Lu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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15
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Zhang G, Lan Y, Xie A, Shi J, Zhao H, Xu L, Zhu S, Luo T, Zhao T, Xiao Y, Li X. Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements. J Biol Chem 2019; 294:15613-15622. [PMID: 31484726 DOI: 10.1074/jbc.ra119.008732] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/30/2019] [Indexed: 12/28/2022] Open
Abstract
Over the past decade, thousands of long noncoding RNAs (lncRNAs) have been identified, many of which play crucial roles in normal physiology and human disease. LncRNAs can interact with chromatin and then recruit protein complexes to remodel chromatin states, thus regulating gene expression. However, how lncRNA-chromatin interactions contribute to their biological functions is largely unknown. Here, we collected and constructed an atlas of 188,647 lncRNA-chromatin interactions in human and mouse. All lncRNAs showed diverse epigenetic modification patterns at their binding sites, especially the marks of enhancer activity. Functional analysis of lncRNA target genes further revealed that lncRNAs could exert their functions by binding to both promoter and distal regulatory elements, especially the distal regulatory elements. Intriguingly, many important pathways were observed to be widely regulated by lncRNAs through distal binding. For example, NEAT1, a cancer lncRNA, controls 13.3% of genes in the PI3K-AKT signaling pathway by interacting with distal regulatory elements. In addition, "two-gene" signatures composed of a lncRNA and its distal target genes, such as HOTAIR-CRIM1, provided significant clinical benefits relative to the lncRNA alone. In summary, our findings underscored that lncRNA-distal interactions were essential for lncRNA functions, which would provide new clues to understand the molecular mechanisms of lncRNAs in complex disease.
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Affiliation(s)
- Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jian Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Shiwei Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tingting Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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16
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Xu Y, Lin S, Zhao H, Wang J, Zhang C, Dong Q, Hu C, Desi S, Wang L, Xu Y. Quantifying Risk Pathway Crosstalk Mediated by miRNA to Screen Precision drugs for Breast Cancer Patients. Genes (Basel) 2019; 10:E657. [PMID: 31466383 PMCID: PMC6770221 DOI: 10.3390/genes10090657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer has become the most common cancer that leads to women's death. Breast cancer is a complex, highly heterogeneous disease classified into various subtypes based on histological features, which determines the therapeutic options. System identification of effective drugs for each subtype remains challenging. In this work, we present a computational network biology approach to screen precision drugs for different breast cancer subtypes by considering the impact intensity of candidate drugs on the pathway crosstalk mediated by miRNAs. Firstly, we constructed and analyzed the subtype-specific risk pathway crosstalk networks mediated by miRNAs. Then, we evaluated 36 Food and Drug Administration (FDA)-approved anticancer drugs by quantifying their effects on these subtype-specific pathway crosstalk networks and combining with survival analysis. Finally, some first-line treatments of breast cancer, such as Paclitaxel and Vincristine, were optimized for each subtype. In particular, we performed precision screening of subtype-specific therapeutic drugs and also confirmed some novel drugs suitable for breast cancer treatment. For example, Sorafenib was applicable for the basal subtype treatment, Irinotecan was optimum for Her2 subtype treatment, Vemurafenib was suitable for the LumA subtype treatment, and Vorinostat could apply to LumB subtype treatment. In addition, the mechanism of these optimal therapeutic drugs in each subtype of breast cancer was further dissected. In summary, our study offers an effective way to screen precision drugs for various breast cancer subtype treatments. We also dissected the mechanism of optimal therapeutic drugs, which may provide novel insight into the precise treatment of cancer and promote researches on the mechanisms of action of drugs.
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Affiliation(s)
- Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shuting Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qun Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shang Desi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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17
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LIFR-AS1 modulates Sufu to inhibit cell proliferation and migration by miR-197-3p in breast cancer. Biosci Rep 2019; 39:BSR20180551. [PMID: 31127025 PMCID: PMC6614576 DOI: 10.1042/bsr20180551] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/16/2019] [Accepted: 05/09/2019] [Indexed: 11/17/2022] Open
Abstract
Numerous evidence has recently demonstrated that long non-coding RNAs (lncRNAs) play vital roles in the oncogenesis and development of a wide range of human neoplasms. Leukemia inhibitory factor receptor antisense RNA 1 (LIFR-AS1), a novel cancer-related lncRNA, has been reported to be under-expressed in breast cancer and associated with poor prognosis. However, the exact role of LIFR-AS1 in breast cancer remains largely unclear. The present study aimed to investigate the biological role of LIFR-AS1 in breast cancer and clarify the potential molecular mechanisms. In the present study, we found that LIFR-AS1 was significantly down-regulated in both tissues and cell lines. Furthermore, over-expression of LIFR-AS1 inhibited breast cancer cell proliferation, colony formation, migration and invasion, whereas knockdown of LIFR-AS1 promoted breast cancer cell proliferation, colony formation, migration and invasion. Moreover, LIFR-AS1 was observed to up-regulate suppressor of fused gene (Sufu) expression by competitively binding to miR-197-3p in breast cancer cells. Notably, miR-197-3p inhibitor reversed the promoting effects of LIFR-AS1 knockdown on breast cancer cell proliferation, colony formation, migration and invasion. Additionally, LIFR-AS1 knockdown promoted tumor growth in vivo. To sum up, our results imply the tumor-suppressing role of LIFR-AS1 in breast cancer.
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18
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Zhang Q, Liu W, Liu C, Lin SY, Guo AY. SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data. Brief Bioinform 2019; 19:1325-1336. [PMID: 28981576 DOI: 10.1093/bib/bbx074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/20/2022] Open
Abstract
Different tissues and diseases have distinct transcriptional profilings with specifically expressed genes (SEGs). So, the identification of SEGs is an important issue in the studies of gene function, biological development, disease mechanism and biomarker discovery. However, few accurate and easy-to-use tools are available for RNA sequencing (RNA-seq) data to detect SEGs. Here, we presented SEGtool, a tool based on fuzzy c-means, Jaccard index and greedy annealing method for SEG detection automatically and self-adaptively ignoring data distribution. Testing result showed that our SEGtool outperforms the existing tools, which was mainly developed for microarray data. By applying SEGtool to Genotype-Tissue Expression (GTEx) human tissue data set, we detected 3181 SEGs with tissue-related functions. Regulatory networks reveal tissue-specific transcription factors regulating many SEGs, such as ETV2 in testis, HNF4A in liver and NEUROD1 in brain. Applied to a case study of single-cell sequencing (SCS) data from embryo cells, we identified many SEGs in specific stages of human embryogenesis. Notably, SEGtool is suitable for RNA-seq data and even SCS data with high specificity and accuracy. An implementation of SEGtool R package is freely available at http://bioinfo.life.hust.edu.cn/SEGtool/.
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Affiliation(s)
- Qiong Zhang
- Huazhong University of Science and Technology, China
| | - Wei Liu
- Huazhong University of Science and Technology, China
| | - Chunjie Liu
- Huazhong University of Science and Technology, China
| | - Sheng-Yan Lin
- Huazhong University of Science and Technology, China
| | - An-Yuan Guo
- Huazhong University of Science and Technology, China
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19
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Zhu Y, Yang L, Chong QY, Yan H, Zhang W, Qian W, Tan S, Wu Z, Lobie PE, Zhu T. Long noncoding RNA Linc00460 promotes breast cancer progression by regulating the miR-489-5p/FGF7/AKT axis. Cancer Manag Res 2019; 11:5983-6001. [PMID: 31308741 PMCID: PMC6612969 DOI: 10.2147/cmar.s207084] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/27/2019] [Indexed: 01/14/2023] Open
Abstract
Purpose: Evidence indicates that long noncoding RNAs (lncRNA) possess important roles in various cellular processes and that dysregulation of lncRNAs promotes tumor progression. However, the expression patterns and biological functions of many specific lncRNAs in breast cancer remain to be determined. Methods: Quantitative real-time polymerase chain reaction was performed to detect Linc00460, miR-489-5p and FGF7 expression. Protein levels were determined using Western blot. MTT and colony formation assay were used to measure cell proliferation. Transwell assays were conducted to determine cell migration and invasion. Luciferase reporter assays were carried out to assess the interaction between miR-489-5p and Linc00460 or FGF7. Biotin pull-down assay was used to detect the direct interaction between miR-489-5p and Linc00460. In vivo experiments were performed to measure tumor formation and lung metastasis. Results: We demonstrated that lncRNA Linc00460 was upregulated in breast cancer, and its expression level was positively associated with lymphatic metastasis and poor overall survival. Forced expression of Linc00460 increased, whereas Linc00460 silencing decreased, breast cancer cell viability, migration and invasion both in vitro and in vivo. Linc00460 was identified as a direct target of miR-489-5p, which further targeted FGF7 and exerted oncogenic functions in breast cancer. Mechanistically, Linc00460 served as a competing endogenous RNA of FGF-7 mRNA by sponging miR-489-5p, resulting in upregulated FGF7 expression and AKT activity. Notably, forced expression of miR-489-5p abrogated Linc00460-mediated oncogenic behavior and activation of the FGF7-AKT pathway in breast cancer cells. Conclusion: We have demonstrated that Linc00460 promotes breast cancer progression partly through the miR-489-5p/FGF7/AKT axis.
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Affiliation(s)
- Yong Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Leiyan Yang
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Qing-Yun Chong
- Cancer Science Institute of Singapore and Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Hong Yan
- Department of Pathology, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Weijie Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Wenchang Qian
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Sheng Tan
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Zhengsheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui 230032, People's Republic of China
| | - Peter E Lobie
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong, People's Republic of China
| | - Tao Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
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20
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Qi G, Kong W, Mou X, Wang S. A new method for excavating feature lncRNA in lung adenocarcinoma based on pathway crosstalk analysis. J Cell Biochem 2018; 120:9034-9046. [DOI: 10.1002/jcb.28177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqiang Qi
- Department of Electronic Engineering College of Information Engineering, Shanghai Maritime University Shanghai China
| | - Wei Kong
- Department of Electronic Engineering College of Information Engineering, Shanghai Maritime University Shanghai China
| | - Xiaoyang Mou
- Department of Biochemistry Rowan University and Guava Medicine Glassboro New Jersey
| | - Shuaiqun Wang
- Department of Electronic Engineering College of Information Engineering, Shanghai Maritime University Shanghai China
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21
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Uramova S, Kubatka P, Dankova Z, Kapinova A, Zolakova B, Samec M, Zubor P, Zulli A, Valentova V, Kwon TK, Solar P, Kello M, Kajo K, Busselberg D, Pec M, Danko J. Plant natural modulators in breast cancer prevention: status quo and future perspectives reinforced by predictive, preventive, and personalized medical approach. EPMA J 2018; 9:403-419. [PMID: 30538792 DOI: 10.1007/s13167-018-0154-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022]
Abstract
In contrast to the genetic component in mammary carcinogenesis, epigenetic alterations are particularly important for the development of sporadic breast cancer (BC) comprising over 90% of all BC cases worldwide. Most of the DNA methylation processes are physiological and essential for human cellular and tissue homeostasis, playing an important role in a number of key mechanisms. However, if dysregulated, DNA methylation contributes to pathological processes such as cancer development and progression. A global hypomethylation of oncogenes and hypermethylation of tumor-suppressor genes are characteristic of most cancer types. Moreover, histone chemical modifications and non-coding RNA-associated multi-gene controls are considered as the key epigenetic mechanisms governing the cellular homeostasis and differentiation states. A number of studies demonstrate dietary plant products as actively affecting the development and progression of cancer. "Nutri-epigenetics" focuses on the influence of dietary agents on epigenetic mechanisms. This approach has gained considerable attention; since in contrast to genetic alterations, epigenetic modifications are reversible affect early carcinogenesis. Currently, there is an evident lack of papers dedicated to the phytochemicals/plant extracts as complex epigenetic modulators, specifically in BC. Our paper highlights the role of plant natural compounds in targeting epigenetic alterations associated with BC development, progression, as well as its potential chemoprevention in the context of preventive medicine. Comprehensive measures are stated with a great potential to advance the overall BC management in favor of predictive, preventive, and personalized medical services and can be considered as "proof-of principle" model, for their potential application to other multifactorial diseases.
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Affiliation(s)
- Sona Uramova
- 1Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Kubatka
- 2Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia.,3Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Dankova
- 3Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinova
- 3Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Barbora Zolakova
- 3Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- 1Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Pavol Zubor
- 1Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Anthony Zulli
- 4Institute for Health and Sport (IHES), Victoria University, Melbourne, Australia
| | | | - Taeg Kyu Kwon
- 6Department of Immunology, School of Medicine, Keimyung University, Daegu, South Korea
| | - Peter Solar
- 7Department of Medical Biology, Faculty of Medicine, P.J. Šafárik University, Košice, Slovakia
| | - Martin Kello
- 8Department of Pharmacology, Faculty of Medicine, P.J. Šafárik University, Košice, Slovakia
| | - Karol Kajo
- Department of Pathology, St. Elisabeth Oncology Institute, Bratislava, Slovakia
| | - Dietrich Busselberg
- 10Qatar Foundation, Weill Cornell Medical College in Qatar, Education City, Doha Qatar
| | - Martin Pec
- 2Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia
| | - Jan Danko
- 1Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
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22
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Liu K, Yao H, Wen Y, Zhao H, Zhou N, Lei S, Xiong L. Functional role of a long non-coding RNA LIFR-AS1/miR-29a/TNFAIP3 axis in colorectal cancer resistance to pohotodynamic therapy. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2871-2880. [DOI: 10.1016/j.bbadis.2018.05.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/04/2018] [Accepted: 05/24/2018] [Indexed: 02/07/2023]
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Zhang H, Liu W, Wang Z, Meng L, Wang Y, Yan H, Li L. MEF2C promotes gefitinib resistance in hepatic cancer cells through regulating MIG6 transcription. TUMORI JOURNAL 2018; 104:221-231. [PMID: 29714661 DOI: 10.1177/0300891618765555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Mitogen-inducible gene 6 ( MIG6) holds a special position in epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) resistance. As MIG6 regulates the activity of EGFR signal pathway negatively, high level of MIG6 can increase the EGFR TKI resistance of cancer cells, and limit the therapeutic action of EGFR TKI, such as gefitinib or erlotinib. Therefore, better understanding of the molecular mechanisms underlying the regulation of EGFR TKI resistance holds great value in cancer therapy. Methods: In our study, we mainly explored the function of transcription activator, myocyte enhancer factor 2C (MEF2C), on MIG6 expression as well as gefitinib-resistant ability of hepatic cancer cells. Results: Our results indicated that both MEF2C and MIG6 could be upregulated in gefitinib-resistant cancer tissues and cancer cell lines compared with gefitinib-sensitive ones. Chromatin immunoprecipitation assay and dual luciferase assay showed that MEF2C could bind to the MEF2C element in the promoter sequence of MIG6 and promote the transcription of MIG6. This effect increased the gefitinib-resistant ability of cancer cells. Therefore, MEF2C knockdown inhibited the gefitinib resistance and limited the proliferation of hepatic cancer cells in vitro and in vivo, while overexpression of MEF2C showed opposite effect on cancer cell proliferation. Conclusion: Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.
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Affiliation(s)
- Hui Zhang
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Wei Liu
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Zhi Wang
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Lin Meng
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Yunhua Wang
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Huawu Yan
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
| | - Lin Li
- Department II of Hepatobiliary Surgery, The People’s Hospital of Chuxiong Yi Autonomous Prefecture, the Fourth Affiliated Hospital of Dali University, Chuxiong, China
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24
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Kapinova A, Kubatka P, Zubor P, Golubnitschaja O, Dankova Z, Uramova S, Pilchova I, Caprnda M, Opatrilova R, Richnavsky J, Kruzliak P, Danko J. The hypoxia-responsive long non-coding RNAs may impact on the tumor biology and subsequent management of breast cancer. Biomed Pharmacother 2018; 99:51-58. [PMID: 29324312 DOI: 10.1016/j.biopha.2017.12.104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/20/2017] [Accepted: 12/28/2017] [Indexed: 02/09/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are DNA transcripts longer than 200 nucleotides without protein-coding potential. As they are key regulators of gene expression at chromatic, transcriptional and posttranscriptional level, they play important role in various biological and pathological processes. Dysregulation of lncRNAs has been observed in several diseases including cancer. Breast cancer is heterogeneous disease with many molecular subtypes specific in different prognosis and treatment responses. Hypoxia, a common micro-environmental feature of rapidly growing tumour is associated with metastases, recurrences and resistance to therapy. Aberrant expression of hypoxia related lncRNAs significantly correlates with poor outcomes in cancer patients, as the lncRNAs play an important regulatory role in the breast cancer-cell survival. Thus, a better understanding of lncRNAs role in the hypoxic conditions of breast cancer is crucial for precise understanding of the tumorigenesis, disease features and poor clinical outcome, especially in highly aggressive breast cancer subtypes (HER2-positive and triple-negative types). Moreover, lncRNAs may represent tumour marker predicting prognosis and therapeutic targets improving precise and personalized therapy for better patient´s survival. In this review, we summarize the recent information on lncRNAs in breast cancer with special focus on the hypoxia-responsive lncRNAs and their potential impact on the prognosis, therapy algorithms and individual outcomes. Presented data helps in better understanding of the specific mechanisms predicting new therapeutic agents and strategies for the pharmacological intervention.
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Affiliation(s)
- Andrea Kapinova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
| | - Peter Kubatka
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia; Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Pavol Zubor
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia; Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Olga Golubnitschaja
- Radiological Clinic, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany; Breast Cancer Research Centre, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - Zuzana Dankova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Sona Uramova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Pilchova
- Division of Neuroscience, Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University in Bratislava and University Hospital, Bratislava, Slovakia
| | - Radka Opatrilova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jan Richnavsky
- Department of Gynecology and Obstetrics, Faculty of Medicine, Pavol Jozef Safarik University and The First Private Hospital Saca, Kosice, Slovakia
| | - Peter Kruzliak
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.
| | - Jan Danko
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
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25
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Alaei S, Sadeghi B, Najafi A, Masoudi-Nejad A. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma. Genomics 2018; 111:76-89. [PMID: 29317304 DOI: 10.1016/j.ygeno.2018.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values. By using microarray expression data for mRNAs and lncRNAs from a large number of ESCC patients, we utilized "Weighted Gene Co-expression Network Analysis" (WGCNA) method to make a big coding-non-coding gene co-expression network, and discovered important functional modules. Gene set enrichment and pathway analysis revealed major biological processes and pathways involved in these modules. After selecting some protein coding genes involved in biological processes and pathways related to cancer, we used "LncTar", a computational tool to predict potential interactions between these genes and lncRNAs. By combining interaction results with Pearson correlations, we introduced some novel lncRNAs with putative key regulatory roles in the network. Survival analysis with Kaplan-Meier estimator and Log-rank test statistic confirmed that most of the introduced genes are associated with poor prognosis in ESCC. Overall, our study reveals novel protein coding genes and lncRNAs associated with ESCC, along with their predicted interactions. Based on the promising results of survival analysis, these genes can be used as good estimators of patients' survival, or even can be analyzed further as new potential signatures or targets for the therapy of ESCC disease.
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Affiliation(s)
- Shervin Alaei
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Balal Sadeghi
- Food Hygiene and Public Health Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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26
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Chen Q, Su Y, He X, Zhao W, Wu C, Zhang W, Si X, Dong B, Zhao L, Gao Y, Yang X, Chen J, Lu J, Qiao X, Zhang Y. Plasma long non-coding RNA MALAT1 is associated with distant metastasis in patients with epithelial ovarian cancer. Oncol Lett 2016; 12:1361-1366. [PMID: 27446438 PMCID: PMC4950178 DOI: 10.3892/ol.2016.4800] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/26/2016] [Indexed: 12/12/2022] Open
Abstract
Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a newly identified metastasis-associated long non-coding RNA. In a previous study, it was identified that plasma levels of MALAT1 were significantly increased in gastric cancer patients with metastasis compared with gastric cancer patients without metastasis and healthy control individuals. However, it is unclear whether plasma levels of MALAT1 may act as a biomarker for evaluating the development of metastasis in epithelial ovarian cancer (EOC). In the present study, groups that consisted of 47 patients with EOC and metastasis (EOC/DM), 47 patients with EOC without metastasis (EOC/NDM), and 47 healthy control (HC) individuals were established. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the level of plasma MALAT1 in these groups. The results showed that levels of plasma MALAT1 were significantly increased in the EOC/DM group compared with the EOC/NDM and HC groups (P<0.001). Receiver operating characteristic (ROC) analysis indicated that plasma MALAT1 yielded an area under the curve (AUC) of 0.820 [95% confidence interval (CI), 0.734–0.905; P<0.001], distinguishing between EOC/DM and EOC/NDM. ROC analysis also yielded an AUC of 0.884 (95% CI, 0.820–0.949; P<0.001), with 89.4% sensitivity and 72.3% specificity for distinguishing between EOC/DM and HC. Furthermore, multivariate analysis indicated that overexpression of MALAT1, differentiation (poor), tumor-node-metastasis stage (IV), lymph node metastasis (N3), peritoneal invasion (present) and higher serum carbohydrate antigen 125 levels were independent predictors of survival (hazard ratio, 3.322; P=0.028) in patients with EOC. Kaplan-Meier analysis revealed that patients with increased MALAT1 expression had a poorer disease-free survival time. In conclusion, the levels of plasma MALAT1 may act as a valuable biomarker for the diagnosis of metastasis.
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Affiliation(s)
- Qingjuan Chen
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Yongyong Su
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Xiaopeng He
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Weian Zhao
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Caixia Wu
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Weibo Zhang
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Xiaomin Si
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Bingwei Dong
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Lianying Zhao
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Yufang Gao
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Xiaowen Yang
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Jianhui Chen
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Jian Lu
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Ximin Qiao
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
| | - Yuchen Zhang
- Department of Medical Oncology, Xianyang Central Hospital, Xianyang, Shaanxi 712000, P.R. China
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