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Eptaminitaki GC, Zaravinos A, Stellas D, Panagopoulou M, Karaliota S, Baltsavia I, Iliopoulos I, Chatzaki E, Iliopoulos D, Baritaki S. Genome-Wide Analysis of lncRNA-mRNA Co-Expression Networks in CD133+/CD44+ Stem-like PDAC Cells. Cancers (Basel) 2023; 15:cancers15041053. [PMID: 36831395 PMCID: PMC9954787 DOI: 10.3390/cancers15041053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the second most prevalent gastrointestinal malignancy and the most common type of pancreatic cancer is linked with poor prognosis and, eventually, with high mortality rates. Early detection is seldom, while tumor heterogeneity and microarchitectural alterations benefit PDAC resistance to conventional therapeutics. Although emerging evidence suggest the core role of cancer stem cells (CSCs) in PDAC aggressiveness, unique stem signatures are poorly available, thus limiting the efforts of anti-CSC-targeted therapy. Herein, we report the findings of the first genome-wide analyses of mRNA/lncRNA transcriptome profiling and co-expression networks in PDAC cell line-derived CD133+/CD44+ cells, which were shown to bear a CSC-like phenotype in vitro and in vivo. Compared to CD133-/CD44- cells, the CD133+/CD44+ population demonstrated significant expression differences in both transcript pools. Using emerging bioinformatic tools, we performed lncRNA target coding gene prediction analysis, which revealed significant Gene Ontology (GO), pathway, and network enrichments in many dyregulated lncRNA nearby (cis or trans) mRNAs, with reported involvement in the regulation of CSC phenotype and functions. In this context, the construction of lncRNA/mRNA networks by ingenuity platforms identified the lncRNAs ATF2, CHEK1, DCAF8, and PAX8 to interact with "hub" SC-associated mRNAs. In addition, the expressions of the above lncRNAs retrieved by TCGA-normalized RNAseq gene expression data of PAAD were significantly correlated with clinicopathological features of PDAC, including tumor grade and stage, nodal metastasis, and overall survival. Overall, our findings shed light on the identification of CSC-specific lncRNA signatures with potential prognostic and therapeutic significance in PDAC.
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Affiliation(s)
- Giasemi C. Eptaminitaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Apostolos Zaravinos
- Basic and Translational Cancer Research Center (BTCRC), Genomics and Systems Biology Laboratory, Cancer Genetics, Nicosia 1516, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
| | - Dimitris Stellas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
| | - Sevasti Karaliota
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ismini Baltsavia
- Laboratory of Computational Biology, Division of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ioannis Iliopoulos
- Laboratory of Computational Biology, Division of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
| | | | - Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Correspondence: ; Tel.: +30-281-039-4727
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Rajabi A, Kayedi M, Rahimi S, Dashti F, Mirazimi SMA, Homayoonfal M, Mahdian SMA, Hamblin MR, Tamtaji OR, Afrasiabi A, Jafari A, Mirzaei H. Non-coding RNAs and glioma: Focus on cancer stem cells. Mol Ther Oncolytics 2022; 27:100-123. [PMID: 36321132 PMCID: PMC9593299 DOI: 10.1016/j.omto.2022.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Glioblastoma and gliomas can have a wide range of histopathologic subtypes. These heterogeneous histologic phenotypes originate from tumor cells with the distinct functions of tumorigenesis and self-renewal, called glioma stem cells (GSCs). GSCs are characterized based on multi-layered epigenetic mechanisms, which control the expression of many genes. This epigenetic regulatory mechanism is often based on functional non-coding RNAs (ncRNAs). ncRNAs have become increasingly important in the pathogenesis of human cancer and work as oncogenes or tumor suppressors to regulate carcinogenesis and progression. These RNAs by being involved in chromatin remodeling and modification, transcriptional regulation, and alternative splicing of pre-mRNA, as well as mRNA stability and protein translation, play a key role in tumor development and progression. Numerous studies have been performed to try to understand the dysregulation pattern of these ncRNAs in tumors and cancer stem cells (CSCs), which show robust differentiation and self-regeneration capacity. This review provides recent findings on the role of ncRNAs in glioma development and progression, particularly their effects on CSCs, thus accelerating the clinical implementation of ncRNAs as promising tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Ali Rajabi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mehrdad Kayedi
- Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Rahimi
- School of Medicine,Fasa University of Medical Sciences, Fasa, Iran
| | - Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mina Homayoonfal
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Mohammad Amin Mahdian
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Afrasiabi
- Department of Internal Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ameneh Jafari
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Yuan E, Liu K, Lee J, Tsung K, Chow F, Attenello FJ. Modulating glioblastoma chemotherapy response: Evaluating long non-coding RNA effects on DNA damage response, glioma stem cell function, and hypoxic processes. Neurooncol Adv 2022; 4:vdac119. [PMID: 36105389 PMCID: PMC9466271 DOI: 10.1093/noajnl/vdac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive primary adult brain tumor, with an estimated annual incidence of 17 000 new cases in the United States. Current treatments for GBM include chemotherapy, surgical resection, radiation therapy, and antiangiogenic therapy. However, despite the various therapeutic options, the 5-year survival rate remains at a dismal 5%. Temozolomide (TMZ) is the first-line chemotherapy drug for GBM; however, poor TMZ response is one of the main contributors to the dismal prognosis. Long non-coding RNAs (lncRNAs) are nonprotein coding transcripts greater than 200 nucleotides that have been implicated to mediate various GBM pathologies, including chemoresistance. In this review, we aim to frame the TMZ response in GBM via exploration of the lncRNAs mediating three major mechanisms of TMZ resistance: (1) regulation of the DNA damage response, (2) maintenance of glioma stem cell identity, and (3) exploitation of hypoxia-associated responses.
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Affiliation(s)
- Edith Yuan
- Corresponding Author: Edith Yuan, BA, Keck School of Medicine, University of Southern California, 1200 North State St. Suite 3300, Los Angeles, CA 90033, USA ()
| | - Kristie Liu
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin Lee
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kathleen Tsung
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frances Chow
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frank J Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Abstract
Glioma, the most common and aggressive type of brain tumor, has a poor prognosis. Glioma stem cells (GSCs) are thought to be responsible for glioma genesis, proliferation, resistance to chemoradiotherapy, and recurrence. Long non-coding RNAs (lncRNAs) have been viewed as a prospective novel target in glioma therapy in recent years due to their functional roles in GSC biological processes. However, how lncRNAs interact with GSCs and the underlining mechanisms associated with these interactions are not yet clear. In this review, we briefly illustrate recent advancements in the functional roles of lncRNA and their potential mechanisms in GSCs.
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Affiliation(s)
- Lei Wang
- Department of Neurosurgery, Hunan Cancer Hospital and The Afliated Cancer Hospital of Xiangya School, Central South University, Changsha, Hunan, China (mainland)
| | - Zhengwen He
- Department of Neurosurgery, Hunan Cancer Hospital and The Afliated Cancer Hospital of Xiangya School, Central South University, Changsha, Hunan, China (mainland)
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Zhou XY, Liu H, Ding ZB, Xi HP, Wang GW. lncRNA SNHG16 Exerts Oncogenic Functions in Promoting Proliferation of Glioma Through Suppressing p21. Pathol Oncol Res 2019; 26:1021-1028. [PMID: 30972632 DOI: 10.1007/s12253-019-00648-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
Glioma is a malignant brain tumor that accounts for 30% of all brain tumors and 80% of malignant brain tumors. This poor clinical outcome makes the study of molecular mechanisms in glioma as an urgent subject. However, the certain mechanism remains unclear. Long non-coding RNAs (lncRNAs) plays a key role in glioma development and progression. In the present study, we aimed to explore the potential mechanisms of lncRNA SNHG16 in glioma. The levels of lncRNA SNHG16 were qualified in both glioma tissues and cell lines using qRT-PCR assay. The ability of cell proliferation was tested via CCK-8 and colony formation assays. Transfections were performed to knockdown SNHG16 and its target gene p21. The cell cycles and cell apoptosis were evaluated using flow cytometry, and the expression of SNHG16, p21 and apoptosis biomarkers were qualified with qRT-PCR and western blot assays. The expression of SNHG16 were up-regulated in both glioma tissues and cell lines. Knockdown of SNHG16 was associated with poor proliferation, decreased monoclonal formation rates, but increased apoptosis rates, which also caused the high expression of p21. Moreover, p21 could mediate cell proliferation and monoclonal formation, promote cell apoptosis in glioma, which was negatively correlated with lncRNA SNHG16. The molecule mechanism experiments revealed that SNHG16 could not only inhibit the expression of p21 but also suppressed the level of caspase 3 and 9, while promoted cyclinD1 and cyclinB1 expression. lncRNA SNHG16 could promote the cell proliferation and inhibit the apoptosis of glioma through suppressing p21, indicating that lncRNA SNHG16 might be quite vital for the diagnosis and progression of glioma and could even be a novel therapeutic target for glioma.
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Affiliation(s)
- Xiang-Yang Zhou
- Department of Neurosurgery, The First Affiliated Hospital of University of South China, No.69, Chuanshan Road, Shigu District, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Hong Liu
- Department of Neurosurgery, The First Affiliated Hospital of University of South China, No.69, Chuanshan Road, Shigu District, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Zheng-Bin Ding
- Department of Neurosurgery, The First Affiliated Hospital of University of South China, No.69, Chuanshan Road, Shigu District, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Hai-Peng Xi
- Department of Neurosurgery, The First Affiliated Hospital of University of South China, No.69, Chuanshan Road, Shigu District, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Guang-Wei Wang
- Department of Neurosurgery, The First Affiliated Hospital of University of South China, No.69, Chuanshan Road, Shigu District, Hengyang, 421001, Hunan Province, People's Republic of China.
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Lei L, Xia S, Liu D, Li X, Feng J, Zhu Y, Hu J, Xia L, Guo L, Chen F, Cheng H, Chen K, Hu H, Chen X, Li F, Zhong S, Mittal N, Yang G, Qian Z, Han L, He C. Genome-wide characterization of lncRNAs in acute myeloid leukemia. Brief Bioinform 2019; 19:627-635. [PMID: 28203711 DOI: 10.1093/bib/bbx007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a large family of noncoding RNAs that play a critical role in various normal bioprocesses as well as tumorigenesis. However, the expression patterns and biological functions of lncRNAs in acute leukemia have not been well studied. Here, we performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) patient samples, along with non-leukemia control hematopoietic samples. We found that lncRNAs were differentially expressed in AML samples relative to control samples. Notably, we identified that lncRNAs upregulated in AML (relative to the control samples) are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2 and ELK-1 compared with those downregulated in AML. Moreover, an enrichment of H3K4me3 and a depletion of H3K27me3 were observed in upregulated lncRNAs in AML. Expression patterns of three types of lncRNAs (antisense, enhancer and intergenic lncRNAs) have previously been characterized. Of the identified lncRNAs, we found that high expression level lncRNA LOC285758 is associated with the poor prognosis in AML patients. Furthermore, we found that LOC285758 regulates proliferation of AML cell lines by enhancing the expression of HDAC2, a key factor in carcinogenesis. Collectively, our study depicts a landscape of important lncRNAs in AML and provides novel potential therapeutic targets and prognostic markers for AML treatment.
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Affiliation(s)
- Lijun Lei
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Siyu Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Dan Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoqing Li
- Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, China
| | - Jing Feng
- International School of Software, Wuhan University, Wuhan, China
| | - Yaqi Zhu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Linjian Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lieping Guo
- Physician in Eastern Hepatobiliary Hospital, Hospital of Second Military Medical University, Wuhan, Hubei, China
| | - Fei Chen
- Zhongnan hospital of Wuhan University, Wuhan, China
| | - Hui Cheng
- Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ke Chen
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Hanyang Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaohua Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | | | - Shan Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Nupur Mittal
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Guohua Yang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhijian Qian
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
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