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Dai J, Zhang S, Shi Y, Xu J, Liu W, Yang J, Shi L, Yan Z, Li C. rs217727 of lncRNA H19 is Associated with Cervical Cancer Risk in the Chinese Han Population. Pharmgenomics Pers Med 2023; 16:933-948. [PMID: 37928407 PMCID: PMC10624116 DOI: 10.2147/pgpm.s422083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/06/2023] [Indexed: 11/07/2023] Open
Abstract
Background Long noncoding RNAs (LncRNAs) have been revealed to involve in cervical cancer (CC) developing. The current study was designed to explore the association of SNPs (rs217727, rs2366152, rs1859168, rs10505477) located in the lncRNA H19, HOTAIR, HOTTIP and CASC8 genes with the risk of CC in a Chinese Han population. Methods Four SNPs were selected and genotyped in 1426 participants (274 CIN patients, 448 CC patients, and 704 healthy control individuals) using MassArray. The association of these SNPs with susceptibility to CC was evaluated. Results Significant differences in allelic distribution of rs217727 were observed in the comparison of CC with control (P = 0.001), indicating the risk of rs217727-A allele in CC (OR = 1.33; 95% CI: 1.12-1.58). The inheritance model analysis revealed that 2AA+GA genotype represented a certain risk of CC (P = 0.001, OR = 1.35; 95% CI: 1.13-1.62). The stratified analysis revealed a risk of the rs217727-A allele for cervical squamous cell carcinoma (SCC) (P = 0.002, OR = 1.33; 95% CI: 1.11-1.60). Conclusion rs217727 in lncRNA H19 exhibited a significant correlation with CC susceptibility, particularly SCC, and A/A genotype of this SNP might present as a risk in CC.
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Affiliation(s)
- Jie Dai
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Shao Zhang
- Department of Gynaecologic Oncology, The No. 3 Affiliated Hospital of Kunming Medical University, Kunming, 650118, People’s Republic of China
| | - Yuhan Shi
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650041, People’s Republic of China
| | - Jinmei Xu
- Department of Gynaecologic Oncology, The No. 3 Affiliated Hospital of Kunming Medical University, Kunming, 650118, People’s Republic of China
| | - Weipeng Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Jia Yang
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The No. 3 Affiliated Hospital of Kunming Medical University, Kunming, 650118, People’s Republic of China
- Department of Gynaecologic Oncology, The Hospital of Yuanmou, Yuanmou, 651300, People’s Republic of China
| | - Chuanyin Li
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, People’s Republic of China
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Sangeeth A, Malleswarapu M, Mishra A, Gutti RK. Long Non-Coding RNAs as Cellular Metabolism and Haematopoiesis Regulators. J Pharmacol Exp Ther 2023; 384:79-91. [PMID: 35667690 DOI: 10.1124/jpet.121.001120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a category of non-coding RNAs (ncRNAs) that are more than 200 bases long and play major regulatory roles in a wide range of biologic processes, including hematopoeisis and metabolism. Metabolism in cells is an immensely complex process that involves the interconnection and unification of numerous signaling pathways. A growing body of affirmation marks that lncRNAs do participate in metabolism, both directly and indirectly, via metabolic regulation of enzymes and signaling pathways, respectively. The complexities are disclosed by the latest studies demonstrating how lncRNAs could indeed alter tissue-specific metabolism. We have entered a new realm for discovery that is both intimidating and intriguing. Understanding the different functions of lncRNAs in various cellular pathways aids in the advancement of predictive and therapeutic capabilities for a wide variety of myelodysplastic and metabolic disorders. This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. We have focused on the pathway of action of several lncRNAs and have also delved into their prognostic value. Their use as biomarkers and possible therapeutic targets has also been discussed. SIGNIFICANCE STATEMENT: This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. The pathway of action of several lncRNAs and their prognostic value was discussed. Their use as biomarkers and possible therapeutic targets has also been elaborated.
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Affiliation(s)
- Anjali Sangeeth
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Mahesh Malleswarapu
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Amit Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
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Li J, Guo S, Sun Z, Fu Y. Noncoding RNAs in Drug Resistance of Gastrointestinal Stromal Tumor. Front Cell Dev Biol 2022; 10:808591. [PMID: 35174150 PMCID: PMC8841737 DOI: 10.3389/fcell.2022.808591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor in the gastrointestinal tracts and a model for the targeted therapy of solid tumors because of the oncogenic driver mutations in KIT and PDGDRA genes, which could be effectively inhibited by the very first targeted agent, imatinib mesylate. Most of the GIST patients could benefit a lot from the targeted treatment of this receptor tyrosine kinase inhibitor. However, more than 50% of the patients developed resistance within 2 years after imatinib administration, limiting the long-term effect of imatinib. Noncoding RNAs (ncRNAs), the non-protein coding transcripts of human, were demonstrated to play pivotal roles in the resistance of various chemotherapy drugs. In this review, we summarized the mechanisms of how ncRNAs functioning on the drug resistance in GIST. During the drug resistance of GIST, there were five regulating mechanisms where the functions of ncRNAs concentrated: oxidative phosphorylation, autophagy, apoptosis, drug target changes, and some signaling pathways. Also, these effects of ncRNAs in drug resistance were divided into two aspects. How ncRNAs regulate drug resistance in GIST was further summarized according to ncRNA types, different drugs and categories of resistance. Moreover, clinical applications of these ncRNAs in GIST chemotherapies concentrated on the prognostic biomarkers and novel therapeutic targets.
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Affiliation(s)
- Jiehan Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuning Guo
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
| | - Yang Fu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
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Calvo Sánchez J, Köhn M. Small but Mighty-The Emerging Role of snoRNAs in Hematological Malignancies. Noncoding RNA 2021; 7:68. [PMID: 34842767 PMCID: PMC8629011 DOI: 10.3390/ncrna7040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Over recent years, the long known class of small nucleolar RNAs (snoRNAs) have gained interest among the scientific community, especially in the clinical context. The main molecular role of this interesting family of non-coding RNAs is to serve as scaffolding RNAs to mediate site-specific RNA modification of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). With the development of new sequencing techniques and sophisticated analysis pipelines, new members of the snoRNA family were identified and global expression patterns in disease backgrounds could be determined. We will herein shed light on the current research progress in snoRNA biology and their clinical role by influencing disease outcome in hematological diseases. Astonishingly, in recent studies snoRNAs emerged as potent biomarkers in a variety of these clinical setups, which is also highlighted by the frequent deregulation of snoRNA levels in the hema-oncological context. However, research is only starting to reveal how snoRNAs might influence cellular functions and the connected disease hallmarks in hematological malignancies.
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Affiliation(s)
| | - Marcel Köhn
- Junior Research Group ‘RBPs and ncRNAs in Human Diseases’, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Saale, Germany;
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Fantini S, Rontauroli S, Sartini S, Mirabile M, Bianchi E, Badii F, Maccaferri M, Guglielmelli P, Ottone T, Palmieri R, Genovese E, Carretta C, Parenti S, Mallia S, Tavernari L, Salvadori C, Gesullo F, Maccari C, Zizza M, Grande A, Salmoiraghi S, Mora B, Potenza L, Rosti V, Passamonti F, Rambaldi A, Voso MT, Mecucci C, Tagliafico E, Luppi M, Vannucchi AM, Manfredini R. Increased Plasma Levels of lncRNAs LINC01268, GAS5 and MALAT1 Correlate with Negative Prognostic Factors in Myelofibrosis. Cancers (Basel) 2021; 13:cancers13194744. [PMID: 34638230 PMCID: PMC8507546 DOI: 10.3390/cancers13194744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 01/31/2023] Open
Abstract
Simple Summary Myelofibrosis (MF) displays the worst prognosis among Philadelphia-negative chronic myeloproliferative neoplasms. There is no curative therapy for MF, except for bone marrow transplantation, which however has a consistent percentage of failure. There is thus an urgent need of novel biomarkers to complement current stratification models and to enable better management of patients. To address this issue, we herein measured the plasma levels of several long noncoding RNAs (lncRNAs). Circulating lncRNAs has been already largely described as potential non-invasive biomarkers in cancers. In our study we unveiled that LINC01268, MALAT1 (both p < 0.0001) and GAS5 (p = 0.0003) plasma levels are significantly higher in MF patients if compared with healthy donors, and their increased plasma levels correlate with several detrimental features in MF. Among them, LINC01268 is an independent variable for both OS (p = 0.0297) and LFS (p = 0.0479), thus representing a putative new biomarker suitable for integrate contemporary prognostic models. Abstract Long non-coding RNAs (lncRNAs) have been recently described as key mediators in the development of hematological malignancies. In the last years, circulating lncRNAs have been proposed as a new class of non-invasive biomarkers for cancer diagnosis and prognosis and to predict treatment response. The present study is aimed to investigate the potential of circulating lncRNAs as non-invasive prognostic biomarkers in myelofibrosis (MF), the most severe among Philadelphia-negative myeloproliferative neoplasms. We detected increased levels of seven circulating lncRNAs in plasma samples of MF patients (n = 143), compared to healthy controls (n = 65). Among these, high levels of LINC01268, MALAT1 or GAS5 correlate with detrimental clinical variables, such as high count of leukocytes and CD34+ cells, severe grade of bone marrow fibrosis and presence of splenomegaly. Strikingly, high plasma levels of LINC01268 (p = 0.0018), GAS5 (p = 0.0008) or MALAT1 (p = 0.0348) are also associated with a poor overall-survival while high levels of LINC01268 correlate with a shorter leukemia-free-survival. Finally, multivariate analysis demonstrated that the plasma level of LINC01268 is an independent prognostic variable, suggesting that, if confirmed in future in an independent patients’ cohort, it could be used for further studies to design an updated classification model for MF patients.
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Affiliation(s)
- Sebastian Fantini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Sebastiano Rontauroli
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Stefano Sartini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Margherita Mirabile
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Elisa Bianchi
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Filippo Badii
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Monica Maccaferri
- Department of Laboratory Medicine and Pathology, Diagnostic Hematology and Clinical Genomics, AUSL/AOU Policlinico, 41124 Modena, Italy;
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
- Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), Neuro-Oncohematology, 00179 Rome, Italy
| | - Raffaele Palmieri
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
| | - Elena Genovese
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Chiara Carretta
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Sandra Parenti
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Selene Mallia
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Lara Tavernari
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Costanza Salvadori
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Francesca Gesullo
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Chiara Maccari
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Michela Zizza
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Alexis Grande
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Silvia Salmoiraghi
- Hematology, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (S.S.); (A.R.)
| | - Barbara Mora
- Division of Hematology, Ospedale ASST Sette Laghi, University of Insubria, 21100 Varese, Italy; (B.M.); (F.P.)
| | - Leonardo Potenza
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
| | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Foundation Policlinico San Matteo, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), 27100 Pavia, Italy;
| | - Francesco Passamonti
- Division of Hematology, Ospedale ASST Sette Laghi, University of Insubria, 21100 Varese, Italy; (B.M.); (F.P.)
| | | | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
- Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), Neuro-Oncohematology, 00179 Rome, Italy
| | - Cristina Mecucci
- Department of Medicine and Surgery, Section of Hematology and Clinical Immunology, University of Perugia, 06129 Perugia, Italy;
| | - Enrico Tagliafico
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
- Center for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Mario Luppi
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
| | - Alessandro Maria Vannucchi
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Rossella Manfredini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
- Correspondence:
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Jin H, Liang G, Yang L, Liu L, Wang B, Yan F. SP1-induced AFAP1-AS1 contributes to proliferation and invasion by regulating miR-497-5p/CELF1 pathway in nasopharyngeal carcinoma. Hum Cell 2021; 34:491-501. [PMID: 33400247 DOI: 10.1007/s13577-020-00475-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Nasopharyngeal carcinoma is a type of otolaryngological malignancy with high incidence. Long non-coding RNAs (lncRNAs) are closely related to nasopharyngeal carcinoma. LncRNA AFAP1-AS1 (AFAP1-AS1) has been found to play important roles in nasopharyngeal carcinoma progression and poor prognosis. However, the mechanism underlying AFAP1-AS1 in regulating nasopharyngeal carcinoma is still unclear. In current study, AFAP1-AS1 was found to be up-regulated in nasopharyngeal carcinoma tissues and cells. AFAP1-AS1 overexpression and knockdown were conducted in nasopharyngeal carcinoma cells. The results proved that AFAP1-AS1 promoted the survival and migration of nasopharyngeal carcinoma cells. Additionally, specificity protein 1 (SP1) was enhanced in nasopharyngeal carcinoma tissues and cells, and induced AFAP1-AS1 expression. The interaction between AFAP1-AS1 and miR-497-5p was confirmed. AFAP1-AS1 was demonstrated to regulate CELF1, a target gene of miR-497-5p. Further functional analysis revealed that AFAP1-AS1 knockdown attenuated SP1-induced nasopharyngeal carcinoma progression. These results indicate that SP1-induced AFAP1-AS1 facilitates nasopharyngeal carcinoma progression by regulating miR-497-5p/CELF1 pathway, which provides a new target for nasopharyngeal carcinoma treatment.
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Affiliation(s)
- Hui Jin
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Gengtian Liang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Liping Yang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Li Liu
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Binru Wang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Fengqin Yan
- Department of Head and Neck Radiation Therapy, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No. 1 Banshan Road, Gongshu District, Hangzhou, 310021, Zhejiang, China.
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310021, Zhejiang, China.
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Feng W, Zhu R, Ma J, Song H. LncRNA ELFN1-AS1 Promotes Retinoblastoma Growth and Invasion via Regulating miR-4270/SBK1 Axis. Cancer Manag Res 2021; 13:1067-1073. [PMID: 33574704 PMCID: PMC7872934 DOI: 10.2147/cmar.s281536] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/06/2020] [Indexed: 12/20/2022] Open
Abstract
Background Long noncoding RNA (lncRNA) has been reported to play important roles in tumor initiation. However, how lncRNA ELFN1-AS1 affects retinoblastoma development remains unclear. Thus, we sought to elucidate its functions in retinoblastoma progression. Methods ELFN1-AS1 expression was measured in retinoblastoma tissues and normal tissues by qRT-PCR. CCK8, colony formation and Transwell assay were carried out to investigate the effects of ELFN1-AS1 knockdown on cell malignant behaviors. Bioinformatics analyses were performed to predict the relationship among ELFN1-AS1, miR-4270 and SBK1. Results ELFN1-AS1 was highly expressed in retinoblastoma tissues and cell lines. ELFN1-AS1 was positively correlated with retinoblastoma progression and prognosis. ELFN1-AS1 knockdown curtailed retinoblastoma proliferation, migration and invasion. ELFN1-AS1 was the competing endogenous RNA for miR-4270 and promoted SBK1expression. Conclusion Altogether, our findings demonstrated that ELFN1-AS1 promotes retinoblastoma progression through mediating miR-4270/SBK1 axis and might be a promising therapeutic target.
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Affiliation(s)
- Wanguo Feng
- Department of Refractive Surgery, Dalian Aier Eye Hospital, Dalian, 116092, People's Republic of China
| | - Ruixi Zhu
- Department of Ophthalmology, Heilongjiang Provincial Hospital, Harbin Institute of Technology, Harbin, 150036, People's Republic of China
| | - Junlong Ma
- Department of Ophthalmology, Dalian University Affiliated Xinhua Hospital, Dalian, 116021, People's Republic of China
| | - Han Song
- Department of Ophthalmology, Heilongjiang Provincial Hospital, Harbin Institute of Technology, Harbin, 150036, People's Republic of China
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Li T, Jin X, Dong J, Deng H. Long noncoding RNA ARSR is associated with a poor prognosis in patients with colorectal cancer. J Gene Med 2020; 22:e3241. [PMID: 32558022 DOI: 10.1002/jgm.3241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As one of the leading cancer-related mortalities worldwide, colorectal cancer (CRC) shows resistance to chemotherapy mainly because of drug resistance. Existing evidence has revealed that long noncoding RNAs (lncRNAs) are related to tumorigenesis and chemoresistance scenarios. However, the mechanism by which lncRNA induces chemoresistance and the postoperative prognosis of CRC both remain unclear. METHODS The expression of a lncRNA named lncARSR in CRC tissue was tested, and its association with clinical and pathological features was analyzed. Gain-of-function and loss-of-function assays were conducted to investigate the role of lncARSR in vivo and in vitro. RESULTS Functional analysis showed that overexpressing lncARSR increased oxaliplatin (OXA) resistance of CRC cells in vitro and in vivo. Moreover, lncARSR conferred chemoresistance to CRC cells. Silencing lncARSR decreased cell viability and promoted cell apoptosis after OXA treatment, whereas overexpression of lncARSR increased cell viability and reduced cell apoptosis after OXA treatment. In addition, lncARSR overexpression induced the tumor formation capacity of colorectal cancer cells. CONCLUSIONS The results obtained in the present study show that up-regulation of lncARSR promoted OXA resistance in CRC. Our results also imply that lncARSR may be a candidate marker for CRC chemoresistance.
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Affiliation(s)
- Ting Li
- Department of Liver and Stomach Diseases, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Xuezhu Jin
- Department of Liver and Stomach Diseases, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Jingrong Dong
- Department of Endoscopy, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Houbo Deng
- Department of Liver and Stomach Diseases, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
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9
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Vafadar A, Shabaninejad Z, Movahedpour A, Mohammadi S, Fathullahzadeh S, Mirzaei HR, Namdar A, Savardashtaki A, Mirzaei H. Long Non-Coding RNAs As Epigenetic Regulators in Cancer. Curr Pharm Des 2020; 25:3563-3577. [PMID: 31470781 DOI: 10.2174/1381612825666190830161528] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/21/2019] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) constitute large portions of the mammalian transcriptome which appeared as a fundamental player, regulating various cellular mechanisms. LncRNAs do not encode proteins, have mRNA-like transcripts and frequently processed similar to the mRNAs. Many investigations have determined that lncRNAs interact with DNA, RNA molecules or proteins and play a significant regulatory function in several biological processes, such as genomic imprinting, epigenetic regulation, cell cycle regulation, apoptosis, and differentiation. LncRNAs can modulate gene expression on three levels: chromatin remodeling, transcription, and post-transcriptional processing. The majority of the identified lncRNAs seem to be transcribed by the RNA polymerase II. Recent evidence has illustrated that dysregulation of lncRNAs can lead to many human diseases, in particular, cancer. The aberrant expression of lncRNAs in malignancies contributes to the dysregulation of proliferation and differentiation process. Consequently, lncRNAs can be useful to the diagnosis, treatment, and prognosis, and have been characterized as potential cancer markers as well. In this review, we highlighted the role and molecular mechanisms of lncRNAs and their correlation with some of the cancers.
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Affiliation(s)
- Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Shabaninejad
- Department of Nanotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student research committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soheila Mohammadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sima Fathullahzadeh
- Medical Biotechnology Research Center, Ashkezar Branch, Islamic Azad University, Ashkezar, Yazd, Iran
| | - Hamid R Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Afshin Namdar
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, 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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10
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Han S, Song L, Chen Y, Hou M, Wei X, Fan D. The long non-coding RNA ILF3-AS1 increases the proliferation and invasion of retinoblastoma through the miR-132-3p/SMAD2 axis. Exp Cell Res 2020; 393:112087. [PMID: 32407730 DOI: 10.1016/j.yexcr.2020.112087] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022]
Abstract
A great deal of evidence suggests that long non-coding RNAs (lncRNAs) function in the tumorigenesis of retinoblastoma (RB). However, the roles of lncRNA ILF3-AS1 in RB are still unclear. In the present study, our work revealed that the lncRNA ILF3-AS1 was increased in both RB tissues and cell lines. Repression of ILF3-AS1 suppressed both RB cell proliferation and invasion in vitro. ILF3-AS1 also promoted tumor growth in vivo. While exploring the mechanisms behind ILF3-AS1 in RB, we identified that ILF3-AS1 sponges with miR-132-3p that is expressed at low levels in RB tissues as well as attenuates RB progression. Furthermore, SMAD2 was confirmed to be a miR-132-3p target. Finally, we found that SMAD2 overexpression or miR-132-3p inhibitors recover the inhibitory effects of ILF3-AS1 suppression on RB progression. Collectively, these data indicate that ILF3-AS1 is involved in RB progression through the miR-132-3p/SMAD2 axis, providing a novel and promising biomarker that can be used for the treatment of RB.
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Affiliation(s)
- Shaoping Han
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China.
| | - Lili Song
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China
| | - Yang Chen
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China
| | - Min Hou
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China
| | - Xiaoyue Wei
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China
| | - Dongsheng Fan
- Department of Ophthalmology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, 471000, China
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11
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Yu Y, Kou D, Liu B, Huang Y, Li S, Qi Y, Guo Y, Huang T, Qi X, Jia L. LncRNA MEG3 contributes to drug resistance in acute myeloid leukemia by positively regulating ALG9 through sponging miR-155. Int J Lab Hematol 2020; 42:464-472. [PMID: 32359033 DOI: 10.1111/ijlh.13225] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/07/2020] [Accepted: 04/11/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The development of drug resistance is the main obstacle for successful treatment in acute myeloid leukemia (AML). Noncoding RNAs have been implicated in biological function in AML drug resistance. Aberrant protein glycosylation is associated with AML progression. The aim of the study was to explore the potential regulatory mechanism of lncRNA MEG3/miR-155/ALG9 axis in drug resistance of AML. METHODS QRT-PCR and Western blot were used for comparison analyses of ALG9, MEG3, and miR-155 levels. CCK-8 and colony formation assays were determined for drug sensitivity and proliferative capability of AML cells. Luciferase reporter assay was used to confirm the targets of miR-155. RESULTS The mannosyltransferase ALG9 and MEG3 was downregulated in peripheral blood mononuclear cells (PBMCs) of M5/multidrug resistance (MDR) AML patients and adriamycin (ADR)-resistant AML cell lines, which determined a positive correlation in AML patients. Low expression of ALG9 and MEG3 predicted poor prognosis of AML patients. The altered level of ALG9 was found corresponding to the drug-resistant phenotype and sphere formation of AML cells. MiR-155 was overexpressed in M5/MDR patients and ADR-resistant AML cells, as well as inversely correlated to ALG9 expression. MEG3 was a direct target of miR-155 and could sponge miR-155 in AML cells. MEG3 interacted with miR-155 to regulate ALG9 expression, which reversed the effects of ALG9 regulation on proliferation and drug resistance in AML cells. CONCLUSION MEG3 sponged miR-155 by competing endogenous RNA (ceRNA) mechanism, which further modulated ALG9 expression and AML procession, providing a novel therapeutic target for AML chemoresistance.
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Affiliation(s)
- Yanan Yu
- College of Laboratory Medicine, Dalian Medical University, Dalian, China.,Department of Emergency, Affiliated Dalian Friend-ship Hospital of Dalian Medical University, Dalian, China
| | - Daqing Kou
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Bing Liu
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Yiran Huang
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Shuangda Li
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Yu Qi
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Yanru Guo
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Tong Huang
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Xia Qi
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
| | - Li Jia
- College of Laboratory Medicine, Dalian Medical University, Dalian, China
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12
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Gao H, Sun X, Wang H, Zheng Y. Long noncoding RNA SNHG22 increases ZEB1 expression via competitive binding with microRNA-429 to promote the malignant development of papillary thyroid cancer. Cell Cycle 2020; 19:1186-1199. [PMID: 32306838 DOI: 10.1080/15384101.2020.1749466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNA termed small nucleolar RNA host gene 22 (SNHG22) is a crucial regulator in epithelial ovarian carcinoma. Nevertheless, the regulatory functions of SNHG22 in papillary thyroid cancer (PTC) progression and its mechanisms of action remain poorly defined. Therefore, the present study aimed to investigate the role of SNHG22 in the malignant phenotype of PTC and determine whether SNHG22 regulates PTC progression via a ceRNA mechanism. SNHG22 expression in PTC was detected using reverse transcription-quantitative polymerase chain reaction analysis. The biological actions of SNHG22 silencing in PTC cells were evaluated both in vitro (using Cell Counting Kit-8 assay, flow cytometry analysis, and cell migration and invasion assays) and in vivo (using tumorigenicity assay). Herein, high SNHG22 expression was observed in PTC tissues and cell lines. This high SNHG22 level was closely associated with unfavorable clinicopathological characteristics and worse overall survival in patients with PTC. SNHG22 knockdown effectively suppressed PTC cell proliferation, migration, and invasion in vitro; accelerated cell apoptosis; and hindered tumor growth in vivo. Mechanistic experiments revealed that SNHG22 directly interacts with microRNA-429 (miR-429) as an miRNA sponge and positively modulates ZEB1 expression. Rescue assays found that miR-429 inhibition or ZEB1 upregulation can offset the actions of SNHG22 knockdown in PTC cells. In sum, SNHG22, miR-429, and ZEB1 form an interactive regulatory network with cancer-promoting roles in PTC cells, suggesting that the SNHG22/miR-429/ZEB1 pathway is a novel diagnostic and therapeutic target.
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Affiliation(s)
- Hong Gao
- Department of Thyroid-Head and Neck Surgery, Jilin Cancer Hospital, Changchun, Jilin, P.R. China
| | - Xiaosong Sun
- Department of Thyroid-Head and Neck Surgery, Jilin Cancer Hospital, Changchun, Jilin, P.R. China
| | - Hongdong Wang
- Department of Thyroid-Head and Neck Surgery, Jilin Cancer Hospital, Changchun, Jilin, P.R. China
| | - Ying Zheng
- Department of Thyroid-Head and Neck Surgery, Jilin Cancer Hospital, Changchun, Jilin, P.R. China
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13
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Association of long non-coding RNA and leukemia: A systematic review. Gene 2020; 735:144405. [DOI: 10.1016/j.gene.2020.144405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/27/2020] [Indexed: 12/12/2022]
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14
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Li X, Rui B, Cao Y, Gong X, Li H. Long non-coding RNA LINC00152 acts as a sponge of miRNA-193b-3p to promote tongue squamous cell carcinoma progression. Oncol Lett 2020; 19:2035-2042. [PMID: 32194700 DOI: 10.3892/ol.2020.11293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 07/26/2019] [Indexed: 12/29/2022] Open
Abstract
Dysregulated expression of long non-coding RNAs has been determined to be important in cancer development; however, their role in tongue squamous cell carcinoma (TSCC) progression and carcinogenesis, to the best of our knowledge, is yet to be elucidated. The present study revealed that long intergenic non-coding RNA 00152 (LINC00152) expression was significantly increased in human TSCC tissues compared with in tissues from matched controls using RT-qPCR. In TSCC cell lines, CAL-27 and SCC-9, LINC00152 was revealed to promote TSCC cell proliferation, enhance cell cycle progression and inhibit cell apoptosis. Additionally, migration and invasion of TSCC cell lines was increased in response to LINC00152 overexpression. Mechanistically, LINC00152 was determined to be localized in the cytoplasm and acted as a microRNA (miR)-193b-3p sponge, and LINC00152 knockdown or miR-193b-3p mimics both inhibited PI3K signaling pathway activation and downstream AKT phosphorylation; therefore, promoting TSCC progression in vitro. Overall, the results of the present study suggested that increased LINC00152 expression in TSCC tissues may act as a sponge of miR-193b-3p to promote cancer progression in vitro.
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Affiliation(s)
- Xiuhua Li
- Department of Stomatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China.,School of Pharmacology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
| | - Bing Rui
- Department of Medical Microbiology and Parasitology, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yongbing Cao
- School of Pharmacology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
| | - Xiaojian Gong
- School of Pharmacology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
| | - Hongjiao Li
- Department of Stomatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
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15
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Jia W, Jia S, Chen P, He Y. Construction and Analysis of a Long Non-Coding RNA (lncRNA)-Associated ceRNA Network in β-Thalassemia and Hereditary Persistence of Fetal Hemoglobin. Med Sci Monit 2019; 25:7079-7086. [PMID: 31541070 PMCID: PMC6767942 DOI: 10.12659/msm.915946] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Higher fetal hemoglobin (HbF) levels can ameliorate the clinical severity of β-thalassemia. The use of integrative strategies to combine results from gene microarray expression profiling, experimental evidence, and bioinformatics helps reveal functional long noncoding RNAs (lncRNAs) in β-thalassemia and HbF induction. Material/Methods In a previous study, a microarray profiling was performed of 7 individuals with high HbF levels and 7 normal individuals. Thirteen paired samples were used for validation. lncRNA NR_001589 and uc002fcj.1 were chosen for further research. The quantitative reverse transcription-PCR was used to detect the expression levels of 2 lncRNAs. The Spearman correlation test was employed. The nuclear and cytoplasmic distribution experiment in K562 cells was used to verify the subcellular localization of 2 lncRNAs. Potential relationships among lncRNAs, predicted microRNAs (miRNAs), and target gene HBG1/2 were based on competitive endogenous RNA theory and bioinformatics analysis. Results Average expression levels of NR_001589 and uc002fcj.1 were significantly higher in the high-HbF group than in the control group. A positive correlation existed between NR_001589, uc002fcj.1, and HbF. The expression of NR_001589 was in both the cytoplasm and the nucleus, mostly (77%) in the cytoplasm. The expression of uc002fcj.1 was in both the cytoplasm and the nucleus; the cytoplasmic proportion was 43% of the total amount. A triple lncRNA-miRNA-mRNA network was established. Conclusions Novel candidate genetic factors associated with the HBG1/2 expression were identified. Further functional investigation of NR_001589 and uc002fcj.1 can help deepen the understanding of molecular mechanisms in β-thalassemia.
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Affiliation(s)
- Wenguang Jia
- Department of Pediatrics, First Affiliated Hospital of Guangxi Medical University, Guangxi Key Laboratory of Thalassemia Research, Nanning, Guangxi, China (mainland)
| | - Siyuan Jia
- Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Ping Chen
- Department of Pediatrics, First Affiliated Hospital of Guangxi Medical University, Guangxi Key Laboratory of Thalassemia Research, Nanning, Guangxi, China (mainland)
| | - Yunyan He
- Department of Pediatrics, First Affiliated Hospital of Guangxi Medical University, Guangxi Key Laboratory of Thalassemia Research, Nanning, Guangxi, China (mainland)
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16
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Thoms JAI, Beck D, Pimanda JE. Transcriptional networks in acute myeloid leukemia. Genes Chromosomes Cancer 2019; 58:859-874. [PMID: 31369171 DOI: 10.1002/gcc.22794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease characterized by a diverse range of recurrent molecular aberrations that occur in many different combinations. Components of transcriptional networks are a common target of these aberrations, leading to network-wide changes and deployment of novel or developmentally inappropriate transcriptional programs. Genome-wide techniques are beginning to reveal the full complexity of normal hematopoietic stem cell transcriptional networks and the extent to which they are deregulated in AML, and new understandings of the mechanisms by which AML cells maintain self-renewal and block differentiation are starting to emerge. The hope is that increased understanding of the network architecture in AML will lead to identification of key oncogenic dependencies that are downstream of multiple network aberrations, and that this knowledge will be translated into new therapies that target these dependencies. Here, we review the current state of knowledge of network perturbation in AML with a focus on major mechanisms of transcription factor dysregulation, including mutation, translocation, and transcriptional dysregulation, and discuss how these perturbations propagate across transcriptional networks. We will also review emerging mechanisms of network disruption, and briefly discuss how increased knowledge of network disruption is already being used to develop new therapies.
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Affiliation(s)
- Julie A I Thoms
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Dominik Beck
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - John E Pimanda
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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17
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Liu W, Wang Z, Wang C, Ai Z. Long non-coding RNA MIAT promotes papillary thyroid cancer progression through upregulating LASP1. Cancer Cell Int 2019; 19:194. [PMID: 31372094 PMCID: PMC6659215 DOI: 10.1186/s12935-019-0913-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023] Open
Abstract
Background Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play an important role in initiation and development of thyroid cancer. However, the underlying molecular mechanism remains elusive. Methods To explore potential oncogenic and tumor suppressive lncRNAs in papillary thyroid cancer (PTC), we performed RNA sequencing to discover differentially expression lncRNAs between PTC tissues and matched normal tissues. RT-qPCR was used to validate differentially expressed lncRNAs. Bioinformatic analysis was performed to predicted potential miRNA and gene which might be regulated by MIAT. Cell proliferation, invasion and cycle assay were conducted to study the function of MIAT and LASP1 in PTC. Results Through analysis of RNA sequencing, we observed that lncRNA-MIAT was overexpressed in PTC tissues. The upregulation of MIAT was further confirmed in 40 pairs of PTC tissues and normal tissues we collected. In the function assays, results suggested that MIAT silencing led to inhibition of cell proliferation, invasion and disruption of cell cycle progression in PTC cells. Mechanistically, MIAT directly bound to miR-324-3p and upregulated LASP1 expression in PTC cells. In addition, expression of MIAT was positively correlated with LASP1 mRNA expression in samples collected from patients with PTC. More importantly, transfection of recombinant LASP1 attenuated MIAT silencing induced inhibition of cell proliferation, invasion and disruption of cell cycle progression in PTC cells. Conclusions In conclusion, the findings suggest that lncRNA-MIAT may promote PTC proliferation and invasion through physically binding miR-324-3p and upregulation of LASP1. Electronic supplementary material The online version of this article (10.1186/s12935-019-0913-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 China
| | - Zhenglin Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 China
| | - Cong Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 China
| | - Zhilong Ai
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 China
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18
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Ng M, Heckl D, Klusmann JH. The Regulatory Roles of Long Noncoding RNAs in Acute Myeloid Leukemia. Front Oncol 2019; 9:570. [PMID: 31338324 PMCID: PMC6629768 DOI: 10.3389/fonc.2019.00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/12/2019] [Indexed: 01/23/2023] Open
Abstract
In this post-genomic era, long noncoding RNAs (lncRNAs) are rapidly gaining recognition for their crucial roles across diverse biological processes and contexts. The human blood system is no exception, where dozens of lncRNAs have been established as regulators of normal and/or malignant hematopoiesis, and where ongoing works continue to uncover novel lncRNA functions. Our review focuses on lncRNAs that are involved in the pathogenesis of acute myeloid leukemia (AML) and the mechanisms through which they control gene expression in this disease context. We also comment on genome-wide sequencing or profiling studies that have implicated large sets of lncRNAs in AML pathophysiology.
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Affiliation(s)
- Michelle Ng
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Heckl
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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19
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Liu Z, Chen Q, Hann SS. The functions and oncogenic roles of CCAT1 in human cancer. Biomed Pharmacother 2019; 115:108943. [PMID: 31078038 DOI: 10.1016/j.biopha.2019.108943] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
In various human cancers, long non-coding RNAs (lncRNAs), a novel class of RNAs longer than 200 nucleotides without protein-coding potential, are implicated in a variety of biological processes, such as cell proliferation, invasion, metastasis, and apoptosis through regulation of gene expression at various levels including chromatin, splicing, transcriptional and post-transcriptional levels. However, the mechanisms underlying these are still elusive. Colon cancer-associated transcript 1(CCAT1) has received increased attention among those lncRNAs. Studies have shown high expression pattern and oncogenic role of CCAT1 in different types of cancer, and aberrant expression of CCAT1 has been involved in tumor-genesis, progression, metastasis, and patient survival via regulating different target genes and signaling pathways. In this review, we first introduce the concept, identification, and biological function of CCAT1; we then describe the mechanisms by which CCAT1 regulate the cancer proliferation and progression. In the last, we discuss emerging insights into the role of CCAT1 as potential biomarker and therapeutic target for novel treatment paradigms in cancer.
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Affiliation(s)
- Zheng Liu
- Laboratory of Tumor Biology, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - QianJun Chen
- Department of Mammary Diseases, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
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20
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Expression profiling of snoRNAs in normal hematopoiesis and AML. Blood Adv 2019; 2:151-163. [PMID: 29365324 DOI: 10.1182/bloodadvances.2017006668] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. We optimized a next-generation sequencing approach and a custom analysis pipeline to identify and quantify expression of snoRNAs in acute myeloid leukemia (AML) and normal hematopoietic cell populations. We show that snoRNAs are expressed in a lineage- and development-specific fashion during hematopoiesis. The most striking examples involve snoRNAs located in 2 imprinted loci, which are highly expressed in hematopoietic progenitors and downregulated during myeloid differentiation. Although most snoRNAs are expressed at similar levels in AML cells compared with CD34+, a subset of snoRNAs showed consistent differential expression, with the great majority of these being decreased in the AML samples. Analysis of host gene expression, splicing patterns, and whole-genome sequence data for mutational events did not identify transcriptional patterns or genetic alterations that account for these expression differences. These data provide a comprehensive analysis of the snoRNA transcriptome in normal and leukemic cells and should be helpful in the design of studies to define the contribution of snoRNAs to normal and malignant hematopoiesis.
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21
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Magilnick N, Boldin MP. Molecular Moirai: Long Noncoding RNA Mediators of HSC Fate. CURRENT STEM CELL REPORTS 2018; 4:158-165. [PMID: 30364527 DOI: 10.1007/s40778-018-0130-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Purpose of Review Hematopoiesis is an ordered developmental process that requires dynamic regulation to warrant proper response to physiological challenges and prevent malignancies. Long noncoding RNAs are emerging as key, multi-faceted regulators of gene expression. This review explores the function of lncRNAs in the control of HSC homeostasis and hematopoietic differentiation. Recent Findings Multiple lncRNAs have been implicated in maintaining HSC stemness and enabling progenitors to carry out the correct programs of lineage differentiation. Specific lncRNAs have been identified that regulate the differentiation of multipotent progenitors into terminally differentiated blood cells. These lncRNAs predominantly act by assisting master regulators that drive specific differentiation programs, either by enhancing or repressing the transcription of particular genomic loci. Summary Long noncoding RNAs contribute to the correct differentiation and maturation of various hematopoietic lineages by assisting with the activation of transcriptional programs in a time- and cell-dependent manner.
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22
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Li W, Ren Y, Si Y, Wang F, Yu J. Long non-coding RNAs in hematopoietic regulation. CELL REGENERATION 2018; 7:27-32. [PMID: 30671227 PMCID: PMC6326246 DOI: 10.1016/j.cr.2018.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/11/2018] [Accepted: 08/21/2018] [Indexed: 02/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles via tethering with DNA, RNA or protein in diverse biological processes. These lncRNA-mediated interactions enhance gene regulatory networks and modulate a wide range of downstream genes. It has been demonstrated that several lncRNAs act as key regulators in hematopoiesis. This review highlights the roles of lncRNAs in normal hematopoietic development and discusses how lncRNA dysregulation correlates with disease prognoses and phenotypes.
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Affiliation(s)
- Weiqian Li
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yue Ren
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
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23
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Yuan F, Lu L, Zhang Y, Wang S, Cai YD. Data mining of the cancer-related lncRNAs GO terms and KEGG pathways by using mRMR method. Math Biosci 2018; 304:1-8. [PMID: 30086268 DOI: 10.1016/j.mbs.2018.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/15/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023]
Abstract
LncRNAs plays an important role in the regulation of gene expression. Identification of cancer-related lncRNAs GO terms and KEGG pathways is great helpful for revealing cancer-related functional biological processes. Therefore, in this study, we proposed a computational method to identify novel cancer-related lncRNAs GO terms and KEGG pathways. By using existing lncRNA database and Max-relevance Min-redundancy (mRMR) method, GO terms and KEGG pathways were evaluated based on their importance on distinguishing cancer-related and non-cancer-related lncRNAs. Finally, GO terms and KEGG pathways with high importance were presented and analyzed. Our literature reviewing showed that the top 10 ranked GO terms and pathways were really related to interpretable tumorigenesis according to recent publications.
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Affiliation(s)
- Fei Yuan
- Department of Science & Technology, Binzhou Medical University Hospital, Binzhou 256603, Shandong, China.
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York 10032, USA.
| | - YuHang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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24
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Li Z, Yang L, Liu X, Nie Z, Luo J. Long noncoding RNA MEG3 inhibits proliferation of chronic myeloid leukemia cells by sponging microRNA21. Biomed Pharmacother 2018; 104:181-192. [PMID: 29772439 DOI: 10.1016/j.biopha.2018.05.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/22/2022] Open
Abstract
The long noncoding RNA (lnc) maternally expressed 3 (MEG3) is downregulated in many types of cancers. However, the relationship between lncRNA MEG3, microRNA-21 (miR-21) and chronic myeloid leukemia (CML) blast crisis is unknown. This study examined bone marrow samples from 40 CML patients and 10 healthy donors. Proliferation and apoptosis assays, real-time polymerase chain reaction (PCR), bisulfite sequencing PCR, Western blotting, luciferase assay, RNA pull-down, RNA immunoprecipitation (RIP), co-immunoprecipitation (CoIP) and Chromatin immunoprecipitation (ChIP) were performed. We found that MEG3 and PTEN expression were down-regulated, whereas, MDM2, DNMT1 and miR-21 were up-regulated in the accelerated and blast phases of CML. Treated with 5-azacytidine decreased the level of MDM2, DNMT1 and miR21, but increased the level of MEG3 and PTEN. Overexpression of MEG3 and silencing the expression of miR-21 inhibited proliferation and induced apoptosis. MEG3 overexpression and silencing the expression of miR21 influence the levels of MMP-2, MMP-9, bcl-2 and Bax. MEG3 was able to interact with MDM2 and EZH2. MDM2 could interact with DNMT1 and PTEN. MYC and AKT can interact with EZH2. ChIP-seq showed that the promoter of KLF4 and SFRP2 interacts with DNMT1. In conclusion, lncRNA MEG3 and its target miR21 may serve as novel therapeutic targets for CML blast crisis; and demethylation drugs might also have potential clinical application in treating CML blast crisis.
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Affiliation(s)
- Ziye Li
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Lin Yang
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaojun Liu
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ziyuan Nie
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jianmin Luo
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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25
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Wang Q, Wu Y, Li F, Zhu H, Zhou B, Qian Y, Ge C, Xu J, Chen L, Chu M, Jiang L, Peng J. Association of genetic polymorphisms in immune-related lncRNA with osteoarthritis susceptibility in Chinese Han population. Per Med 2018; 15:103-110. [PMID: 29714128 DOI: 10.2217/pme-2017-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aim: Immune-related lncRNA may influence osteoarthritis (OA) susceptibility. We conducted this study to assess whether the genetic variants in several immune-related lncRNA influence OA susceptibility. Methods: The current research genotyped four SNPs in 306 OA patients and 316 healthy controls, including PRNCR1 rs7463708, PRNCR1 rs1456315, PRNCR1 rs16901946 and KIF13B1 rs643472, to investigate their associations with OA susceptibility. Results: We identified that PRNCR1 rs1456315 was associated with OA susceptibility in Chinese Han population (recessive model: odds ratio = 2.24; 95% CI: 1.05–4.81; additive model: odds ratio = 1.36; 95% CI: 1.03–1.80). Conclusion: Individuals with PRNCR1 rs1456315 mutant G allele were more likely to suffer from OA in Chinese Han population.
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Affiliation(s)
- Qiang Wang
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Yinliang Wu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Fanian Li
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Heping Zhu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Bo Zhou
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Yuqiang Qian
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Chi Ge
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Jing Xu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Liang Chen
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Miao Chu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Long Jiang
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Jun Peng
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
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26
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Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 2017; 130:1965-1975. [PMID: 28928124 DOI: 10.1182/blood-2017-06-788695] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate cell fate in the hematopoietic system. We focus on a growing number of mechanistic studies to synthesize emerging principles of lncRNA function, emphasizing how they facilitate diversification of gene programming during development. We also survey how disrupted lncRNA function can contribute to malignant transformation, highlighting opportunities for therapeutic intervention in specific myeloid and lymphoid cancers. Finally, we discuss challenges and prospects for further elucidation of lncRNA mechanisms.
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27
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A 4-lncRNA scoring system for prognostication of adult myelodysplastic syndromes. Blood Adv 2017; 1:1505-1516. [PMID: 29296792 DOI: 10.1182/bloodadvances.2017008284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/06/2017] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) not only participate in normal hematopoiesis but also contribute to the pathogenesis of acute leukemia. However, their clinical and prognostic relevance in myelodysplastic syndromes (MDSs) remains unclear to date. In this study, we profiled lncRNA expressions in 176 adult patients with primary MDS, and identified 4 lncRNAs whose expression levels were significantly associated with overall survival (OS). We then constructed a risk-scoring system with the weighted sum of these 4 lncRNAs. Higher lncRNA scores were associated with higher marrow blast percentages, higher-risk subtypes of MDSs (based on both the Revised International Prognostic Scoring System [IPSS-R] and World Health Organization classification), complex cytogenetic changes, and mutations in RUNX1, ASXL1, TP53, SRSF2, and ZRSR2, whereas they were inversely correlated with SF3B1 mutation. Patients with higher lncRNA scores had a significantly shorter OS and a higher 5-year leukemic transformation rate compared with those with lower scores. The prognostic significance of our 4-lncRNA risk score could be validated in an independent MDS cohort. In multivariate analysis, higher lncRNA scores remained an independent unfavorable risk factor for OS (relative risk, 4.783; P < .001) irrespective of age, cytogenetics, IPSS-R, and gene mutations. To our knowledge, this is the first report to provide a lncRNA platform for risk stratification of MDS patients. In conclusion, our integrated 4-lncRNA risk-scoring system is correlated with distinctive clinical and biological features in MDS patients, and serves as an independent prognostic factor for survival and leukemic transformation. This concise yet powerful lncRNA-based scoring system holds the potential to improve the current risk stratification of MDS patients.
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28
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Wang L, Hu Y, Xiang X, Qu K, Teng Y. Identification of long non-coding RNA signature for paclitaxel-resistant patients with advanced ovarian cancer. Oncotarget 2017; 8:64191-64202. [PMID: 28969062 PMCID: PMC5609994 DOI: 10.18632/oncotarget.19828] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/19/2017] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer is the most lethal gynecologic malignancy, characterized by late diagnosis, frequent relapse, and easy development of chemoresistance. Recent studies suggest that lncRNAs are involved in ovarian cancer onset and progression, as well as the resistance in paclitaxel-containing chemotherapy. However, the genome-wide expression pattern and associated functional implications of lncRNAs in paclitaxel-resistant ovarian cancer cells remain undetermined. In the present study, we identified a panel of lncRNAs aberrantly expressed in both paclitaxel resistant ovarian cancer tissues and cell lines, including XR_948297, XR_947831, XR_938728, XR_938392, NR_103801, NR_073113, and NR_036503. Moreover, the seven-lncRNA signature showed a relatively high predictive accuracy of chemoresistance with an area under the ROC curve (AUC) of 0.93, and was associated with progression-free survival inovarian cancer patients (HR=2.05, p=0.015). Our function prediction demonstrated that the seven-lncRNA signature was positively correlated with a cluster containing 129 genes enriched in insulin secretion-related pathway. Our findings suggest that the seven-lncRNA signature may be utilized as potent biomarkers for predicting chemoresistance for ovarian cancer patients with paclitaxel-containing chemotherapy.
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Affiliation(s)
- Luqing Wang
- Department of Nuclear Medicine, Liaocheng People's Hospital, Taishan Medical College, Liaocheng 252000, China
| | - Yanjun Hu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Taishan Medical College, Liaocheng 252000, China
| | - Xiaohong Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Kai Qu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yue Teng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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29
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Bhan A, Soleimani M, Mandal SS. Long Noncoding RNA and Cancer: A New Paradigm. Cancer Res 2017; 77:3965-3981. [PMID: 28701486 DOI: 10.1158/0008-5472.can-16-2634] [Citation(s) in RCA: 1915] [Impact Index Per Article: 273.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 04/05/2017] [Accepted: 05/04/2017] [Indexed: 12/11/2022]
Abstract
In addition to mutations or aberrant expression in the protein-coding genes, mutations and misregulation of noncoding RNAs, in particular long noncoding RNAs (lncRNA), appear to play major roles in cancer. Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer. Alterations in lncRNA expression and their mutations promote tumorigenesis and metastasis. LncRNAs may exhibit tumor-suppressive and -promoting (oncogenic) functions. Because of their genome-wide expression patterns in a variety of tissues and their tissue-specific expression characteristics, lncRNAs hold strong promise as novel biomarkers and therapeutic targets for cancer. In this article, we have reviewed the emerging functions and association of lncRNAs in different types of cancer and discussed their potential implications in cancer diagnosis and therapy. Cancer Res; 77(15); 3965-81. ©2017 AACR.
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Affiliation(s)
- Arunoday Bhan
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas
| | - Milad Soleimani
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas.
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30
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A four-gene LincRNA expression signature predicts risk in multiple cohorts of acute myeloid leukemia patients. Leukemia 2017; 32:263-272. [PMID: 28674423 DOI: 10.1038/leu.2017.210] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/08/2017] [Accepted: 06/21/2017] [Indexed: 12/16/2022]
Abstract
Prognostic gene expression signatures have been proposed as clinical tools to clarify therapeutic options in acute myeloid leukemia (AML). However, these signatures rely on measuring large numbers of genes and often perform poorly when applied to independent cohorts or those with older patients. Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of cell identity and oncogenesis, but knowledge of their utility as prognostic markers in AML is limited. Here we analyze transcriptomic data from multiple cohorts of clinically annotated AML patients and report that (i) microarrays designed for coding gene expression can be repurposed to yield robust lincRNA expression data, (ii) some lincRNA genes are located in close proximity to hematopoietic coding genes and show strong expression correlations in AML, (iii) lincRNA gene expression patterns distinguish cytogenetic and molecular subtypes of AML, (iv) lincRNA signatures composed of three or four genes are independent predictors of clinical outcome and further dichotomize survival in European Leukemia Net (ELN) risk groups and (v) an analytical tool based on logistic regression analysis of quantitative PCR measurement of four lincRNA genes (LINC4) can be used to determine risk in AML.
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31
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Guo H, Wu L, Zhao P, Feng A. Overexpression of long non-coding RNA zinc finger antisense 1 in acute myeloid leukemia cell lines influences cell growth and apoptosis. Exp Ther Med 2017; 14:647-651. [PMID: 28672980 PMCID: PMC5488414 DOI: 10.3892/etm.2017.4535] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/06/2017] [Indexed: 01/17/2023] Open
Abstract
The association between long non-coding RNA zinc finger antisense 1 (ZFAS1) and acute myeloid leukemia (AML) has not yet been investigated. The present study aimed to assess the potential role of ZFAS1 in AML cell proliferation and apoptosis. The expression of ZFAS1 mRNA in various AML cell lines (HL-60, KG-1, ML-1 and SKNO-1) was measured by reverse transcription-quantitative polymerase chain reaction. The results showed that ZFAS1 expression was increased in all four human AML cell lines compared with the control cell lines (T lymphocytic leukemia or Burkitt's lymphoma). Transfection with small interfering RNA into human AML cells established ZFAS1 knockdown. A cell-counting kit-8 (CCK-8) assay was used to investigate the effect of ZFAS1 on AML cell proliferation and the effect of ZFAS1 on the cell cycle and cell apoptosis was assessed using flow cytometry. Notably, the CCK-8 assay demonstrated that ZFAS1 knockdown inhibited cell proliferation in HL-60 and SKNO-1 cell lines and flow cytometry analysis indicated that ZFAS1 knockdown induced AML cell cycle G1 phase arrest and triggered cell apoptosis. Therefore, the present study indicated that ZFAS1 promoted the proliferation and inhibited the apoptosis of AML cells.
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Affiliation(s)
- Haifei Guo
- Department of Hematology, Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang 325200, P.R. China
| | - Lili Wu
- Department of Medical Oncology, Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang 325200, P.R. China
| | - Pu Zhao
- Department of Hematology, Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang 325200, P.R. China
| | - Aimei Feng
- Department of Hematology, Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang 325200, P.R. China
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32
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Lyu Y, Lou J, Yang Y, Feng J, Hao Y, Huang S, Yin L, Xu J, Huang D, Ma B, Zou D, Wang Y, Zhang Y, Zhang B, Chen P, Yu K, Lam EWF, Wang X, Liu Q, Yan J, Jin B. Dysfunction of the WT1-MEG3 signaling promotes AML leukemogenesis via p53-dependent and -independent pathways. Leukemia 2017; 31:2543-2551. [PMID: 28400619 PMCID: PMC5729340 DOI: 10.1038/leu.2017.116] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/16/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a pivotal role in tumorigenesis, exemplified by the recent finding that lncRNA maternally expressed gene 3 (MEG3) inhibits tumor growth in a p53-dependent manner. Acute myeloid leukemia (AML) is the most common malignant myeloid disorder in adults, and TP53 mutations or loss are frequently detected in patients with therapy-related AML or AML with complex karyotype. Here, we reveal that MEG3 is significantly downregulated in AML and suppresses leukemogenesis not only in a p53-dependent, but also a p53-independent manner. In addition, MEG3 is proven to be transcriptionally activated by Wilms’ tumor 1 (WT1), dysregulation of which by epigenetic silencing or mutations is causally involved in AML. Therefore MEG3 is identified as a novel target of the WT1 molecule. Ten–eleven translocation-2 (TET2) mutations frequently occur in AML and significantly promote leukemogenesis of this disorder. In our study, TET2, acting as a cofactor of WT1, increases MEG3 expression. Taken together, our work demonstrates that TET2 dysregulated WT1-MEG3 axis significantly promotes AML leukemogenesis, paving a new avenue for diagnosis and treatment of AML patients.
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Affiliation(s)
- Y Lyu
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - J Lou
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Neurosurgery, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Y Yang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - J Feng
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Y Hao
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - S Huang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - L Yin
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - J Xu
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - D Huang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - B Ma
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Neurosurgery, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - D Zou
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Y Wang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - Y Zhang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - B Zhang
- Department of Neurosurgery, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - P Chen
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - K Yu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - E W-F Lam
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - X Wang
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Q Liu
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - J Yan
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,Department of Hematology, the Second Affiliated Hospital, Institute of Hematopoeitic Stem Cell Transplantation of Dalian Medical University, Liaoning Hematopoeitic Stem Cell Transplantation Medical Center, Dalian Key Laboratory of Hematology, Dalian Medical University, Dalian, China
| | - B Jin
- Department of Hematology, the Second Affiliated Hospital, Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
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33
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Wahlster L, Daley GQ. Progress towards generation of human haematopoietic stem cells. Nat Cell Biol 2016; 18:1111-1117. [PMID: 27723718 DOI: 10.1038/ncb3419] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
De novo generation of haematopoietic stem cells from different human pluripotent stem cell sources remains a high priority for haematology and regenerative medicine. At present, efficient derivation of functional haematopoietic stem cells with the capability for definitive in vivo engraftment and multi-lineage potential remains challenging. Here, we discuss recent progress and strategies to overcome obstacles that have thwarted past efforts. In addition, we review promising advances in the generation of mature blood lineages and the potential of induced pluripotent stem cells.
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Affiliation(s)
- Lara Wahlster
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, 02115 Massachusetts, USA; in the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115 Massachusetts, USA; and at the Harvard Stem Cell Institute, Boston, 02115 Massachusetts, USA.,Department of General Pediatrics, Heidelberg University Hospital, Ruprecht-Karls-University Heidelberg, Heidelberg, 69120 Germany
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, 02115 Massachusetts, USA; in the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115 Massachusetts, USA; and at the Harvard Stem Cell Institute, Boston, 02115 Massachusetts, USA
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34
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Identification of long noncoding RNA expression profile in oxaliplatin-resistant hepatocellular carcinoma cells. Gene 2016; 596:53-88. [PMID: 27729273 DOI: 10.1016/j.gene.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 09/23/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent and malignant type of liver cancer. Besides the high incidence, the resistance to chemotherapy is a major problem that leads to the high mortality of HCC. Recently, aberrant expression of long noncoding RNAs (lncRNAs) has been considered as a primary feature of many types of cancer. However, the genome-wide expression pattern and associated functional implications of lncRNAs in chemo-resistant HCC cells remain unknown. In this study, we identified 120 differentially expressed lncRNAs with 61 up-regulated and 59 down-regulated (fold change>2, p<0.05) along with 421 differentially expressed mRNAs with 228 up-regulated and 193 down-regulated (fold change>2, p<0.05) in oxaliplatin-resistant (MHCC97H-OXA) HCC cells, compared to parental oxaliplatin-sensitive (MHCC97H) by microarray. The underlying pathways were related to cell death, proliferation, cellular response to stimulus, including p53 pathway, ErbB pathway and MAPK pathway. Further, 16 lncRNAs were selected for validation of microarray results with quantitative PCR, and a strong correlation was identified between the qPCR results and microarray data. We demonstrated for the first time that ENST00000438347, NR_073453 and ENST00000502804 were up-regulated in MHCC97H-OXA cells as well as chemo-resistant HCC cancerous tissues. Moreover, the expression of ENST00000518376 was significantly associated with the tumor size and differentiation. Overall survival analysis showed that high expression of ENST00000438347 and ENST00000518376 was associated with poor prognosis in HCC patients. Taken together, our results reveal that the expression profile in oxaliplatin-resistant HCC is significantly altered including lncRNAs. And a series of de novo lncRNAs play important functions in HCC oxaliplatin resistance and HCC progression.
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Ding N, Xi J, Li Y, Xie X, Shi J, Zhang Z, Li Y, Fang F, Wang S, Yue W, Pei X, Fang X. Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. Front Med 2016; 10:297-310. [PMID: 27272188 DOI: 10.1007/s11684-016-0452-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022]
Abstract
Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.
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Affiliation(s)
- Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiafei Xi
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Yanming Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoyan Xie
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Jian Shi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaojun Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhua Li
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Fang Fang
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Sihan Wang
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Wen Yue
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Xuetao Pei
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China. .,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China.
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Abstract
The daily production of up to 1011 erythrocytes is tightly controlled to maintain the number of erythrocytes in peripheral blood between narrow boundaries. Availability of growth factors and nutrients, particularly iron, control the proliferation and survival of precursor cells partly through control of mRNA translation. General translation initiation mechanisms can selectively control translation of transcripts that carry specific structures in the UTRs. This selective mRNA translation is an important layer of gene expression regulation in erythropoiesis. Ribosome profiling is a recently developed high throughput sequencing technique for global mapping of translation initiation sites across the transcriptome. Here we describe what is known about control of mRNA translation in erythropoiesis and how ribosome profiling will help to further our knowledge. Ribosome footprinting will give insight in transcript-specific translation at codon resolution, which is of great value to understand many cellular processes during erythropoiesis. It will be of particular interest to understand responses to iron availability and reactive oxygen species (ROS), which affects translation initiation of transcripts harbouring upstream ORFs (uORF) and potential alternative downstream ORFs (aORF).
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Rodríguez-Malavé NI, Fernando TR, Patel PC, Contreras JR, Palanichamy JK, Tran TM, Anguiano J, Davoren MJ, Alberti MO, Pioli KT, Sandoval S, Crooks GM, Rao DS. BALR-6 regulates cell growth and cell survival in B-lymphoblastic leukemia. Mol Cancer 2015; 14:214. [PMID: 26694754 PMCID: PMC4688921 DOI: 10.1186/s12943-015-0485-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 12/11/2015] [Indexed: 12/31/2022] Open
Abstract
Background A new class of non-coding RNAs, known as long non-coding RNAs (lncRNAs), has been recently described. These lncRNAs are implicated to play pivotal roles in various molecular processes, including development and oncogenesis. Gene expression profiling of human B-ALL samples showed differential lncRNA expression in samples with particular cytogenetic abnormalities. One of the most promising lncRNAs identified, designated B-ALL associated long RNA-6 (BALR-6), had the highest expression in patient samples carrying the MLL rearrangement, and is the focus of this study. Results Here, we performed a series of experiments to define the function of BALR-6, including several novel splice forms that we identified. Functionally, siRNA-mediated knockdown of BALR-6 in human B-ALL cell lines caused reduced cell proliferation and increased cell death. Conversely, overexpression of BALR-6 isoforms in both human and mouse cell lines caused increased proliferation and decreased apoptosis. Overexpression of BALR-6 in murine bone marrow transplantation experiments caused a significant increase in early hematopoietic progenitor populations, suggesting that its dysregulation may cause developmental changes. Notably, the knockdown of BALR-6 resulted in global dysregulation of gene expression. The gene set was enriched for leukemia-associated genes, as well as for the transcriptome regulated by Specificity Protein 1 (SP1). We confirmed changes in the expression of SP1, as well as its known interactor and downstream target CREB1. Luciferase reporter assays demonstrated an enhancement of SP1-mediated transcription in the presence of BALR-6. These data provide a putative mechanism for regulation by BALR-6 in B-ALL. Conclusions Our findings support a role for the novel lncRNA BALR-6 in promoting cell survival in B-ALL. Furthermore, this lncRNA influences gene expression in B-ALL in a manner consistent with a function in transcriptional regulation. Specifically, our findings suggest that BALR-6 expression regulates the transcriptome downstream of SP1, and that this may underlie the function of BALR-6 in B-ALL. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0485-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Norma I Rodríguez-Malavé
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA. .,Cellular and Molecular Pathology Ph.D. Program, UCLA, Los Angeles, USA.
| | - Thilini R Fernando
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Parth C Patel
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Jorge R Contreras
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA. .,Cellular and Molecular Pathology Ph.D. Program, UCLA, Los Angeles, USA.
| | - Jayanth Kumar Palanichamy
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA. .,All India Institute of Medical Sciences (AIIMS), New Delhi, India.
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Jaime Anguiano
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Michael J Davoren
- Department of Environmental Health Sciences, UCLA, Los Angeles, USA. .,Molecular Toxicology Interdepartmental Ph.D. Program, UCLA, Los Angeles, USA.
| | - Michael O Alberti
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Kimanh T Pioli
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Salemiz Sandoval
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
| | - Gay M Crooks
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA. .,Cellular and Molecular Pathology Ph.D. Program, UCLA, Los Angeles, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, USA. .,Broad Stem Cell Research Center, UCLA, 650 Charles E. Young Drive, Factor 12-272, Los Angeles, CA, 90095, USA.
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA. .,Cellular and Molecular Pathology Ph.D. Program, UCLA, Los Angeles, USA. .,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, USA. .,Broad Stem Cell Research Center, UCLA, 650 Charles E. Young Drive, Factor 12-272, Los Angeles, CA, 90095, USA.
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38
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Alvarez-Dominguez JR, Bai Z, Xu D, Yuan B, Lo KA, Yoon MJ, Lim YC, Knoll M, Slavov N, Chen S, Peng C, Lodish HF, Sun L. De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development. Cell Metab 2015; 21:764-776. [PMID: 25921091 PMCID: PMC4429916 DOI: 10.1016/j.cmet.2015.04.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/17/2014] [Accepted: 03/31/2015] [Indexed: 12/21/2022]
Abstract
Brown adipose tissue (BAT) protects against obesity by promoting energy expenditure via uncoupled respiration. To uncover BAT-specific long non-coding RNAs (lncRNAs), we used RNA-seq to reconstruct de novo transcriptomes of mouse brown, inguinal white, and epididymal white fat and identified ∼1,500 lncRNAs, including 127 BAT-restricted loci induced during differentiation and often targeted by key regulators PPARγ, C/EBPα, and C/EBPβ. One of them, lnc-BATE1, is required for establishment and maintenance of BAT identity and thermogenic capacity. lnc-BATE1 inhibition impairs concurrent activation of brown fat and repression of white fat genes and is partially rescued by exogenous lnc-BATE1 with mutated siRNA-targeting sites, demonstrating a function in trans. We show that lnc-BATE1 binds heterogeneous nuclear ribonucleoprotein U and that both are required for brown adipogenesis. Our work provides an annotated catalog for the study of fat depot-selective lncRNAs and establishes lnc-BATE1 as a regulator of BAT development and physiology.
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Affiliation(s)
- Juan R Alvarez-Dominguez
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Zhiqiang Bai
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Dan Xu
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Bingbing Yuan
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Kinyui Alice Lo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Myeong Jin Yoon
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yen Ching Lim
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Marko Knoll
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Nikolai Slavov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Shuai Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | - Chen Peng
- Division of Bioengineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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39
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Abstract
EB virus (EBV) is associated with heterogeneous lymphomas. In these lymphomas EBV+ lymphoma cells are embedded in non-neoplastic bystanders: B and T cells, macrophages. Without these bystander cells, the lymphoma cells are incapable of being engrafted in immunodeficient mice. In this context, the bystanders are tumor-supportive "inflammatory niche". Recently, EBV-infected cells produce exosomes that contain EBV specifically encoded miRNAs (EBV-miRNAs). Accordingly, we hypothesized that exosomal EBV-miRNAs might redirect tumor surrounding immune cells from tumor reactive into tumor-supportive "inflammatory niche". The EBV-miRNAs in the exosome secreted from EBV positive lymphoma cells significantly influenced on monocyte/macrophage Mo/Mf in inducing CD69, IL-10, and TNF, suggesting that EBV-miRNAs might polarize Mo/Mf into tumor associated Mf (TAM). EBV-miRNAs were required to develop lymphoproliferative disease (LPD) in vivo mouse model. Moreover, when Mfs were depleted by clodronate liposome, EBV positive tumor cells disappeared. These results suggest that lymphoma-derived secretary EBV-miRNAs regulate Mo/Mf to support the lymphoma survival or development. Most importantly, exosomal EBV-miRNAs derived from the lymphoma cells were transferred to Mf in human EBV+ lymphoma samples, which showed correlation with prognosis.
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Affiliation(s)
- Ai Kotani
- Tokai University the Institute of Medical Science Devision of Hematological malignancy, Tokai University School of Medicien, Internal Medicien, Hematology and Oncology
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