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Karoii DH, Azizi H, Skutella T. Whole transcriptome analysis to identify non-coding RNA regulators and hub genes in sperm of non-obstructive azoospermia by microarray, single-cell RNA sequencing, weighted gene co-expression network analysis, and mRNA-miRNA-lncRNA interaction analysis. BMC Genomics 2024; 25:583. [PMID: 38858625 PMCID: PMC11165898 DOI: 10.1186/s12864-024-10506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The issue of male fertility is becoming increasingly common due to genetic differences inherited over generations. Gene expression and evaluation of non-coding RNA (ncRNA), crucial for sperm development, are significant factors. This gene expression can affect sperm motility and, consequently, fertility. Understanding the intricate protein interactions that play essential roles in sperm differentiation and development is vital. This knowledge could lead to more effective treatments and interventions for male infertility. MATERIALS AND METHODS Our research aim to identify new and key genes and ncRNA involved in non-obstructive azoospermia (NOA), improving genetic diagnosis and offering more accurate estimates for successful sperm extraction based on an individual's genotype. RESULTS We analyzed the transcript of three NOA patients who tested negative for genetic sperm issues, employing comprehensive genome-wide analysis of approximately 50,000 transcript sequences using microarray technology. This compared gene expression profiles between NOA sperm and normal sperm. We found significant gene expression differences: 150 genes were up-regulated, and 78 genes were down-regulated, along with 24 ncRNAs up-regulated and 13 ncRNAs down-regulated compared to normal conditions. By cross-referencing our results with a single-cell genomics database, we identified overexpressed biological process terms in differentially expressed genes, such as "protein localization to endosomes" and "xenobiotic transport." Overrepresented molecular function terms in up-regulated genes included "voltage-gated calcium channel activity," "growth hormone-releasing hormone receptor activity," and "sialic acid transmembrane transporter activity." Analysis revealed nine hub genes associated with NOA sperm: RPL34, CYB5B, GOL6A6, LSM1, ARL4A, DHX57, STARD9, HSP90B1, and VPS36. CONCLUSIONS These genes and their interacting proteins may play a role in the pathophysiology of germ cell abnormalities and infertility.
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Affiliation(s)
- Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran.
| | - Thomas Skutella
- Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
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2
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Sabaghi F, Sadat SY, Mirsaeedi Z, Salahi A, Vazifehshenas S, Kesh NZ, Balavar M, Ghoraeian P. The Role of Long Noncoding RNAs in Progression of Leukemia: Based on Chromosomal Location. Microrna 2024; 13:14-32. [PMID: 38275047 DOI: 10.2174/0122115366265540231201065341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 10/12/2023] [Indexed: 01/27/2024]
Abstract
Long non-coding RNA [LncRNA] dysregulation has been seen in many human cancers, including several kinds of leukemia, which is still a fatal disease with a poor prognosis. LncRNAs have been demonstrated to function as tumor suppressors or oncogenes in leukemia. This study covers current research findings on the role of lncRNAs in the prognosis and diagnosis of leukemia. Based on recent results, several lncRNAs are emerging as biomarkers for the prognosis, diagnosis, and even treatment outcome prediction of leukemia and have been shown to play critical roles in controlling leukemia cell activities, such as proliferation, cell death, metastasis, and drug resistance. As a result, lncRNA profiles may have superior predictive and diagnostic potential in leukemia. Accordingly, this review concentrates on the significance of lncRNAs in leukemia progression based on their chromosomal position.
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Affiliation(s)
- Fatemeh Sabaghi
- Department of Molecular cell biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saina Yousefi Sadat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zohreh Mirsaeedi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Aref Salahi
- Department of Molecular cell biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sara Vazifehshenas
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Neda Zahmat Kesh
- Department of Genetics, Zanjan Branch Islamic Azad University, Zanjan, Iran
| | - Mahdieh Balavar
- Department of Genetics, Falavarjan Branch Islamic Azad University, Falavarjan, Iran
| | - Pegah Ghoraeian
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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3
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Xu Q, Guo T. Somatic mutation-associated risk index based on lncRNA expression for predicting prognosis in acute myeloid leukemia. Hematology 2022; 27:659-671. [PMID: 35666642 DOI: 10.1080/16078454.2022.2056677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Objectives: Genomic instability has several implications for acute myeloid leukemia (AML) prognosis. This article aims to construct a somatic mutation-associated risk index (SMRI) of genomic instability for AML to predict prognosis and explore the potential determinants of AML prognosis.Methods: We obtained differentially expressed lncRNAs from genomic instability subtypes and selected six lncRNAs to construct the SMRI through multivariate Cox regression analysis. The median SMRI classified patients into high and low SMRI groups. Kaplan-Meier survival analysis was used to clarify the prognostic differences of SMRI subtypes. Receiver operating characteristic curve analysis was performed to elucidate the value of SMRI as a prognostic indicator. Gene set variation analysis, tumor mutation burden (TMB) analysis, immune infiltration, and immune checkpoint expression analysis were performed to investigate possible causes for the differences in prognosis of SMRI subtypes.Results: The high SMRI group exhibited a poor prognosis, which was characterized by elevated levels of TMB, mutation counts (TP53, NPM1, DNMT3A, and FLT3-TKD), CD8+ T cell infiltration, and immune checkpoint (PD-1, PD-L2, CTLA4, LAG3) expression. The SMRI was still associated with prognosis, even after adjustment for age, sex, cytogenetic risk, DNMT3A status, FLT3 status, and NPM1 status. Gene set variation analysis showed that AML with FLT3-ITD mutation, CEBPA mutation, and LSCs (leukemia stem cells) were enriched in the high SMRI group.Conclusion: Our research suggests that the SMRI derived from genomic instability subtypes is a useful biomarker for predicting prognosis and may be beneficial for improving the clinical outcome of patients with AML.
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Affiliation(s)
- Qiang Xu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Tao Guo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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4
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Hola MAM, Ali MAM, ElNahass Y, Salem TAE, Mohamed MR. Expression and prognostic relevance of long noncoding RNAs CRNDE and AOX2P in adult acute myeloid leukemia. Int J Lab Hematol 2021; 43:732-742. [PMID: 34129278 DOI: 10.1111/ijlh.13586] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/06/2021] [Accepted: 04/29/2021] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Several long noncoding RNAs (lncRNAs) have been demonstrated to play a critical role in the tumorigenesis of acute myeloid leukemia (AML), and altered expression of certain lncRNAs has been recognized as a potential prognostic marker in AML patients. Here, we sought to determine whether the expression of the lncRNA colorectal neoplasia differentially expressed (CRNDE) and aldehyde oxidase 2 pseudogene (AOX2P) is associated with clinicopathological features and clinical outcome of patients with AML. METHODS CRNDE and AOX2P expression levels were measured in diagnostic blood samples from 200 adult patients with de novo AML, along with 50 healthy control blood samples, using quantitative real-time polymerase chain reaction (qRT-PCR). The association of CRNDE and AOX2P expression with the clinicopathological characteristics and outcome of AML patients was analyzed. RESULTS Upregulated CRNDE expression was independently associated with lower complete remission (CR) rates in the whole cohort of AML (P < .001). AOX2P overexpression was identified as an independent adverse prognostic marker for CR in the CN-AML (P = .009) and non-t (15;17) AML (P < .001) subgroups. Patients with high CRNDE expression had a significantly shorter event-free survival (EFS, whole cohort of AML: P = .017; CN-AML: P = .001; non-t (15;17) AML: P = .006) and inferior overall survival (OS, whole cohort of AML: P = .002; t(15;17) AML: P = .001) than those with low CRNDE expression. EFS and OS did not differ significantly between patients with high AOX2P expression and those with low expression. CONCLUSION Aberrantly upregulated CRNDE expression and, to a lesser extent, AOX2P overexpression, are associated with poor prognosis in AML patients, suggesting that the determination of CRNDE and, perhaps, AOX2P, expression level at diagnosis provides valuable prognostic information, allows refinement of risk stratification, and helps clinical decision-making in AML.
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Affiliation(s)
- Mona A M Hola
- Cytogenetics and Molecular Biology Laboratory, Nasser Institute for Research and Treatment, Cairo, Egypt
| | - Mohamed A M Ali
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Yasser ElNahass
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Tarek A E Salem
- Department of Molecular Biology, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Menofia, Egypt.,Department of Pathology, Biochemistry Unit, College of Medicine, Qassim University, Buraydah, Qassim, Saudi Arabia
| | - Mohamed R Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
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5
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Elcheva IA, Spiegelman VS. The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia. Cancers (Basel) 2020; 12:E3854. [PMID: 33419342 PMCID: PMC7766907 DOI: 10.3390/cancers12123854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
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Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
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6
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Zhang W, Liu Y, Zhang J, Zheng N. Long Non-Coding RNA Taurine Upregulated Gene 1 Targets miR-185 to Regulate Cell Proliferation and Glycolysis in Acute Myeloid Leukemia Cells in vitro. Onco Targets Ther 2020; 13:7887-7896. [PMID: 32982274 PMCID: PMC7493018 DOI: 10.2147/ott.s238189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a group of malignant hematopoietic system diseases. Taurine-upregulated gene 1 (TUG1) is a long non-coding RNA that has been associated with human cancers, including AML. However, the role and molecular mechanisms of TUG1 in AML remains to be defined. Methods Expression of TUG1 and miR-185 was detected using RT-qPCR. Cell viability and apoptotic rate were measured by MTT assay and flow cytometry, respectively. Glycolysis was determined by commercial glucose and lactate assay kits and Western blot. The target binding between TUG1 and miR-185 was predicted on Starbase online database and confirmed by luciferase reporter assay and RNA immunoprecipitation. Results TUG1 was upregulated and miR-185 was downregulated in the peripheral blood mononuclear cells of AML specimens and cells (HL-60, KG-1, MOLM-14, and MOLM-13). Both TUG1 knockdown and miR-185 overexpression via transfection could suppress cell viability, glucose consumption, lactate production, and hexokinase 2 expression, but promote apoptotic rate in HL-60 and KG-1 cells. Notably, TUG1 functioned as a sponge of miR-185 by target binding. Moreover, downregulation of miR-185 could partially overturn the effect of TUG1 knockdown on cell proliferation and glycolysis in HL-60 and KG-1 cells. Conclusion Expression of TUG1 was upregulated in AML patients and cells, and its knockdown repressed cell proliferation and glycolysis in AML cells in vitro by targeting miR-185.
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Affiliation(s)
- Weide Zhang
- Department of Hematology, The People's Hospital of Shouguang, Shouguang, Shandong, People's Republic of China
| | - Yuhua Liu
- Department of Digestive Oncology, The Gansu Provincial Cancer Hospital, Lanzhou, Gansu, People's Republic of China
| | - Jing Zhang
- Department of Psychiatry, Shouguang Mental and Health Care Center, Shouguang, Shandong, People's Republic of China
| | - Ni Zheng
- Department of Clinical Laboratory, Shengli Oilfield Central Hospital, Dongying, Shandong, People's Republic of China
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7
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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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8
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Chen L, Fan X, Zhu J, Chen X, Liu Y, Zhou H. LncRNA MAGI2-AS3 inhibits the self-renewal of leukaemic stem cells by promoting TET2-dependent DNA demethylation of the LRIG1 promoter in acute myeloid leukaemia. RNA Biol 2020; 17:784-793. [PMID: 32174258 DOI: 10.1080/15476286.2020.1726637] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The presence or absence of cytogenetic mutations is proposed to be responsible for the pathogenesis of acute myeloid leukaemia (AML). However, the current classification system is inadequate to elucidate the molecular heterogeneity of the disease, and therapy failures frequently occur. Leukaemia stem cells (LSCs) initiate and maintain the clonal hierarchy of AML and exhibit properties of self-renewal remaining recalcitrant to conventional chemotherapy. In this study, we identified a novel long non-coding RNA (lncRNA) MAGI2 antisense RNA 3 (MAGI2-AS3) in AML and investigated its functional role in regulating LSCs self-renewal. LSCs were identified by immunoprofiling of CD34+ CD123+ in AML patients' marrow. MAGI2-AS3 exhibited a poor expression level in LSCs than the normal human haematopoietic stem cells. Lentivirus-mediated upregulation of MAGI2-AS3 or leucine-rich repeats and Ig-like domains 1 (LRIG1) impaired LSCs self-renewal. MAGI2-AS3-overexpressed LSCs acquired the ability of self-renewal following lentivirus-mediated knockdown of LRIG1. Methylation-dependent inhibition of LRIG1 was evident in LSCs. MAGI2-AS3 was found to induce occupancy of TET2 at the LRIG1 promoter. Lentivirus-mediated downregulation of TET2 could impair MAGI2-AS3-mediated elevation of LRIG1 and neutralize the inhibitory effect of MAGI2-AS3 on LSCs self-renewal. In vivo analysis indicated an elevated overall survival of NOD/SCID mice injected with LSCs in the presence of MAGI2-AS3. Altogether, the key findings support the potential of lncRNA MAGI2-AS3 to serve as a novel candidate for the improvement of AML treatment.
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Affiliation(s)
- Lijuan Chen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Xu Fan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University , Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis & National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jianhua Zhu
- Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Xuexin Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Yiling Liu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Hao Zhou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
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9
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Bárcenas-López DA, Núñez-Enríquez JC, Hidalgo-Miranda A, Beltrán-Anaya FO, May-Hau DI, Jiménez-Hernández E, Bekker-Méndez VC, Flores-Lujano J, Medina-Sansón A, Tamez-Gómez EL, López-García VH, Lara-Ramos JR, Núñez-Villegas NN, Peñaloza-González JG, Flores-Villegas LV, Amador-Sánchez R, Espinosa-Elizondo RM, Martín-Trejo JA, Velázquez-Aviña MM, Merino-Pasaye LE, Pérez-Saldívar ML, Duarte-Rodríguez DA, Torres-Nava JR, Cortés-Herrera B, Solís-Labastida KA, González-Ávila AI, Santillán-Juárez JD, García-Velázquez AJ, Rosas-Vargas H, Mata-Rocha M, Sepúlveda-Robles OA, Mejía-Aranguré JM, Jiménez-Morales S. Transcriptome Analysis Identifies LINC00152 as a Biomarker of Early Relapse and Mortality in Acute Lymphoblastic Leukemia. Genes (Basel) 2020; 11:genes11030302. [PMID: 32183133 PMCID: PMC7140896 DOI: 10.3390/genes11030302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Evidence showing the role of long non-coding RNAs (lncRNAs) in leukemogenesis have emerged in the last decade. It has been proposed that these genes can be used as diagnosis and/or prognosis biomarkers in childhood acute lymphoblastic leukemia (ALL). To know if lncRNAs are associated with early relapse and early mortality, a microarray-based gene expression analysis in children with B-lineage ALL (B-ALL) was conducted. Cox regression analyses were performed. Hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated. LINC00152 and LINC01013 were among the most differentially expressed genes in patients with early relapse and early mortality. For LINC00152 high expression, the risks of relapse and death were HR: 4.16 (95% CI: 1.46–11.86) and HR: 1.99 (95% CI: 0.66–6.02), respectively; for LINC01013 low expression, the risks of relapse and death were HR: 3.03 (95% CI: 1.14–8.05) and HR: 6.87 (95% CI: 1.50–31.48), respectively. These results were adjusted by NCI risk criteria and chemotherapy regimen. The lncRNA–mRNA co-expression analysis showed that LINC00152 potentially regulates genes involved in cell substrate adhesion and peptidyl–tyrosine autophosphorylation biological processes. The results of the present study point out that LINC00152 could be a potential biomarker of relapse in children with B-ALL.
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Affiliation(s)
- Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Fredy Omar Beltrán-Anaya
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Didier Ismael May-Hau
- Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico;
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Aurora Medina-Sansón
- Servicio de Hemato-Oncologia, Hospital Infantil de México Federico Gómez, Secretaria de Salud (SS), Mexico City 06720, Mexico;
| | - Edna Liliana Tamez-Gómez
- Servicio de Hemato-Oncología Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Víctor Hugo López-García
- Servicio de Ortopedia Pediátrica, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - José Ramón Lara-Ramos
- Departamento de Genética, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Nora Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - José Gabriel Peñaloza-González
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - Raquel Amador-Sánchez
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Rosa Martha Espinosa-Elizondo
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Martha Margarita Velázquez-Aviña
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaria de Salud del D.F., Mexico City 15530, Mexico;
| | - Beatriz Cortés-Herrera
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Ana Itamar González-Ávila
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Jessica Denisse Santillán-Juárez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Alejandra Jimena García-Velázquez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Haydee Rosas-Vargas
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Minerva Mata-Rocha
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
- Coordinación de Investigación en Salud, IMSS, Mexico City 06720, Mexico
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
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Cao L, Hu SY, Pan J, Wang Y, He HL, Lu J, Xiao PF, Du ZZ, Gu GX, Chai YH. [The effects of long non-coding RNA AC002454.1 on the biological behaviour of NB4 leukemia cells]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 40:862-865. [PMID: 31775489 PMCID: PMC7364985 DOI: 10.3760/cma.j.issn.0253-2727.2019.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- L Cao
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - S Y Hu
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - J Pan
- Institute of Pediatrics, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Y Wang
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - H L He
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - J Lu
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - P F Xiao
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Z Z Du
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
| | - G X Gu
- Institute of Pediatrics, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Y H Chai
- Hematology-Oncology Department, Children's Hospital of Soochow University, Suzhou 215025, China
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11
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Zheng J, Song Y, Li Z, Tang A, Fei Y, He W. The implication of lncRNA expression pattern and potential function of lncRNA RP4-576H24.2 in acute myeloid leukemia. Cancer Med 2019; 8:7143-7160. [PMID: 31568697 PMCID: PMC6885877 DOI: 10.1002/cam4.2518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent studies have revealed that long noncoding RNAs (lncRNAs) may hold crucial triggers of the pathogenesis of hematological malignancies, while the studies evaluating the expression pattern of lncRNA in acute myeloid leukemia (AML) are few. Thus, this study aimed to investigate the implication of lncRNA expression pattern in AML development and progression. METHODS Bone marrow samples from four AML patients and four controls were subjected to lncRNA sequencing. Then, bone marrow samples from 110 AML patients and 40 controls were proposed to real-time quantitative polymerase chain reaction (RT-qPCR) validation for 10 candidate lncRNAs. Clinical data and survival profiles were recorded in AML patients. Furthermore, lncRNA RP4-576H24.2 expression in AML cell lines and its effect on AML cell proliferation and apoptosis were detected. RESULTS LncRNA expression pattern by sequencing clearly distinguished AML patients from controls, and 630 upregulated and 621 downregulated lncRNAs were identified in AML patients compared to controls, which were mainly enriched in AML oncogene-related biological process and pathways (such as neutrophil degranulation, leukocyte transendothelial migration, and hematopoietic cell lineage). RT-qPCR validation observed that six lncRNAs correlated with AML risk, one lncRNA associated with risk stratification, and three lncRNAs correlated with survivals, among which lncRNA RP4-576H24.2 was the only one correlated with AML susceptibility, risk stratification, and survivals. Further in vitro experiments showed that lncRNA RP4-576H24.2 was upregulated in AML cell lines compared to normal bone marrow mononuclear cells (BMMCs), and promoted proliferation while inhibited apoptosis in HL-60 and KG-1 cells. CONCLUSIONS LncRNA expression pattern is closely involved in the development and progression of AML, and several specific lncRNAs exhibit potential to be biomarkers for AML risk and prognosis. Besides, lncRNA RP4-576H24.2 might be a potential oncogene in AML pathogenesis.
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Affiliation(s)
- Jifu Zheng
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuan Song
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenjiang Li
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Aiping Tang
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yan Fei
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenfeng He
- Key Laboratory of Molecular Medicine of Jiangxi, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Liu J, Wang Y, Chen P, Ma Y, Wang S, Tian Y, Wang A, Wang D. AC002454.1 and CDK6 synergistically promote endometrial cell migration and invasion in endometriosis. Reproduction 2019; 157:535-543. [DOI: 10.1530/rep-19-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
Previous lncRNA microarray screening found that the AC002454.1 gene was highly expressed in endometriosis (EMS), and these expression levels were highly correlated with cyclin-dependent kinase-6 (CDK6). This study investigated the expression level and correlation between AC002454.1 and CDK6 in endometrium tissues and the influence of these changes in expression upon the biological behavior of eutopic endometrial cells. We confirmed AC002454.1 and CDK6 mRNA and protein were highly expressed in ectopic and eutopic endometrial tissue from patients with EMS and were clearly correlated. In vitro, both AC002454.1 and CDK6 positively regulated the proliferation, migration and invasion ability of eutopic endometrial cells and could promote the transformation of cells from G0/G1 phase to S phase. AC002454.1 and CDK6 may have synergistic effects, thereby affecting the biological behavior of endometrial cells, and thus promote the progression of EMS.
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Luo W, Yu H, Zou X, Ni X, Wei J. Long non-coding RNA taurine-upregulated gene 1 correlates with unfavorable prognosis in patients with refractory or relapsed acute myeloid leukemia treated by purine analogue based chemotherapy regimens. Cancer Biomark 2019; 23:485-494. [PMID: 30347595 DOI: 10.3233/cbm-181405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study aimed to explore the correlation of long non-coding RNA taurine-upregulated gene 1 (lncRNA TUG1) expression with clinicopathological features and its predictive value for treatment response and survival profiles in refractory or relapsed acute myeloid leukemia (R/R AML) patients. METHODS Seventy three R/R AML patients who received cladribine combined with cytarabine and granulocyte colony-stimulating factor (G-CSF) (CLAG) or fludarabine combined with cytarabine and G-CSF (FLAG) based chemotherapy and 37 non-malignant controls were recruited. LncRNA TUG1 expression was detected in bone marrow sample obtained before treatment. Complete response (CR), partial response (PR), overall response rate (ORR) and overall survival (OS) were evaluated. RESULTS LncRNA TUG1 expression was upregulated in R/R AML patients compared to controls. It was also elevated in R/R AML patients with age ⩾ 60 years (vs. age < 60 years, P= 0.030) and in patients with secondary AML (vs. primary AML, P= 0.035). R/R AML patients with lncRNA TUG1 high expression achieved numerically lower CR (P= 0.053), decreased ORR (P= 0.028) and shorter OS (P< 0.001) than patients with lncRNA TUG1 low expression. Univariate logistic regression and COX's regression disclosed that lncRNA TUG1 high expression correlated with declined ORR, numerically decreased CR, and reduced OS. Furthermore, multivariate analyses verified that lncRNA TUG1 high expression was an independent predictive factor for decreased ORR and worse OS. CONCLUSIONS In conclusion, lncRNA TUG1 expression was elevated in R/R AML patients, and it might serve as a potential biomarker for poor prognosis in R/R AML patients treated with CLAG or FLAG based chemotherapy.
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Guan X, Wen X, Xiao J, An X, Yu J, Guo Y. Lnc-SOX6-1 upregulation correlates with poor risk stratification and worse treatment outcomes, and promotes cell proliferation while inhibits apoptosis in pediatric acute myeloid leukemia. Int J Lab Hematol 2019; 41:234-241. [PMID: 30624855 DOI: 10.1111/ijlh.12952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/20/2018] [Accepted: 11/01/2018] [Indexed: 12/22/2022]
Abstract
INTRODUCTION To investigate the correlation of long noncoding RNA-SOX6-1 (lnc-SOX6-1) with clinicopathological features and treatment outcomes in pediatric acute myeloid leukemia (AML) patients, and further explore its function in AML cell proliferation and apoptosis. METHODS A total of 146 de novo pediatric AML patients and 73 nonhematologic malignancy patients/donors were recruited. Bone marrow samples were obtained, followed by measurement of lnc-SOX6-1 expression by qPCR. Besides, lnc-SOX6-1 expression in various AML cells and control cells was detected. Blank overexpression (NC (+)), lnc-SOX6-1 overexpression (Lnc RNA (+)), blank shRNA (NC (-)), and lnc-SOX6-1 shRNA plasmids (Lnc RNA (-)) were transferred into KG-1 cells and THP-1 cells. Cell proliferation rate and cell apoptosis rate were detected by CCK-8 assay and AV/PI assay, respectively. RESULTS Lnc-SOX6-1 expression was upregulated in pediatric AML patients compared to controls, and its high expression correlated with the presence of monosomal karyotype, severer risk stratification, lower possibility of complete response achievement, shorter event-free survival, and poor overall survival. Furthermore, lnc-SOX6-1 expression was elevated in various AML cells compared to normal cells. In KG-1 cells and THP-1 cells, cell proliferation rate was elevated in Lnc RNA (+) group but reduced in Lnc RNA (-) group at 48 and 72 hours, and cell apoptosis rate was decreased in Lnc RNA (+) group but increased in Lnc RNA (-) group at 72 hours compared to the corresponding control groups. CONCLUSION Lnc-SOX6-1 is highly expressed and correlates with worse risk stratification and poor treatment outcomes, and promotes cell proliferation while represses apoptosis in pediatric AML.
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Affiliation(s)
- Xianmin Guan
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xianhao Wen
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jianwen Xiao
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - Xizhou An
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Jie Yu
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxia Guo
- Department of Hematology and Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
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Wang J, Chen X, Shen D, Ge D, Chen J, Pei J, Li Y, Yue Z, Feng J, Chu M, Nie Y. A long noncoding RNA NR_045363 controls cardiomyocyte proliferation and cardiac repair. J Mol Cell Cardiol 2018; 127:105-114. [PMID: 30553885 DOI: 10.1016/j.yjmcc.2018.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/26/2018] [Accepted: 12/09/2018] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in the regulation of genes involved in cell proliferation. We have previously sought to more globally understand the differences of lncRNA expression between human fetal heart and adult heart to identify some functional lncRNAs which involve in the process of heart repair. We found that a highly conserved long noncoding RNA NR_045363 was mainly expressed in cardiomyocytes and rarely in non-cardiomyocytes. NR_045363 overexpression in 7-day-old mice heart could improve cardiac function and stimulate cardiomyocyte proliferation after myocardial infarction. Furthermore, NR_045363 knockdown inhibited proliferation of primary embryonic cardiomyocytes, while NR_045363 overexpression enhanced DNA synthesis and cytokinesis in neonatal cardiomyocytes in vitro. Mechanistic analysis revealed that NR_045363 promoted cardiomyocyte proliferation through interaction with miR-216a, which regulated the JAK2-STAT3 pathway. Our results showed that NR_045363 is a potent lncRNA modulator essential for cardiomyocyte proliferation.
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Affiliation(s)
- Jue Wang
- Department of Cardiac Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xianda Chen
- Children's Heart Center, The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Cardiovascular Development and Translational Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Danping Shen
- Children's Heart Center, The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Cardiovascular Development and Translational Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Donghui Ge
- Children's Heart Center, The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Cardiovascular Development and Translational Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiuling Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jianqiu Pei
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yandong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhang Yue
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jie Feng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Maoping Chu
- Children's Heart Center, The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Cardiovascular Development and Translational Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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Lin Y, Wu W, Sun Z, Shen L, Shen B. MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. RNA Biol 2018; 15:1093-1105. [PMID: 30081733 DOI: 10.1080/15476286.2018.1502590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the potential as biomarkers for disease diagnosis, prognosis and therapy. In the era of big data and biomedical informatics, computer-aided biomarker discovery has become the current frontier. However, most of the computational models are highly dependent on specific prior knowledge and training-testing procedures, very few are mechanism-guided or evidence-based. To the best of our knowledge, untill now no general rules have been uncovered and applied to miRNA biomarker screening. In this study, we manually collected literature-reported cancer miRNA biomarkers and analyzed their regulatory patterns, including the regulatory modes, biological functions and evolutionary characteristics of their targets in the human miRNA-mRNA network. Two evidences were statistically detected and used to distinguish biomarker miRNAs from others. Based on these observations, we developed a novel bioinformatics model and software tool for miRNA biomarker discovery ( http://sysbio.suda.edu.cn/MiRNA-BD/ ). In contrast to routine methods that focus on miRNA synergic functions, our method searches for vulnerable sites in the miRNA-mRNA network and considers the independent regulatory power of miRNAs, i.e., single-line regulations between miRNAs and mRNAs. The performance comparison demonstrates the generality and precision of our model, which identifies miRNA biomarkers for cancers as well as other complex diseases without training or specific prior knowledge.
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Affiliation(s)
- Yuxin Lin
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Wentao Wu
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Zhandong Sun
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Li Shen
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China.,b Department of Genetics & Systems Biology Institute , Yale University School of Medicine , West Haven , CT USA
| | - Bairong Shen
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China.,c Center for Translational Biomedical Informatics , Guizhou University School of Medicine , Guiyang , China.,d Institute for Systems Genetics, West China Hospital , Sichuan University , Chengdu , China
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Yan H, Xu R, Zhang X, Wang Q, Pang J, Zhang X, Chang X, Zhang Y. Identifying differentially expressed long non-coding RNAs in PBMCs in response to the infection of multidrug-resistant tuberculosis. Infect Drug Resist 2018; 11:945-959. [PMID: 30034244 PMCID: PMC6047615 DOI: 10.2147/idr.s154255] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this paper was to identify differentially expressed long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) influenced by the infection of multidrug-resistant tuberculosis (MDR-TB). Materials and methods IncRNA and mRNA expression profiles in PBMCs derived from healthy controls (HCs) and individuals with MDR-TB and drug-sensitive tuberculosis (DS-TB) were analyzed and compared by microarray assay. Six lncRNAs were randomly selected for validation by using real-time quantitative polymerase chain reaction (RT-qPCR). The biological functions and signaling pathways affected by the differentially expressed mRNAs were investigated by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-based approaches. Results Compared with the HC group, 1,429 lncRNAs (983 mRNAs) and 2,040 lncRNAs (1,407 mRNAs) were identified to be deregulated in the MDR-TB group and in the DS-TB group, respectively, and 1,511 lncRNAs and 1,047 mRNAs were identified to be differentially expressed in both MDR-TB and DS-TB groups. Between the three groups, 22 lncRNAs and 38 mRNAs were found deregulated. Most deregulated lncRNAs were from intergenic regions (~55% of the total), natural antisense to protein-coding loci (~32% of the total), or intronic antisense to protein-coding loci (~5% of the total). Significantly enriched signaling pathways regulated by the deregulated mRNAs were mainly associated with natural killer cell-mediated cytotoxicity, antigen processing and presentation, graft-vs-host disease, the transforming growth factor-β signaling pathway, and the Hippo signaling pathway. Conclusion This study is the first to report differentially expressed lncRNAs in PBMCs in response to MDR-TB infection. It revealed that some lncRNAs might be associated with regulating host immune response to MDR-TB infection. Further elucidation of the potential of these deregulated lncRNAs in MDR-TB and its reactivation requires further study.
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Affiliation(s)
- Hong Yan
- Department of Laboratory Medicine, Nanjing Chest Hospital, Nanjing 210029, China
| | - Rufeng Xu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Xiangrong Zhang
- Nanjing Public Health Clinical Center, Nanjing, Jiangsu 211133, China
| | - Qian Wang
- Department of Laboratory Medicine, Nanjing Chest Hospital, Nanjing 210029, China
| | - Jing Pang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Xia Zhang
- Nanjing Public Health Clinical Center, Nanjing, Jiangsu 211133, China
| | - Xiaoai Chang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
| | - Yaqin Zhang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 210029, China,
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Chandra Gupta S, Nandan Tripathi Y. Potential of long non-coding RNAs in cancer patients: From biomarkers to therapeutic targets. Int J Cancer 2016; 140:1955-1967. [DOI: 10.1002/ijc.30546] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/11/2016] [Accepted: 11/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Subash Chandra Gupta
- Laboratory for Translational Cancer Research; Department of Biochemistry, Institute of Science, Banaras Hindu University; Varanasi 221 005 India
| | - Yashoda Nandan Tripathi
- Laboratory for Translational Cancer Research; Department of Biochemistry, Institute of Science, Banaras Hindu University; Varanasi 221 005 India
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