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Yang M, Tang Y, Zhu P, Lu H, Wan X, Guo Q, Xiao L, Liu C, Guo L, Liu W, Yang Y. The advances of E2A-PBX1 fusion in B-cell acute lymphoblastic Leukaemia. Ann Hematol 2024; 103:3385-3398. [PMID: 38148344 DOI: 10.1007/s00277-023-05595-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
The E2A-PBX1 gene fusion is a common translocation in B-cell acute lymphoblastic leukaemia. Patients harbouring the E2A-PBX1 fusion gene typically exhibit an intermediate prognosis. Furthermore, minimal residual disease has unsatisfactory prognostic value in E2A-PBX1 B-cell acute lymphoblastic leukaemia. However, the mechanism of E2A-PBX1 in the occurrence and progression of B-cell acute lymphoblastic leukaemia is not well understood. Here, we mainly review the roles of E2A and PBX1 in the differentiation and development of B lymphocytes, the mechanism of E2A-PBX1 gene fusion in B-cell acute lymphoblastic leukaemia, and the potential therapeutic approaches.
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Affiliation(s)
- Mengting Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Yanhui Tang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Peng Zhu
- School of Pharmacy, Wannan Medical College, Wuhu, 241000, People's Republic of China
| | - Haiquan Lu
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaohong Wan
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Lan Xiao
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Chunyan Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
| | - You Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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2
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Altieri F, Buono L, Lanzilli M, Mirabelli P, Cianflone A, Beneduce G, De Matteo A, Parasole R, Salvatore M, Smaldone G. LINC00958 as new diagnostic and prognostic biomarker of childhood acute lymphoblastic leukaemia of B cells. Front Oncol 2024; 14:1388154. [PMID: 38884090 PMCID: PMC11176504 DOI: 10.3389/fonc.2024.1388154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Background Paediatric acute B-cell lymphoblastic leukaemia is the most common cancer of the paediatric age. Although the advancement of scientific and technological knowledge has ensured a huge step forward in the management of this disease, there are 15%-20% cases of recurrence leading to serious complications for the patient and sometimes even death. It is therefore necessary to identify new and increasingly personalised biomarkers capable of predicting the degree of risk of B-ALL in order to allow the correct management of paediatric leukaemia patients. Methods Starting from our previously published results, we validate the expression level of LINC00958 in a cohort of 33 B-ALL and 9 T-ALL childhood patients, using in-silico public datasets as support. Expression levels of LINC00958 in B-ALL patients stratified by risk (high risk vs. standard/medium risk) and who relapsed 3 years after the first leukaemia diagnosis were also evaluated. Results We identified the lncRNA LINC00958 as a biomarker of B-ALL, capable of discriminating B-ALL from T-ALL and healthy subjects. Furthermore, we associated LINC00958 expression levels with the disease risk classification (high risk and standard risk). Finally, we show that LINC00958 can be used as a predictor of relapses in patients who are usually stratified as standard risk and thus not always targeted for marrow transplantation. Conclusions Our results open the way to new diagnostic perspectives that can be directly used in clinical practice for a better management of B-ALL paediatric patients.
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Affiliation(s)
| | | | | | - Peppino Mirabelli
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Alessandra Cianflone
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Giuliana Beneduce
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Antonia De Matteo
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Rosanna Parasole
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
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3
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [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: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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4
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Sharma P, Kaur P, Bhatia P, Trehan A, Sreedharanunni S, Singh M. Novel lncRNAs LINC01221, RP11-472G21.2 and CRNDE are markers of differential expression in pediatric patients with T cell acute lymphoblastic leukemia. Cancer Cell Int 2024; 24:65. [PMID: 38336706 PMCID: PMC10858595 DOI: 10.1186/s12935-024-03255-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
INTRODUCTION Pediatric T-cell acute lymphoblastic leukemia (T-ALL) poses significant challenges due to its aggressive nature and resistance to standard treatments. Long non-coding RNAs (lncRNAs) have emerged as potential biomarkers and therapeutic targets in leukemia. This study aims to characterize the lncRNA landscape in pediatric T-ALL, identify specific lncRNAs signatures, and assess their clinical relevance. METHODS RNA sequencing was performed on T-ALL patient and control samples. Differential expression analysis identified dysregulated lncRNAs and mRNAs. Functional enrichment analysis revealed potential roles of these lncRNAs in cancer pathogenesis. Validation of candidate lncRNAs was conducted using real-time PCR. Clinical correlations were assessed, including associations with patients' clinical characteristics and survival outcomes. RESULTS Analysis identified 674 dysregulated lncRNAs in pediatric T-ALL, with LINC01221 and CRNDE showing the most interactions in cancer progression pathways. Functional enrichment indicated involvement in apoptosis, survival, proliferation, and metastasis. Top 10 lncRNAs based on adjusted p value < 0.05 and Fold Change > 2 were selected for validation. Seven lncRNAs LINC01221, PCAT18, LINC00977, RP11-620J15.3, RP11-472G21.2, CTD-2291D10.4, and CRNDE showed correlation with RNA sequencing data. RP11-472G21.2 and CTD-2291D10.4 were highly expressed in T-ALL patients, with RP11-620J15.3 correlating significantly with better overall survival (p = 0.0007) at a median follow up of 32 months. The identified lncRNAs were further analysed in B-ALL patients. Distinct lncRNAs signatures were noted, distinguishing T-ALL from B-ALL and healthy controls, with lineage-specific overexpression of LINC01221 (p < 0.0001), RP11-472G21.2 (p < 0.001) and CRNDE (p = 0.04) in T-ALL. CONCLUSION This study provides insights into the lncRNA landscape of pediatric T-ALL, offering potential diagnostic and prognostic markers. RP11-620J15.3 emerges as a promising prognostic marker, and distinct lncRNAs signatures may aid in the differentiation of T-ALL subtypes. Further research with larger cohorts is warranted to validate these findings and advance personalized treatment strategies for pediatric T-ALL patients.
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Affiliation(s)
- Pankaj Sharma
- Hematology-Oncology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Parminder Kaur
- Hematology-Oncology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prateek Bhatia
- Hematology-Oncology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amita Trehan
- Hematology-Oncology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Minu Singh
- Hematology-Oncology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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5
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Cruz-Miranda GM, Olarte-Carrillo I, Bárcenas-López DA, Martínez-Tovar A, Ramírez-Bello J, Ramos-Peñafiel CO, García-Laguna AI, Cerón-Maldonado R, May-Hau D, Jiménez-Morales S. Transcriptome Analysis in Mexican Adults with Acute Lymphoblastic Leukemia. Int J Mol Sci 2024; 25:1750. [PMID: 38339034 PMCID: PMC10855968 DOI: 10.3390/ijms25031750] [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: 11/23/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) represents around 25% of adult acute leukemias. Despite the increasing improvement in the survival rate of ALL patients during the last decade, the heterogeneous clinical and molecular features of this malignancy still represent a major challenge for treatment and achieving better outcomes. To identify aberrantly expressed genes in bone marrow (BM) samples from adults with ALL, transcriptomic analysis was performed using Affymetrix Human Transcriptome Array 2.0 (HTA 2.0). Differentially expressed genes (DEGs) (±2-fold change, p-value < 0.05, and FDR < 0.05) were detected using the Transcriptome Analysis Console. Gene Ontology (GO), Database for Annotation, Visualization, and Integrated Discovery (DAVID), and Ingenuity Pathway Analysis (IPA) were employed to identify gene function and define the enriched pathways of DEGs. The protein-protein interactions (PPIs) of DEGs were constructed. A total of 871 genes were differentially expressed, and DNTT, MYB, EBF1, SOX4, and ERG were the top five up-regulated genes. Meanwhile, the top five down-regulated genes were PTGS2, PPBP, ADGRE3, LUCAT1, and VCAN. An association between ERG, CDK6, and SOX4 expression levels and the probability of relapse and death was observed. Regulation of the immune system, immune response, cellular response to stimulus, as well as apoptosis signaling, inflammation mediated by chemokines and cytokines, and T cell activation were among the most altered biological processes and pathways, respectively. Transcriptome analysis of ALL in adults reveals a group of genes consistently associated with hematological malignancies and underscores their relevance in the development of ALL in adults.
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Affiliation(s)
- Gabriela Marisol Cruz-Miranda
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Irma Olarte-Carrillo
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Adolfo Martínez-Tovar
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Julian Ramírez-Bello
- Subdirección de Investigación Clínica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
| | | | - Anel Irais García-Laguna
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Rafael Cerón-Maldonado
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Didier May-Hau
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
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6
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Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
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Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
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7
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Palanichamy JK, Tran TM, King JK, Katzman S, Ritter AJ, Sharma G, Tso C, Contreras JR, Fernando TR, Sanford JR, Rao DS. Distinct oncogenic phenotypes in hematopoietic specific deletions of Trp53. Sci Rep 2023; 13:7490. [PMID: 37160922 PMCID: PMC10169790 DOI: 10.1038/s41598-023-33949-8] [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: 08/27/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
Loss of function in the tumor suppressor gene TP53 is the most common alteration seen in human cancer. In mice, P53 deletion in all cells leads predominantly to the development of T-cell lymphomas, followed by B-cell lymphomas, sarcomas and teratomas. In order to dissect the role of P53 in the hematopoietic system, we generated and analyzed two different mouse models deficient for P53. A pan-hematopoietic P53 deletion mouse was created using Vav1-Cre based deletion; and a B-cell-specific deletion mouse was created using a CD19-Cre based deletion. The Vav1-P53CKO mice predominantly developed T-cell malignancies in younger mice, and myeloid malignancies in older mice. In T-cell malignancies, there was accelerated thymic cell maturation with overexpression of Notch1 and its downstream effectors. CD19-P53CKO mice developed marginal zone expansion in the spleen, followed by marginal zone lymphoma, some of which progressed to diffuse large B-cell lymphomas. Interestingly, marginal zone and diffuse large B-cell lymphomas had a unique gene expression signature characterized by activation of the PI3K pathway, compared with wild type marginal zone or follicular cells of the spleen. This study demonstrates lineage specific P53 deletion leading to distinct phenotypes secondary to unique gene expression programs set in motion.
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Affiliation(s)
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA
- Molecular, Cellular and Integrative Physiology Graduate Program, UCLA, Los Angeles, USA
| | | | - Sol Katzman
- Center for Biomolecular Science & Engineering, UCSC, Santa Cruz, USA
| | - Alexander J Ritter
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, UCSC, Santa Cruz, USA
| | - Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Christine Tso
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA
| | - Jorge R Contreras
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA
| | | | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, UCSC, Santa Cruz, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, 650 Charles E Young Drive, Los Angeles, CA, 90095, USA.
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8
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Gallo Cantafio ME, Torcasio R, Viglietto G, Amodio N. Non-Coding RNA-Dependent Regulation of Mitochondrial Dynamics in Cancer Pathophysiology. Noncoding RNA 2023; 9:ncrna9010016. [PMID: 36827549 PMCID: PMC9964195 DOI: 10.3390/ncrna9010016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/07/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
Mitochondria are essential organelles which dynamically change their shape and number to adapt to various environmental signals in diverse physio-pathological contexts. Mitochondrial dynamics refers to the delicate balance between mitochondrial fission (or fragmentation) and fusion, that plays a pivotal role in maintaining mitochondrial homeostasis and quality control, impinging on other mitochondrial processes such as metabolism, apoptosis, mitophagy, and autophagy. In this review, we will discuss how dysregulated mitochondrial dynamics can affect different cancer hallmarks, significantly impacting tumor growth, survival, invasion, and chemoresistance. Special emphasis will be given to emerging non-coding RNA molecules targeting the main fusion/fission effectors, acting as novel relevant upstream regulators of the mitochondrial dynamics rheostat in a wide range of tumors.
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Affiliation(s)
| | - Roberta Torcasio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Laboratory of Cellular and Molecular Cardiovascular Pathophysiology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Arcavacata di Rende, 87036 Cosenza, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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9
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Jafari-Raddani F, Davoodi-Moghaddam Z, Yousefi AM, Ghaffari SH, Bashash D. An overview of long noncoding RNAs: Biology, functions, therapeutics, analysis methods, and bioinformatics tools. Cell Biochem Funct 2022; 40:800-825. [PMID: 36111699 DOI: 10.1002/cbf.3748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a diverse class of RNAs whose functions are widespread in all branches of life and have been the focus of attention in the last decade. While a huge number of lncRNAs have been identified, there is still much work to be done and plenty to be learned. In the current review, we begin with the biogenesis and function of lncRNAs as they are involved in the different cellular processes from regulating the architecture of chromosomes to controlling translation and post-translation modifications. Questions on how overexpression, mutations, or deficiency of lncRNAs can affect the cellular status and result in the pathogenesis of various human diseases are responded to. Besides, we allocate an overview of several studies, concerning the application of lncRNAs either as diagnostic and prognostic biomarkers or novel therapeutics. We also introduce the currently available techniques to explore details of lncRNAs such as their function, cellular localization, and structure. In the last section, as exponentially growing data in this area need to be gathered and organized in comprehensive databases, we have a particular focus on presenting general and specialized databases. Taken together, with this review, we aim to provide the latest information on different aspects of lncRNAs to highlight their importance in physiopathologic states and take a step towards helping future studies.
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Affiliation(s)
- Farideh Jafari-Raddani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Davoodi-Moghaddam
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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Gasic V, Karan-Djurasevic T, Pavlovic D, Zukic B, Pavlovic S, Tosic N. Diagnostic and Therapeutic Implications of Long Non-Coding RNAs in Leukemia. Life (Basel) 2022; 12:1770. [PMID: 36362925 PMCID: PMC9695865 DOI: 10.3390/life12111770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Leukemia is a heterogenous group of hematological malignancies categorized in four main types (acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and chronic lymphocytic leukemia (CLL). Several cytogenetic and molecular markers have become a part of routine analysis for leukemia patients. These markers have been used in diagnosis, risk-stratification and targeted therapy application. Recent studies have indicated that numerous regulatory RNAs, such as long non-coding RNAs (lncRNAs), have a role in tumor initiation and progression. When it comes to leukemia, data for lncRNA involvement in its etiology, progression, diagnosis, treatment and prognosis is limited. The aim of this review is to summarize research data on lncRNAs in different types of leukemia, on their expression pattern, their role in leukemic transformation and disease progression. The usefulness of this information in the clinical setting, i.e., for diagnostic and prognostic purposes, will be emphasized. Finally, how particular lncRNAs could be used as potential targets for the application of targeted therapy will be considered.
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Affiliation(s)
- Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
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11
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Ousati Ashtiani Z, Abbasi S, Pourmand G, Ghafouri-Fard S. Overexpression of long intergenic noncoding RNAs in bladder cancer: A new insight to cancer diagnosis. Pathol Res Pract 2022; 235:153961. [DOI: 10.1016/j.prp.2022.153961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 12/24/2022]
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12
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May-Hau DI, Bárcenas-López DA, Núñez-Enríquez JC, Bekker-Méndez VC, Beltrán-Anaya FO, Jiménez-Hernández E, Ortíz-Maganda MP, Guerra-Castillo FX, Medina-Sanson A, Flores-Lujano J, Martín-Trejo JA, Peñaloza-González JG, Velázquez-Aviña MM, Torres-Nava JR, Hernández-Echáurregui GA, Espinosa-Elizondo RM, Gutiérrez-Rivera MDL, Sanchez-Hernandez R, Pérez-Saldívar ML, Flores-Villegas LV, Merino-Pasaye LE, Duarte-Rodríguez DA, Mata-Rocha M, Sepúlveda-Robles OA, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM, Jiménez-Morales S. Underexpression of LINC00173 in TCF3/PBX1-Positive Cases Is Associated With Poor Prognosis in Children With B-Cell Precursor Acute Lymphoblastic Leukemia. Front Oncol 2022; 12:887766. [PMID: 35719952 PMCID: PMC9201104 DOI: 10.3389/fonc.2022.887766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most frequent pediatric cancer worldwide. Despite improvements in treatment regimens, approximately 20% of the cases cannot be cured, highlighting the necessity for identifying new biomarkers to improve the current clinical and molecular risk stratification schemes. We aimed to investigate whether LINC00173 is a biomarker in ALL and to explore its expression level in other human cancer types. Methods A nested case-control study including Mexican children with BCP-ALL was conducted. LINC00173 expression was evaluated by qRT-PCR using hydrolysis probes. To validate our findings, RNA-seq expression data from BCP-ALL and normal tissues were retrieved from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) repositories, respectively. LINC00173 expression was also evaluated in solid tumors by downloading available data from The Cancer Genome Atlas (TCGA). Results A lower expression of LINC00173 in BCP-ALL cases compared to normal subjects was observed (p < 0.05). ALL patients who carry the TCF3/PBX1 fusion gene displayed lower expression of LINC00173 in contrast to other BCP-ALL molecular subtypes (p < 0.04). LINC00173 underexpression was associated with a high risk to relapse (HR = 1.946, 95% CI = 1.213-3.120) and die (HR = 2.073, 95% CI = 1.211-3.547). Patients with TCF3/PBX1 and underexpression of LINC00173 had the worst prognosis (DFS: HR = 12.24, 95% CI = 5.04-29.71; OS: HR = 11.19, 95% CI = 26-32). TCGA data analysis revealed that underexpression of LINC00173 is also associated with poor clinical outcomes in six new reported tumor types. Conclusion Our findings suggest that LINC00173 is a biomarker of poor prognosis in BCP-ALL and other types of cancer. We observed an association between the expression of LINC00173 and TCF3/PBX1 and the risk to relapse and die in BCP-ALL, which is worse in TCF3/PBX1-positive cases displaying underexpression of LINC00173. Experimental studies are needed to provide insight into the LINC00173 and TCF3/PBX relationship.
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Affiliation(s)
- Didier Ismael May-Hau
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de Mexico, México City, Mexico
| | - Diego Alberto Bárcenas-López
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Epidemiología Clínica y Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Mónica Patricia Ortíz-Maganda
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Francisco Xavier Guerra-Castillo
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México, Mexico City, Mexico
| | | | | | - María de Lourdes Gutiérrez-Rivera
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rodrigo Sanchez-Hernandez
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - 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, Mexico City, Mexico
| | - 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, Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Medicine Faculty, Universidad Autónoma de México, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Noncoding RNAs as novel immunotherapeutic tools against cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 129:135-161. [PMID: 35305717 DOI: 10.1016/bs.apcsb.2021.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Immunotherapy is implemented as an important treatment strategy in various malignancies. In cancer, immunotherapy is employed for successful killing of tumor cells with high specificity and greater efficacy, with minimum side effects. Despite various available strategies, cellular immunotherapy including innate (NK cells, macrophages, dendritic cells) and adaptive (B cells and T cells) immune cells plays a critical role in tumor microenvironment. Since past few years, many drugs targeting immune checkpoint proteins including CTLA-4 and PD-1/PD-L1 have been investigated as immunotherapy approach against cancer but complete effectiveness still remains a question, as diverse mechanisms involved in tumorigenesis may result in the development of cancer cell resistance. Number of evidences have highlighted the significant role of non-coding RNAs (ncRNAs) in regulating multiple stages of cancer initiation, progression & immunity. ncRNAs comprises 98% human transcriptome and are basically considered as dark genome. Among ncRNAs, miRNAs and lncRNAs have been extensively studied in regulating diverse processes of cancer tumorigenesis. Upregulation of oncogenic and downregulation of tumor suppressive miRNAs/lncRNAs has been reported to facilitate the cancer progression and invasiveness. This chapter summarizes how an interplay between ncRNAs and immune cells in cancer pathogenesis can be therapeutically targeted to improve current treatment regimen. Strategies should be employed to improve the efficacy and reduce off-target effects of ncRNA based immunotherapy. Henceforth, combination of ncRNAs and available immunotherapy can be argued to enhance the efficacy of existing immunotherapeutic approaches against cancer to improve patient's survival.
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Maimaitiyiming Y, Ye L, Yang T, Yu W, Naranmandura H. Linear and Circular Long Non-Coding RNAs in Acute Lymphoblastic Leukemia: From Pathogenesis to Classification and Treatment. Int J Mol Sci 2022; 23:ijms23084442. [PMID: 35457264 PMCID: PMC9033105 DOI: 10.3390/ijms23084442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The coding regions account for only a small part of the human genome, and the remaining vast majority of the regions generate large amounts of non-coding RNAs. Although non-coding RNAs do not code for any protein, they are suggested to work as either tumor suppressers or oncogenes through modulating the expression of genes and functions of proteins at transcriptional, posttranscriptional and post-translational levels. Acute Lymphoblastic Leukemia (ALL) originates from malignant transformed B/T-precursor-stage lymphoid progenitors in the bone marrow (BM). The pathogenesis of ALL is closely associated with aberrant genetic alterations that block lymphoid differentiation and drive abnormal cell proliferation as well as survival. While treatment of pediatric ALL represents a major success story in chemotherapy-based elimination of a malignancy, adult ALL remains a devastating disease with relatively poor prognosis. Thus, novel aspects in the pathogenesis and progression of ALL, especially in the adult population, need to be further explored. Accumulating evidence indicated that genetic changes alone are rarely sufficient for development of ALL. Recent advances in cytogenic and sequencing technologies revealed epigenetic alterations including that of non-coding RNAs as cooperating events in ALL etiology and progression. While the role of micro RNAs in ALL has been extensively reviewed, less attention, relatively, has been paid to other non-coding RNAs. Herein, we review the involvement of linear and circular long non-coding RNAs in the etiology, maintenance, and progression of ALL, highlighting the contribution of these non-coding RNAs in ALL classification and diagnosis, risk stratification as well as treatment.
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Affiliation(s)
- Yasen Maimaitiyiming
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linyan Ye
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tao Yang
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Wenjuan Yu
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Correspondence: (W.Y.); (H.N.)
| | - Hua Naranmandura
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Correspondence: (W.Y.); (H.N.)
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Illarregi U, Telleria J, Bilbao‑Aldaiturriaga N, Lopez‑Lopez E, Ballesteros J, Martin‑Guerrero I, Gutierrez‑Camino A. lncRNA deregulation in childhood acute lymphoblastic leukemia: A systematic review. Int J Oncol 2022; 60:59. [DOI: 10.3892/ijo.2022.5348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/03/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Unai Illarregi
- Department of Genetics, Physical Anthropology and Animal Physiology, University of The Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Jaione Telleria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of The Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Nerea Bilbao‑Aldaiturriaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of The Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Elixabet Lopez‑Lopez
- Department of Biochemistry and Molecular Biology, University of The Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Javier Ballesteros
- Department of Neuroscience, University of The Basque Country (UPV/EHU) and CIBERSAM, Medical School, 48940 Leioa, Spain
| | - Idoia Martin‑Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of The Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Angela Gutierrez‑Camino
- Division of Hematology‑Oncology, CHU Sainte‑Justine Research Center, Montreal, QC H3T 1C5, Canada
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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Jamali E. The emerging role non-coding RNAs in B cell-related disorders. Cancer Cell Int 2022; 22:91. [PMID: 35193592 PMCID: PMC8862212 DOI: 10.1186/s12935-022-02521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs and microRNAs have recently attained much attention regarding their role in the development of B cell lineage as well as participation in the lymphomagenesis. These transcripts have a highly cell type specific signature which endows them the potential to be used as biomarkers for clinical situations. Aberrant expression of several non-coding RNAs has been linked with B cell malignancies and immune related disorders such as rheumatoid arthritis, systemic lupus erythematous, asthma and graft-versus-host disease. Moreover, these transcripts can alter response of immune system to infectious conditions. miR-7, miR-16-1, miR-15a, miR-150, miR-146a, miR-155, miR-212 and miR-132 are among microRNAs whose role in the development of B cell-associated disorders has been investigated. Similarly, SNHG14, MALAT1, CRNDE, AL133346.1, NEAT1, SMAD5-AS1, OR3A4 and some other long non-coding RNAs participate in this process. In the current review, we describe the role of non-coding RNAs in B cell malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ju JK, Han WN, Shi CL. Long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 gene (PVT1) modulates the proliferation and apoptosis of acute lymphoblastic leukemia cells by sponging miR-486-5p. Bioengineered 2022; 13:4587-4597. [PMID: 35152842 PMCID: PMC8973597 DOI: 10.1080/21655979.2022.2031405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 gene (PVT1) is related to the progress of various cancers. Here, we illuminated the role of PVT1 in acute lymphoblastic leukemia (ALL) cell proliferation and apoptosis. PVT1 was upregulated in plasma samples from patients with ALL and ALL cell lines. PVT1 silencing repressed cell viability and enhanced cell apoptosis in Jurkat and SUP-B15 cells. PVT1 targeted microRNA-486-5p (miR-486-5p) and negatively modulated miR-486-5p expression. Upregulation of miR-486-5p decreased cell viability and increased ALL cell apoptosis. Mastermind Like Transcriptional Coactivator 3 (MAML3) was a downstream molecule of miR-486-5p and miR-486-5p mimic transfection weakened its expression in ALL cells. Rescue experiments proved that reintroduction of PVT1 counteracted the impacts of miR-486-5p in ALL cell proliferation and apoptosis. In vivo, PVT1 silencing repressed the tumor growth of SUP-B15 cells and reduced the expression of MAML3. Altogether, silencing of PVT1 inhibited ALL cell growth and induced cell apoptosis through sponging miR-486-5p.
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Affiliation(s)
- Jin-Ke Ju
- Department of Pediatrics, Changyi People’s Hospital, Changyi, China
| | - Wei-Na Han
- Department of General Surgery, Changyi People’s Hospital, Changyi, China
| | - Cai-Ling Shi
- Department of Pediatrics, Changyi People’s Hospital, Changyi, China
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19
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Xia J, Wang M, Zhu Y, Bu C, Li T. Differential mRNA and long noncoding RNA expression profiles in pediatric B-cell acute lymphoblastic leukemia patients. BMC Pediatr 2022; 22:10. [PMID: 34980027 PMCID: PMC8722040 DOI: 10.1186/s12887-021-03073-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/10/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are involved in the pathogenesis and development of various cancers including B cell acute lymphoblastic leukemia (B-ALL). To determine the potential roles of lncRNAs involved in pathogenesis of B-ALL, we analyzed the expression profile of lncRNAs and mRNAs in B-ALL, respectively, and constructed lncRNAs/mRNAs interaction network. METHODS We performed RNA sequencing of 10 non-leukemic blood disease donors and 10 B-ALL patients for Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Interactions among mRNAs were predicted using the STRING database. Quantitative real time PCR (qRT-PCR) was performed to verify the RNA-seq data of lncRNAs and mRNAs. Potential functions of subtype-specific lncRNAs were determined by using coexpression-based analysis on distally (trans-pattern) located protein-coding genes. RESULTS A total of 1813 differentially expressed transcripts (DETs) and 2203 lncRNAs were identified. Moreover, 10 dysregulated lncRNAs and 10 mRNAs were randomly selected, and further assessed by RT-qPCR in vitro. Go and KEGG analysis demonstrated that the differentially expressed mRNAs were most closely associated with myeloid leukocyte activation and in transcriptional misregulation in cancer, respectively. In addition, co-expression analysis demonstrated that these lncRNAs, including MSTRG.27994.3, MSTRG.21740.1, ENST00000456341, MSTRG.14224.1 and MSTRG.20153.1, may mediate the pathogenesis and development of B-ALL via lncRNA-mRNA network interactions. CONCLUSIONS These results showed that several mRNAs and lncRNAs are aberrantly expressed in the bone marrow of B-ALL patients and play potential roles in B-ALL development, and be useful for diagnostic and/or prognostic purposes in pediatric B-ALL. DATA AVAILABILITY The datasets used during our study are available through HARVARD Dataverse Persistent ID doi: https://doi.org/10.7910/DVN/LK9T4Z .
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Affiliation(s)
- Jing Xia
- Department of Pediatric Laboratory, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Mengjie Wang
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Yi Zhu
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Chaozhi Bu
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, Jiangsu, China.
| | - Tianyu Li
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China.
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20
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Ahani M, Ghaderian SMH, Mehr Azma M, Kamali K, Naghavi Gargari B, Bahramali G, Akbarzadeh R. Differential gene expression of BCL-2, ZEB2-AS1 and BALR-2 in prostate cancer and benign prostatic hyperplasia. Andrologia 2021; 54:e14344. [PMID: 34866225 DOI: 10.1111/and.14344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/15/2021] [Accepted: 11/27/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) and benign prostate hyperplasia (BPH) are highly prevalent heterogeneous disorders among men. Whereas PCa and BPH underline common pathological features, apoptotic-related genes might be differentially expressed in these diseases. This study was aimed at testing BCL-2 as well as BALR-2 and ZEB2-AS1 apoptosis-related long non-coding RNA (lncRNA) in patients with PCa and BPH. The expression levels of the BCL-2 gene and ZEB2-AS1 lncRNA were upregulated in tumoural tissues in comparison to adjacent non-cancerous tissues (ANCTs) and BPH tissues. In contrast, the expression level of BALR-2 lncRNA was significantly higher in BPH compared with tumoural tissues. Furthermore, while no association was noticed between the relative expression of ZEB2-AS1 and the tumour grade, the relative expression of BCL-2 and BALR-2 is strongly associated with a higher grade of the tumour in PCa samples compared with the ANCTs. The receiver operating characteristic (ROC) curve analysis indicated the highest specificity and diagnostic value in distinguishing PCa and ANCTs as well as PCa and BPH, respectively. In conclusion, altered expression of BCL-2 and BALR-2 was observed to be associated with tumoural progression and could be used as potential candidates for distinguishing PCa tissues from ANCTs or BPH samples.
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Affiliation(s)
- Maryam Ahani
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Mohammad Hossein Ghaderian
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mitra Mehr Azma
- Aliasghar Children's Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Koosha Kamali
- Department of Urology, Hasheminejad Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Bahar Naghavi Gargari
- Department of Basic Sciences, Faculty of Nursing & Midwifery, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Golnaz Bahramali
- Hepatitis, AIDS and Bloodborne Diseases Department, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Akbarzadeh
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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21
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Porcù E, Benetton M, Bisio V, Da Ros A, Tregnago C, Borella G, Zanon C, Bordi M, Germano G, Manni S, Campello S, Rao DS, Locatelli F, Pigazzi M. The long non-coding RNA CDK6-AS1 overexpression impacts on acute myeloid leukemia differentiation and mitochondrial dynamics. iScience 2021; 24:103350. [PMID: 34816103 PMCID: PMC8591413 DOI: 10.1016/j.isci.2021.103350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/30/2021] [Accepted: 10/22/2021] [Indexed: 12/17/2022] Open
Abstract
Patients with acute myeloid leukemia (AML) carrying high-risk genetic lesions or high residual disease levels after therapy are particularly exposed to the risk of relapse. Here, we identified the long non-coding RNA CDK6-AS1 able to cluster an AML subgroup with peculiar gene signatures linked to hematopoietic cell differentiation and mitochondrial dynamics. CDK6-AS1 silencing triggered hematopoietic commitment in healthy CD34+ cells, whereas in AML cells the pathological undifferentiated state was rescued. This latter phenomenon derived from RUNX1 transcriptional control, responsible for the stemness of hematopoietic precursors and for the block of differentiation in AML. By CDK6-AS1 silencing in vitro, AML mitochondrial mass decreased with augmented pharmacological sensitivity to mitochondria-targeting drugs. In vivo, the combination of tigecycline and cytarabine reduced leukemia progression in the AML-PDX model with high CDK6-AS1 levels, supporting the concept of a mitochondrial vulnerability. Together, these findings uncover CDK6-AS1 as crucial in myeloid differentiation and mitochondrial mass regulation. CDK6-AS1 acts in concert with CDK6 High CDK6-AS1 levels trigger RUNX1 early differentiation arrest in myeloid cells CDK6-AS1 controls mitochondrial mass of AML blasts CDK6-AS1 levels impact on mitochondrial-targeted agents sensitivity
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Affiliation(s)
- Elena Porcù
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Maddalena Benetton
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Valeria Bisio
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Ambra Da Ros
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Claudia Tregnago
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Giulia Borella
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy
| | - Carlo Zanon
- Pediatric Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, Istituto di Ricerca Pediatrica - Città della Speranza, 35127 Padova, Italy
| | - Matteo Bordi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy.,Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00143 Rome, Italy
| | - Giuseppe Germano
- Pediatric Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, Istituto di Ricerca Pediatrica - Città della Speranza, 35127 Padova, Italy
| | - Sabrina Manni
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padova, Padova, and Veneto Institute of Molecular Medicine (VIMM), 35129 Padova, Italy
| | - Silvia Campello
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Children's Hospital, Sapienza University of Rome, 00165 Roma, Italy
| | - Martina Pigazzi
- Pediatric Hematology, Oncology and Hematopoietic Cell&Gene Therapy Division of Women's and Children's Health Department, University-Hospital of Padova, Via N. Giustiniani, 3, 35128 Padova, Italy.,Pediatric Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, Istituto di Ricerca Pediatrica - Città della Speranza, 35127 Padova, Italy
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22
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Wu L, Zhang R, Lin S, Lin M, Wang J. Silencing CDK6-AS1 inhibits LPS-induced inflammatory damage in HK-2 cells. Open Med (Wars) 2021; 16:1256-1264. [PMID: 34514170 PMCID: PMC8395588 DOI: 10.1515/med-2021-0314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 11/15/2022] Open
Abstract
In this study, we aim to discover the importance of long non-coding RNA cyclin-dependent kinase 6 (CDK6)-AS1 in lipopolysaccharide (LPS)-induced HK-2 cells. We treated the HK-2 cells with LPS and knocked down CDK6-AS1 in HK-2 cells and then analyzed the effects of CDK6-AS1 on the viability of cell, cell apoptosis, the expression of cytokines via MTT, flow cytometry, enzyme-linked immunosorbent assay (ELISA), and qPCR. The results showed that silencing CDK6-AS1 alleviated LPS-induced inhibition of HK-2 cell proliferation, release of IL-1β, IL-8, IL-6, and TNF-α, cell apoptosis, and decrease in mitochondrial membrane potential. In addition, decreasing the level of CDK6-AS1 inhibited the reduction of Bcl-2 levels, the expression of Bax, cleaved caspade-9, and cleaved caspase-3, induced by LPS. In conclusion, lowering CDK6-AS1 level alleviates LPS-induced inflammatory damage in HK-2 cells.
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Affiliation(s)
- Ling Wu
- Department of Pediatrics, Fujian Maternity and Child Health Hospital, Fuzhou 350001, Fujian, China
| | - Rui Zhang
- Department of Pediatrics, Fujian Maternity and Child Health Hospital, Fuzhou 350001, Fujian, China
| | - Sheng Lin
- Department of Pediatrics, Fujian Maternity and Child Health Hospital, Fuzhou 350001, Fujian, China
| | - Min Lin
- Pediatric Intensive Care Unit, Fujian Maternity and Child Health Hospital, Fuzhou 350001, Fujian, China
| | - Jing Wang
- Department of Nosocomial Infection Management, Fujian Maternity and Child Health Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou 350001, Fujian, China
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23
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Orlandella FM, Smaldone G, Salvatore G, Vitagliano L, Cianflone A, Parasole R, Beneduce G, Menna G, Salvatore M, Mirabelli P. The lncRNA TEX41 is upregulated in pediatric B-Cells Acute Lymphoblastic Leukemia and it is necessary for leukemic cell growth. Biomark Res 2021; 9:54. [PMID: 34233751 PMCID: PMC8261931 DOI: 10.1186/s40364-021-00307-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs involved in the regulation of various physiological and pathological cellular processes, including transcription, intracellular trafficking, and chromosome remodeling. LncRNAs deregulation was linked to the development and progression of various cancer types, such as acute leukemias. In this context, lncRNAs were also evaluated as a novel class of biomarkers for cancer diagnosis and prognosis. Here, we analyzed TEX41 in childhood B cell acute lymphoid leukemia (B-ALL). Methods Total RNA was extracted from pediatric B-ALL patients (at diagnosis and after induction of therapy) and from healthy subjects. Total RNA was also extracted from different leukemia cell line models. The expression level of TEX41 was evaluated by q-RT-PCR. Also, the dataset deposited by St. Jude Children’s Research Hospital was consulted. Furthermore, the silencing of TEX41 in RS4;11 cell line was obtained by 2′-Deoxy, 2′Fluroarabino Nucleic Acids (2′F-ANAs) Oligonucleotides, and the effect on cell proliferation was evaluated. Cell cycle progression and its regulators were analyzed by flow cytometry and immunoblotting. Results We exploited the St Jude Cloud database and found that TEX41 is a lncRNA primarily expressed in the case of B-ALL (n = 79) while its expression levels are low/absent for T-cell ALL (n = 25) and acute myeloid leukemia (n = 38). The association of TEX41 with B-ALL was confirmed by real-time PCR assays. TEX41 disclosed increased expression levels in bone marrow from patients with B-ALL at diagnosis, while its expression levels became low or absent when retested in Bone Marrow cells of the same patient after 1 month of induction therapy. Also, silencing experiments performed on RS4;11 cells showed that TEX41 downregulation impaired in vitro leukemic cell growth determining their arrest in the G2-M phase and the deregulation of cell cycle proteins. Conclusions Our findings highlight that TEX41 is an upregulated lncRNA in the case of B-ALL and this feature makes it a novel potential biomarker for the diagnosis of this leukemia subtype in pediatric patients. Finally, TEX41 expression seems to be critical for leukemic proliferation, indeed, silencing experiments targeting TEX41 mRNA in the RS4;11 cell line hampered in vitro cell growth and cell cycle progression, by inducing G2-M arrest as confirmed propidium iodide staining and by the upregulation of p53 and p21 proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-021-00307-7.
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Affiliation(s)
| | | | - Giuliana Salvatore
- IRCCS, SDN, Via E. Gianturco 113, 80143, Naples, Italy.,Dipartimento di Scienze Motorie e del Benessere, University of Naples Parthenope, Via Medina 40, 80133, Naples, Italy.,CEINGE - Biotecnologie Avanzate S.c.a.r.l, Via Gaetano Salvatore 486, 80145, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R, Via Mezzocannone 16, 80134, Napoli, Italy
| | | | - Rosanna Parasole
- Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples, Italy
| | - Giuliana Beneduce
- Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples, Italy
| | - Giuseppe Menna
- Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples, Italy
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24
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Chen Z, Yang F, Liu H, Fan F, Lin Y, Zhou J, Cai Y, Zhang X, Wu Y, Mao R, Zhang T. Identification of a nomogram based on an 8-lncRNA signature as a novel diagnostic biomarker for childhood acute lymphoblastic leukemia. Aging (Albany NY) 2021; 13:15548-15568. [PMID: 34106877 PMCID: PMC8221355 DOI: 10.18632/aging.203116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022]
Abstract
Childhood acute lymphoblastic leukemia (cALL) still represents a major cause of disease-related death in children. This study aimed to explore the prognostic value of long non-coding RNAs (lncRNAs) in cALL. We downloaded lncRNA expression profiles from the TARGET and GEO databases. Univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses were applied to identify lncRNA-based signatures. We identified an eight-lncRNA signature (LINC00630, HDAC2-AS2, LINC01278, AL356599.1, AC114490.1, AL132639.3, FUT8.AS1, and TTC28.AS1), which separated the patients into two groups with significantly different overall survival rates. A nomogram based on the signature, BCR ABL1 status and white blood cell count at diagnosis was developed and showed good accuracy for predicting the 3-, 5- and 7-year survival probability of cALL patients. The C-index values of the nomogram in the training and internal validation set reached 0.8 (95% CI, 0.757 to 0.843) and 0.806 (95% CI, 0.728 to 0.884), respectively. The nomogram proposed in this study objectively and accurately predicted the prognosis of cALL. In vitro experiments suggested that LINC01278 promoted the proliferation of leukemic cells and inhibited leukemic cell apoptosis by targeting the inhibition of miR-500b-3p in cALL, and LINC01278 may be a biological target for the treatment of cALL in the future.
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Affiliation(s)
- Zhang Chen
- Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China
| | - Fan Yang
- Emergency Department, Peking University Third Hospital, Peking University School of Medicine, Beijing 100083, China
| | - Hui Liu
- Department of Neurology, General Hospital of Western Theater Command, Chengdu 610500, China
| | - Fan Fan
- Department of Neurology, General Hospital of Western Theater Command, Chengdu 610500, China
| | - Yanggang Lin
- Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China
| | - Jinhua Zhou
- Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China
| | - Yun Cai
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu 610083, China
| | - Xiaoxiao Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yingxin Wu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China
| | - Rui Mao
- Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China.,Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China
| | - Tongtong Zhang
- Medical Research Center, The Third People's Hospital of Chengdu, The Second Chengdu Hospital Affiliated to Chongqing Medical University, Chengdu 610031, China
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25
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Yu W, Wang W, Yu X. Investigation of lncRNA-mRNA co-expression network in ETV6-RUNX1-positive pediatric B-cell acute lymphoblastic leukemia. PLoS One 2021; 16:e0253012. [PMID: 34101758 PMCID: PMC8186766 DOI: 10.1371/journal.pone.0253012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/17/2021] [Indexed: 12/04/2022] Open
Abstract
ETV6/RUNX1 gene fusion is the most common chromosomal translocation abnormality occurred in pediatric B-cell acute lymphoblastic leukemia (B-ALL). Compared with ETV6-RUNX1-negative patients, ETV6-RUNX1-positive patients possess more improved treatment strategies but higher risk to relapse. In this research, the potential gene interaction networks were constructed intending for elucidating the pathogenesis of B-ALL. We performed the weighted gene co-expression network analysis (WGCNA) to assess the involvement of lncRNA-mRNA pairs in B-ALL patients consisting of 24 ETV6-RUNX1-positive patients and 18 ETV6-RUNX1-negative patients and found a module that was significantly associated with positive/negative trait. Gene Ontology analysis showed that mRNAs in this module were enriched in the positive regulation of MAPK cascade, positive regulation of JNK cascade, and myeloid cell differentiation pathway. To further investigate the relationship between lncRNAs and mRNAs in this significant module, we constructed the lncRNA-mRNA co-expression network. 3 lncRNAs (RP11-170J3.2, RP11-135F9.1 and RP1-151B14.9) were found at the core of the lncRNA-mRNA co-expression network, which had the most co-expression connections with mRNAs. And several related mRNAs (ACTN1, TNFRSF21 and NLRP3) had a significant correlation with the patient survival prediction. Our findings may explicate the pathogenesis of B-ALL, and the disease-associated genes could provide clues to find novel biomarkers for prognosis.
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Affiliation(s)
- Weijuan Yu
- Department of Hematology Laboratory, Yantai Yuhuangding Hospital, Yantai, P.R. China
| | - Weihua Wang
- Department of Hematology Laboratory, Yantai Yuhuangding Hospital, Yantai, P.R. China
| | - Xiumei Yu
- Department of Hematology Laboratory, Yantai Yuhuangding Hospital, Yantai, P.R. China
- * E-mail:
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26
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Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
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Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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27
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Rodriguez PD, Paculova H, Kogut S, Heath J, Schjerven H, Frietze S. Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22052683. [PMID: 33799946 PMCID: PMC7961854 DOI: 10.3390/ijms22052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Jessica Heath
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Department of Pediatrics, University of Vermont, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Correspondence:
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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: 14] [Impact Index Per Article: 3.5] [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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29
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Cuadros M, García DJ, Andrades A, Arenas AM, Coira IF, Baliñas-Gavira C, Peinado P, Rodríguez MI, Álvarez-Pérez JC, Ruiz-Cabello F, Camós M, Jiménez-Velasco A, Medina PP. LncRNA-mRNA Co-Expression Analysis Identifies AL133346.1/CCN2 as Biomarkers in Pediatric B-Cell Acute Lymphoblastic Leukemia. Cancers (Basel) 2020; 12:cancers12123803. [PMID: 33348573 PMCID: PMC7765782 DOI: 10.3390/cancers12123803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Dysregulation of noncoding RNAs has been described in numerous types of cancers and it has been associated with oncogenic or tumor suppressor activities. However, the signature of clinically relevant noncoding RNAs in pediatric B-cell acute lymphoblastic leukemia is still poorly understood. In a search for long non-coding RNAs that characterize pediatric B-cell acute lymphoblastic leukemia, we found that the long non-coding RNA AL133346.1 and a neighbouring protein-coding mRNA (CCN2) were significantly over-expressed in leukemia samples compared to healthy bone marrow. Survival analysis showed that patients with high CCN2 expression had a significantly better prognosis. These data suggest that AL133346.1/CCN2 could be useful for discriminating subtypes of leukemia and that CCN2 expression could predict the prognosis of pediatric patients with B-cell acute lymphoblastic leukemia. Abstract Pediatric acute B-cell lymphoblastic leukemia (B-ALL) constitutes a heterogeneous and aggressive neoplasia in which new targeted therapies are required. Long non-coding RNAs have recently emerged as promising disease-specific biomarkers for the clinic. Here, we identified pediatric B-ALL-specific lncRNAs and associated mRNAs by comparing the transcriptomic signatures of tumoral and non-tumoral samples. We identified 48 lncRNAs that were differentially expressed between pediatric B-ALL and healthy bone marrow samples. The most relevant lncRNA/mRNA pair was AL133346.1/CCN2 (previously known as RP11-69I8.3/CTGF), whose expression was positively correlated and increased in B-ALL samples. Their differential expression pattern and their strong correlation were validated in external B-ALL datasets (Therapeutically Applicable Research to Generate Effective Treatments, Cancer Cell Line Encyclopedia). Survival curve analysis demonstrated that patients with “high” expression levels of CCN2 had higher overall survival than those with “low” levels (p = 0.042), and this gene might be an independent prognostic biomarker in pediatric B-ALL. These findings provide one of the first detailed descriptions of lncRNA expression profiles in pediatric B-ALL and indicate that these potential biomarkers could help in the classification of leukemia subtypes and that CCN2 expression could predict the survival outcome of pediatric B-cell acute lymphoblastic leukemia patients.
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Affiliation(s)
- Marta Cuadros
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Av. de la Investigación 11, 18016 Granada, Spain
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Daniel J García
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Av. de la Investigación 11, 18016 Granada, Spain
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
| | - Alvaro Andrades
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - Alberto M Arenas
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - Isabel F Coira
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - Carlos Baliñas-Gavira
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - Paola Peinado
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - María I Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Av. de la Investigación 11, 18016 Granada, Spain
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Juan Carlos Álvarez-Pérez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
| | - Francisco Ruiz-Cabello
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Av. de la Investigación 11, 18016 Granada, Spain
- Department of Clinical Analysis and Immunology, UGC Laboratorio Clínico, University Hospital Virgen de las Nieves, 18014 Granada, Spain
| | - Mireia Camós
- Hematology Laboratory, Institut de Recerca Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Antonio Jiménez-Velasco
- Hematology Laboratory, Universitary Regional Hospital, Av. de Carlos Haya, 29010 Málaga, Spain
| | - Pedro P Medina
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (ibs. Granada), Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Av. de Fuente Nueva S/N, 18071 Granada, Spain
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Abstract
Long noncoding RNAs (lncRNAs) have recently been discovered and are increasingly recognized as vital components of modern molecular biology. Accumulating evidence shows that lncRNAs have emerged as important mediators in diverse biological processes such as cell differentiation, pluripotency, and tumorigenesis, while the function of lncRNAs in the field of normal and malignant hematopoiesis remains to be further elucidated. Here, we widely reviewed recent advances and summarize the characteristics and basic mechanisms of lncRNAs and keep abreast of developments of lncRNAs within the field of normal and malignant hematopoiesis. Based on gene regulatory networks at different levels of lncRNAs participation, lncRNAs have been shown to regulate gene expression from epigenetics, transcription and post transcription. The expression of lncRNAs is highly cell-specific and critical for the development and activation of hematopoiesis. Moreover, we also summarized the role of lncRNAs involved in hematological malignancies in recent years. LncRNAs have been found to play an emerging role in normal and malignant hematopoiesis, which may provide novel ideas for the diagnosis and therapeutic targets of hematological diseases in the foreseeable future.
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Xiao Y, Xiao Z, Feng X, Chen Z, Kuang L, Wang L. A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs. BMC Bioinformatics 2020; 21:555. [PMID: 33267800 PMCID: PMC7709313 DOI: 10.1186/s12859-020-03906-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/25/2020] [Indexed: 12/25/2022] Open
Abstract
Background Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, in recent years, more and more computational methods have been proposed by researchers to infer potential lncRNA-disease associations. However, there exist all kinds of limitations in these state-of-the-art prediction methods as well. Results In this manuscript, a novel computational model named FVTLDA is proposed to infer potential lncRNA-disease associations. In FVTLDA, its major novelty lies in the integration of direct and indirect features related to lncRNA-disease associations such as the feature vectors of lncRNA-disease pairs and their corresponding association probability fractions, which guarantees that FVTLDA can be utilized to predict diseases without known related-lncRNAs and lncRNAs without known related-diseases. Moreover, FVTLDA neither relies solely on known lncRNA-disease nor requires any negative samples, which guarantee that it can infer potential lncRNA-disease associations more equitably and effectively than traditional state-of-the-art prediction methods. Additionally, to avoid the limitations of single model prediction techniques, we combine FVTLDA with the Multiple Linear Regression (MLR) and the Artificial Neural Network (ANN) for data analysis respectively. Simulation experiment results show that FVTLDA with MLR can achieve reliable AUCs of 0.8909, 0.8936 and 0.8970 in 5-Fold Cross Validation (fivefold CV), 10-Fold Cross Validation (tenfold CV) and Leave-One-Out Cross Validation (LOOCV), separately, while FVTLDA with ANN can achieve reliable AUCs of 0.8766, 0.8830 and 0.8807 in fivefold CV, tenfold CV, and LOOCV respectively. Furthermore, in case studies of gastric cancer, leukemia and lung cancer, experiment results show that there are 8, 8 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with MLR, and 8, 7 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with ANN, having been verified by recent literature. Comparing with the representative prediction model of KATZLDA, comparison results illustrate that FVTLDA with MLR and FVTLDA with ANN can achieve the average case study contrast scores of 0.8429 and 0.8515 respectively, which are both notably higher than the average case study contrast score of 0.6375 achieved by KATZLDA. Conclusion The simulation results show that FVTLDA has good prediction performance, which is a good supplement to future bioinformatics research.
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Affiliation(s)
- Yubin Xiao
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China.,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Zheng Xiao
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiang Feng
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Zhiping Chen
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Linai Kuang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China. .,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China.
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Mousavi Z, Ghorbian S, Rezamand A, Roshangar L, Jafari B. Expression Profile of LncRNAs in Childhood Acute Lymphoblastic Leukemia: A Pilot Study. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.84] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Childhood acute lymphoblastic leukemia (ALL) explains 26% of pediatricmalignancies and is one of the leading causes of disease-related deaths in children. A novelmolecular class of non-coding genes, long non-coding RNAs (lncRNAs) having over 200nucleotides, have been defined as regulators of different cellular processes including pluripotency,oncogenesis, and transcription. It has been demonstrated that lncRNA transcription profilescan distinguish pre B-cell subtype of ALL accurately and act as early diagnostic and prognosticbiomarkers. Hence, the aim of this pilot study was the prior evaluation of expression profileof several lncRNA candidates including RP11-68I18.10, RP11-624C23.1, RP11-446E9, RP11-137H2.4, and RP11-203E8 in patients with ALL. Methods: In this study, 80 blood samples were obtained from patients, definitely diagnosed bypathologists with ALL, and from healthy subjects. Total RNA was extracted from blood samples,and cDNA was synthesized. Real-time PCR was applied to determine the expression of lncRNAs.A P-value of 0.010 was considered statistically significant. Results: Our findings revealed that the expression levels of lncRNAs RP11-624C23.1, RP11-446E9, RP11-137H2.4, RP11-68I18.10, and RP11-203E8 were significantly decreased in ALLsamples compared to those of healthy samples (P<0.0001, P =0.0616, P =0.0292, P<0.0001, andP = 0.0007). Moreover, the relationship between these five lncRNA expression changes and theimmunophenotype in ALL patients was not significant. Conclusion: The dysregulation of lncRNAs in ALL samples could provide a novel and interestingpossibility for early diagnosis and prognosis, as well as mastering the treatment of ALL.
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Affiliation(s)
- Zohreh Mousavi
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Azim Rezamand
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leyla Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behboud Jafari
- Department of Microbiology, Ahar Branch, Islamic Azad University, Ahar, Iran
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lncRNAs-mRNAs Co-Expression Network Underlying Childhood B-Cell Acute Lymphoblastic Leukaemia: A Pilot Study. Cancers (Basel) 2020; 12:cancers12092489. [PMID: 32887470 PMCID: PMC7564554 DOI: 10.3390/cancers12092489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Acute lymphoblastic leukemia (ALL) is one of the most common childhood cancers. The ALL onset involves abnormal proliferation and arrest of differentiation of B or T cell progenitors. Recently, long non–coding RNAs (lncRNAs) gained great interest in the B–ALL leukemogenesis, however, so far few “omic” studies investigate lncRNAs and protein–coding gene networks. In our retrospective study, we conceived an integrated bioinformatic approach, by using NGS platform, to discover lncRNAs strongly correlated with aberrantly expressed protein–coding genes. We provided dysregulated lncRNA–mRNA pairs potentially underlying B–ALL pathogenesis. Diagnosis incidence peak of ALL appears approximatively between 1 and 19 years old. lncRNAs may be of clinical utility as non–invasive biomarker for B–ALL onset or therapy response in support of precision medicine. The identification of lncRNA as key regulators in B–ALL could lead to the identification of the altered pathways able to sustain the leukemic growth. Abstract Long non–coding RNAs (lncRNAs) are emerging as key gene regulators in the pathogenesis and development of various cancers including B lymphoblastic leukaemia (B–ALL). In this pilot study, we used RNA–Seq transcriptomic data for identifying novel lncRNA–mRNA cooperative pairs involved in childhood B–ALL pathogenesis. We conceived a bioinformatic pipeline based on unsupervised PCA feature extraction approach and stringent statistical criteria to extract potential childhood B–ALL lncRNA signatures. We then constructed a co–expression network of the aberrantly expressed lncRNAs (30) and protein–coding genes (754). We cross–validated our in–silico findings on an independent dataset and assessed the expression levels of the most differentially expressed lncRNAs and their co–expressed mRNAs through ex vivo experiments. Using the guilt–by–association approach, we predicted lncRNA functions based on their perfectly co–expressed mRNAs (Spearman’s correlation) that resulted closely disease–associated. We shed light on 24 key lncRNAs and their co–expressed mRNAs which may play an important role in B–ALL pathogenesis. Our results may be of clinical utility for diagnostic and/or prognostic purposes in paediatric B–ALL management.
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Piao M, Zhang L. Knockdown of SNHG16 suppresses the proliferation and induces the apoptosis of leukemia cells via miR‑193a‑5p/CDK8. Int J Mol Med 2020; 46:1175-1185. [PMID: 32705162 PMCID: PMC7387099 DOI: 10.3892/ijmm.2020.4671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
Although small nucleolar RNA host gene 16 (SNHG16) is known to exhibit auxo‑action in certain types of tumor, its role in leukemia remains unclear. The present study analyzed the role and mechanisms of action of SNHG16 in leukemia cells in order to identify therapeutic targets for this disease. Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed to determine SNHG16 expression in human leukemia cell lines. Using TargetScan 7.2 and dual‑luciferase reporter assay, the target genes of SNHG16 were verified. Following the downregulation of the expression of SNHG16 or its target genes, Cell Counting kit‑8 (CCK‑8) assay was performed to examine the viability of the leukemia cells. In addition, flow cytometry was performed to analyze the cell apoptotic rates, and colony formation assays were used to determine the cell proliferative ability. RT‑qPCR and western blot analysis were used to determine the association between SNHG16 and its target genes. SNHG16 was found to be abnormally highly expressed in acute myeloblastic leukemia cell lines, the knockdown of which weakened the viability of the leukemia cells, suppressed cell proliferation and promoted cell apoptosis. miR‑193a‑5p could bind to SNHG16, and its target gene was CDK8. Moreover, the expression of miR‑193a‑5p increased with the decrease in SNHG16 expression, while the inhibition of miR‑193a‑5p promoted the expression of CDK8. The downregulation of miR‑193a‑5p enhanced the viability of the leukemia cells, accelerated cell cloning and reduced cell apoptosis, which was completely opposite to the effects observed with the silencing of CDK8. The knockdown of SNHG16 suppressed the viability of the leukemia cells, suppressed cell proliferation, and induced cell apoptosis by regulating miR‑193a‑5p/CDK8. Thus, SNHG16 may prove to be a potential therapeutic target for the treatment of leukemia.
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Affiliation(s)
- Meihua Piao
- Clinical Laboratory, Yanbian University Hospital (Yanbian Hospital), Yanji, Jilin 133000
| | - Li Zhang
- Department of Neonatology, Weinan Maternal and Child Health Hospital, Weinan, Shaanxi 714000, P.R. China
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Liu Y, Sun P, Zhao Y, Liu B. The role of long non-coding RNAs and downstream signaling pathways in leukemia progression. Hematol Oncol 2020; 39:27-40. [PMID: 32621547 DOI: 10.1002/hon.2776] [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] [Received: 05/14/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 01/17/2023]
Abstract
The study of long non-coding RNAs (lncRNA) is a newly established field and our knowledge about them is rapidly growing. These kinds of RNAs are unchanged parts of the genome throughout evolution, that modulate cell growth, differentiation, and apoptosis during diverse physiological and pathological processes including leukemia development. They have the capability to be useful biomarkers for the diagnosis, clinical typing, prognosis, as well as potential therapeutic targets. In this study, we summarized the role of lncRNAs in the expression and function of white blood cells and oncogenic transformation into four main types of leukemia.
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Affiliation(s)
- Yadong Liu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Penghao Sun
- Department of Andrology, The First Hospital of Jilin University, Changchun, China
| | - Yuhao Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Bin Liu
- Department of Hand Surgery, The First Hospital of Jilin University, Changchun, China
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Expression of non-coding RNAs in hematological malignancies. Eur J Pharmacol 2020; 875:172976. [DOI: 10.1016/j.ejphar.2020.172976] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/18/2020] [Accepted: 01/29/2020] [Indexed: 12/22/2022]
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Gao J, Wang F, Wu P, Chen Y, Jia Y. Aberrant LncRNA Expression in Leukemia. J Cancer 2020; 11:4284-4296. [PMID: 32368311 PMCID: PMC7196264 DOI: 10.7150/jca.42093] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Leukemia is a common malignant cancer of the hematopoietic system, whose pathogenesis has not been fully elucidated. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides without protein-coding function. Recent studies report their role in cellular processes such as the regulation of gene expression, as well as in the carcinogenesis, occurrence, development, and prognosis of various tumors. Evidence indicating relationships between a variety of lncRNAs and leukemia pathophysiology has increased dramatically in the previous decade, with specific lncRNAs expected to serve as diagnostic biomarkers, novel therapeutic targets, and predictors of clinical outcomes. Furthermore, these lncRNAs might offer insight into disease pathogenesis and novel treatment options. This review summarizes progress in studies on the role(s) of lncRNAs in leukemia.
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Affiliation(s)
- Jie Gao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fujue Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pengqiang Wu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingying Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yongqian Jia
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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Ying X, Zhang W, Fang M, Wang C, Han L, Yang C. LncRNA SNHG5 regulates SOX4 expression through competitive binding to miR-489-3p in acute myeloid leukemia. Inflamm Res 2020; 69:607-618. [PMID: 32266420 DOI: 10.1007/s00011-020-01345-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/01/2020] [Accepted: 03/30/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Currently, lncRNA plays an important role in the occurrence and development of acute myeloid leukemia (AML), including SNHG5. However, the role and mechanism of SNHG5 in AML remains unclear. In this study, we explored the regulatory mechanism of SNHG5 in the development of AML. METHODS AND RESULTS QRT-PCR was used to investigate the expression of SNHG5, miR-489-3p, and SOX. The proliferation and apoptosis of AML cells were analyzed by cell transfection, cell counting kit-8 (CCK8), and flow cytometric analysis. Moreover, the expression analysis of marker proteins was detected by western blot. Through luciferase activity assay, RNA pull-down, and RNA-binding protein immunoprecipitation (RIP), we proved that SNHG5 could bind miR-489-3p and SOX4 which might be the target gene of miR-489-3p. RESULTS We first found that SNHG5 was up-regulated in both AML patient bone marrow samples and various AML cell lines. Second, we found that knockdown of SNHG5 inhibited proliferation of AML cells and promoted apoptosis. It was found that SNHG5 could bind miR-489-3p, and the relative expression of SNHG5 was negatively correlated with miR-489-3p. Further results suggested that SOX4 might be the target gene of miR-489-3p. Finally, our experimental data indicated that knockdown of SNHG5 could reduce the tumor volume and down-regulated SOX4 levels in vivo. CONCLUSIONS Our results demonstrated that SNHG5 affected the expression of SOX4 through binding miR-489-3p to regulate proliferation and apoptosis of AML, which might act as a prospective prognostic biological marker and a promising therapeutic target for AML.
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Affiliation(s)
- Xiaoyang Ying
- Department of Clinical Hematology, Affiliated No. 2 Hospital School of Medicine, Xi'an Jiaotong University, Xi'an Jiaotong University West Five Road, No 157, Xi'an, 710004, People's Republic of China.,Department of Hematology, Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, 116001, China
| | - Wanggang Zhang
- Department of Clinical Hematology, Affiliated No. 2 Hospital School of Medicine, Xi'an Jiaotong University, Xi'an Jiaotong University West Five Road, No 157, Xi'an, 710004, People's Republic of China.
| | - Meiyun Fang
- Department of Hematology, Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, 116001, China
| | - Chenchen Wang
- Department of Hematology, Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, 116001, China
| | - Li Han
- Department of Hematology, Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, 116001, China
| | - Chenmeng Yang
- Department of Hematology, Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, 116001, China
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40
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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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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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Zhang L, Xu X, Su X. Noncoding RNAs in cancer immunity: functions, regulatory mechanisms, and clinical application. Mol Cancer 2020; 19:48. [PMID: 32122338 PMCID: PMC7050126 DOI: 10.1186/s12943-020-01154-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
It is well acknowledged that immune system is deeply involved in cancer initiation and progression, and can exert both pro-tumorigenic and anti-tumorigenic effects, depending on specific microenvironment. With the better understanding of cancer-associated immune cells, especially T cells, immunotherapy was developed and applied in multiple cancers and exhibits remarkable efficacy. However, currently only a subset of patients have responses to immunotherapy, suggesting that a boarder view of cancer immunity is required. Non-coding RNAs (ncRNAs), mainly including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are identified as critical regulators in both cancer cells and immune cells, thus show great potential to serve as new therapeutic targets to improve the response of immunotherapy. In this review, we summarize the functions and regulatory mechanisms of ncRNAs in cancer immunity, and highlight the potential of ncRNAs as novel targets for immunotherapy.
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Affiliation(s)
- Le Zhang
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, 1 Tong Dao Street, Huimin District, Hohhot, 010050, Inner Mongolia, China
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, FL, 33612-9497, USA
| | - Xiulan Su
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, 1 Tong Dao Street, Huimin District, Hohhot, 010050, Inner Mongolia, China.
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Inferences of Individual Drug Response-Related Long Non-coding RNAs Based on Integrating Multi-omics Data in Breast Cancer. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:128-139. [PMID: 32163894 PMCID: PMC7066040 DOI: 10.1016/j.omtn.2020.01.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/19/2020] [Accepted: 01/31/2020] [Indexed: 12/25/2022]
Abstract
Differences in individual drug responses are obstacles in breast cancer (BRCA) treatment, so predicting responses would help to plan treatment strategies. The accumulation of cancer molecular profiling and drug response data provide opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs in BRCA. This study evaluated drug responses with a multi-omics integrated system that depended on long non-coding RNAs (lncRNAs). We identified drug response-related lncRNAs (DRlncs) by combining expression data of lncRNA, microRNA, messenger RNA, methylation levels, somatic mutations, and the survival data of cancer patients treated with drugs. We constructed an integrated and computational multi-omics approach to identify DRlncs for diverse chemotherapeutic drugs in BRCA. Some DRlncs were identified with Adriamycin, Cytoxan, Tamoxifen, and all samples for BRCA patients. These DRlncs showed specific features regarding both expression and computational accuracies. The DRlnc-gene co-expression networks were constructed and analyzed. Key DRlncs, such as HOXA-AS2 (Ensembl: ENSG00000253552), in the drug Adriamycin were characterized. The experimental analysis also suggested that HOXA-AS2 (Ensembl: ENSG00000253552) was a key DRlnc in Adriamycin drug resistance in BRCA patients. Some DRlncs were associated with survival and some specific functions. A possible mechanism of DRlnc HOXA-AS2 (Ensembl: ENSG00000253552) in the Adriamycin drug response for BRCA resistance was inferred. In summary, this study provides a framework for lncRNA-based evaluation of clinical drug responses in BRCA. Understanding the underlying molecular mechanisms of drug responses will facilitate improved responses to chemotherapy and outcomes of BRCA treatment.
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Aberuyi N, Rahgozar S, Ghodousi ES, Ghaedi K. Drug Resistance Biomarkers and Their Clinical Applications in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 9:1496. [PMID: 32010613 PMCID: PMC6978753 DOI: 10.3389/fonc.2019.01496] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are biological molecules found in body fluids or tissues, which can be considered as indications of a normal or abnormal process, or of a condition or disease. There are various types of biomarkers based on their application and molecular alterations. Treatment-sensitivity or drug resistance biomarkers include prognostic and predictive molecules with utmost importance in selecting appropriate treatment protocols and improving survival rates. Acute lymphoblastic leukemia (ALL) is the most prevalent hematological malignancy diagnosed in children with nearly 80% cure rate. Despite the favorable survival rates of childhood ALL (chALL), resistance to chemotherapeutic agents and, as a consequence, a dismal prognosis develops in a significant number of patients. Therefore, there are urgent needs to have robust, sensitive, and disease-specific molecular prognostic and predictive biomarkers, which could allow better risk classification and then better clinical results. In this article, we review the currently known drug resistance biomarkers, including somatic or germ line nucleic acids, epigenetic alterations, protein expressions and metabolic variations. Moreover, biomarkers with potential clinical applications are discussed.
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Affiliation(s)
- Narges Aberuyi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Elaheh Sadat Ghodousi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
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Cuadros M, Andrades Á, Coira IF, Baliñas C, Rodríguez MI, Álvarez-Pérez JC, Peinado P, Arenas AM, García DJ, Jiménez P, Camós M, Jiménez-Velasco A, Medina PP. Expression of the long non-coding RNA TCL6 is associated with clinical outcome in pediatric B-cell acute lymphoblastic leukemia. Blood Cancer J 2019; 9:93. [PMID: 31767830 PMCID: PMC6877621 DOI: 10.1038/s41408-019-0258-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022] Open
Affiliation(s)
- Marta Cuadros
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain.,GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Health Research Institute of Granada (ibs.Granada), Granada, Spain
| | - Álvaro Andrades
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Isabel F Coira
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Carlos Baliñas
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - María I Rodríguez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Health Research Institute of Granada (ibs.Granada), Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Juan Carlos Álvarez-Pérez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Health Research Institute of Granada (ibs.Granada), Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Paola Peinado
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Alberto M Arenas
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Daniel J García
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain.,GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Pilar Jiménez
- Health Research Institute of Granada (ibs.Granada), Granada, Spain.,Department of Clinical Analysis and Immunology, UGC Laboratorio Clínico, University Hospital Virgen de las Nieves, Granada, Spain
| | - Mireia Camós
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, University of Barcelona; Institut de Recerca Hospital Sant Joan de Deu Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Pedro P Medina
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain. .,Health Research Institute of Granada (ibs.Granada), Granada, Spain. .,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain.
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Chen CT, Wang PP, Mo WJ, Zhang YP, Zhou W, Deng TF, Zhou M, Chen XW, Wang SQ, Wang CX. Expression profile analysis of prognostic long non-coding RNA in adult acute myeloid leukemia by weighted gene co-expression network analysis (WGCNA). J Cancer 2019; 10:4707-4718. [PMID: 31528236 PMCID: PMC6746144 DOI: 10.7150/jca.31234] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/25/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs), which are over 200 nt in length, have a key role in tumorigenesis and disease progression. To explore the role of prognostic lncRNAs in adult acute myeloid leukemia (AML), the expression profiles of lncRNAs and mRNAs in AML were analyzed. Methods: The RNAseq data of 167 adult AML patients and the corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA), which is a publicly available database. The RPKM values of the RNAseq data were subjected to weighted gene co-expression network analysis (WGCNA) in modularization. Results: We identified survival specific lncRNAs and mRNAs, which were divided into modules by coexpression analysis. The lncRNAs were mainly annotated into "Fc gamma R-mediated phagocytosis". The hub lncRNA and co-expressed mRNAs were further selected for analysis of risk stratification. LncRNA-LOC646762 may contribute to AML through the "endocytosis" signaling pathway. Finally, the expression levels of LOC646762 and co-expressed CCND3, CBR1, C10orf54, CD97 and BLOC1S1 in the adult AML patients and healthy volunteers were validated by qRT-PCR, and then their roles in prognosis and risk stratification were identified. Conclusions: Prognostic lncRNA-LOC646762, which may contribute to AML through the "endocytosis" signaling pathway, may act as a biomarker for predicting the survival of adult AML patients, as well as for risk stratification.
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Affiliation(s)
- Cun-Te Chen
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Pei-Pei Wang
- Department of Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Wen-Jian Mo
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Yu-Ping Zhang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Wei Zhou
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Ting-Fen Deng
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Ming Zhou
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiao-Wei Chen
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shun-Qing Wang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Cai-Xia Wang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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47
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Long Non-Coding RNA and Acute Leukemia. Int J Mol Sci 2019; 20:ijms20030735. [PMID: 30744139 PMCID: PMC6387068 DOI: 10.3390/ijms20030735] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022] Open
Abstract
Acute leukemia (AL) is the main type of cancer in children worldwide. Mortality by this disease is high in developing countries and its etiology remains unanswered. Evidences showing the role of the long non-coding RNAs (lncRNAs) in the pathophysiology of hematological malignancies have increased drastically in the last decade. In addition to the contribution of these lncRNAs in leukemogenesis, recent studies have suggested that lncRNAs could be used as biomarkers in the diagnosis, prognosis, and therapeutic response in leukemia patients. The focus of this review is to describe the functional classification, biogenesis, and the role of lncRNAs in leukemogenesis, to summarize the evidence about the lncRNAs which are playing a role in AL, and how these genes could be useful as potential therapeutic targets.
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48
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Tschumper RC, Shanafelt TD, Kay NE, Jelinek DF. Role of long non-coding RNAs in disease progression of early stage unmutated chronic lymphocytic leukemia. Oncotarget 2019; 10:60-75. [PMID: 30713603 PMCID: PMC6343752 DOI: 10.18632/oncotarget.26538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Predicting disease progression in chronic lymphocytic leukemia (CLL) remains challenging particularly in patients with Rai Stage 0/I disease that have an unmutated immunoglobulin heavy chain variable region (UM IGHV). Even though patients with UM IGHV have a poor prognosis and generally require earlier treatment, not all UM IGHV patients experience more rapid disease progression with some remaining treatment free for many years. This observation suggests biologic characteristics other than known prognostic factors influence disease progression. Alterations in long non-coding RNA (lncRNA) expression levels have been implicated in diagnosis and prognosis of various cancers, however, their role in disease progression of early Rai stage UM CLL is unknown. Here we use microarray analysis to compare lncRNA and mRNA profiles of Rai 0/I UM IGHV patients who progressed in <2 years relative to patients who had not progressed for >5 years. Over 1,300 lncRNAs and 940 mRNAs were differentially expressed (fold change ≥ 2.0; p-value ≤ 0.05). Of interest, the differentially expressed lncRNAs T204050, NR_002947, and uc.436+, have known associated genes that have been linked to CLL. Thus, our study reveals differentially expressed lncRNAs in progressive early stage CLL requiring therapy versus indolent early Rai stage UM CLL. These lncRNAs have the potential to impact relevant biological processes and pathways that influence clinical outcome in CLL.
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Affiliation(s)
| | - Tait D Shanafelt
- Department of Hematology/Oncology, Stanford University, Stanford, CA, USA
| | - Neil E Kay
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Diane F Jelinek
- Department of Immunology, Mayo Clinic, Scottsdale, AZ, USA.,Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
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49
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Mohseni M, Uludag H, Brandwein JM. Advances in biology of acute lymphoblastic leukemia (ALL) and therapeutic implications. AMERICAN JOURNAL OF BLOOD RESEARCH 2018; 8:29-56. [PMID: 30697448 PMCID: PMC6334189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and also occurs in adults. Although the outcomes of multi-agent chemotherapy regimens have greatly improved, high toxicity and relapses in many patients necessitate the development of novel therapeutic approaches. Advances in molecular profiling and cytogenetics have identified a broad range of genetic abnormalities, including gene mutations, chromosome translocations and aneuploidy, which has provided a more comprehensive understanding of the biology and pathogenesis of ALL. This understanding has also led to new targeted therapeutic approaches, including the use of selective small molecule inhibitors, nucleic acid-based therapies and immune-based therapies mediated by specific monoclonal antibodies and cellular immunotherapy, which are poised to revolutionize the treatment of various ALL subtypes. The main focus of this review is to highlight the latest advances in ALL biology, including the identification of prognostic factors and putative therapeutic targets. We also review the current status of, and ongoing progress in, the development of targeted therapies for ALL.
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Affiliation(s)
- Mahsa Mohseni
- Department of Medicine, University of Alberta Edmonton, Alberta, Canada
| | - Hasan Uludag
- Department of Chemical and Materials Engineering, University of Alberta Edmonton, Alberta, Canada
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50
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Wong NK, Huang CL, Islam R, Yip SP. Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies. J Hematol Oncol 2018; 11:131. [PMID: 30466456 PMCID: PMC6251105 DOI: 10.1186/s13045-018-0673-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/23/2018] [Indexed: 12/26/2022] Open
Abstract
Recent studies have revealed that non-coding regions comprise the vast majority of the human genome and long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs that has been implicated in a variety of biological processes. Abnormal expression of lncRNAs has also been linked to different human diseases including cancers, yet the regulatory mechanisms and functional effects of lncRNAs are still ambiguous, and the molecular details also need to be confirmed. Unlike protein-coding gene, it is much more challenging to unravel the roles of lncRNAs owing to their unique and complex features such as functional diversity and low conservation among species, which greatly hamper their experimental characterization. In this review, we summarize and discuss both conventional and advanced approaches for the identification and functional characterization of lncRNAs related to hematological malignancies. In particular, the utility and advancement of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system as gene-editing tools are envisioned to facilitate the molecular dissection of lncRNAs via different knock-in/out strategies. Besides experimental considerations specific to lncRNAs, the roles of lncRNAs in the pathogenesis and progression of leukemia are also highlighted in the review. We expect that these insights may ultimately lead to clinical applications including development of biomarkers and novel therapeutic approaches targeting lncRNAs.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
| | - Rashidul Islam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
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