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Forabosco P, Pala M, Crobu F, Diana MA, Marongiu M, Cusano R, Angius A, Steri M, Orrù V, Schlessinger D, Fiorillo E, Devoto M, Cucca F. Transcriptome organization of white blood cells through gene co-expression network analysis in a large RNA-seq dataset. Front Immunol 2024; 15:1350111. [PMID: 38629067 PMCID: PMC11018966 DOI: 10.3389/fimmu.2024.1350111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Gene co-expression network analysis enables identification of biologically meaningful clusters of co-regulated genes (modules) in an unsupervised manner. We present here the largest study conducted thus far of co-expression networks in white blood cells (WBC) based on RNA-seq data from 624 individuals. We identify 41 modules, 13 of them related to specific immune-related functions and cell types (e.g. neutrophils, B and T cells, NK cells, and plasmacytoid dendritic cells); we highlight biologically relevant lncRNAs for each annotated module of co-expressed genes. We further characterize with unprecedented resolution the modules in T cell sub-types, through the availability of 95 immune phenotypes obtained by flow cytometry in the same individuals. This study provides novel insights into the transcriptional architecture of human leukocytes, showing how network analysis can advance our understanding of coding and non-coding gene interactions in immune system cells.
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Affiliation(s)
- Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Francesca Crobu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maria Antonietta Diana
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Mara Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Roberto Cusano
- CRS4-Next Generation Sequencing (NGS) Core, Parco POLARIS, Cagliari, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health (NIH), Baltimore, MA, United States
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Marcella Devoto
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Roma, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
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2
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Lobo-Alves SC, Oliveira LAD, Kretzschmar GC, Valengo AE, Rosati R. Long noncoding RNA expression in acute lymphoblastic leukemia: A systematic review. Crit Rev Oncol Hematol 2024; 196:104290. [PMID: 38341118 DOI: 10.1016/j.critrevonc.2024.104290] [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: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), as gene expression modulators, are potential players in Acute Lymphoblastic Leukemia (ALL) pathogenesis. We systematically explored current literature on lncRNA expression in ALL to identify lncRNAs consistently reported as differentially expressed (DE) either in ALL versus controls or between ALL subtypes. By comparing articles that provided global expression data for DE lncRNAs in the ETV6::RUNX1-positive ALL subtype, we identified four DE lncRNAs in three independent studies (two versus other subtypes and one versus controls), showing concordant expression of LINC01013, CRNDE and lnc-KLF7-1. Additionally, LINC01503 was consistently downregulated on ALL versus controls. Within RT-qPCR studies, twelve lncRNA were DE in more than one source. Thus, several lncRNAs were supported as DE in ALL by multiple sources, highlighting their potential role as candidate biomarkers or therapeutic targets. Finally, as lncRNA annotation is rapidly expanding, standardization of reporting and nomenclature is urgently needed to improve data verifiability and compilation.
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Affiliation(s)
- Sara Cristina Lobo-Alves
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Liana Alves de Oliveira
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Gabriela Canalli Kretzschmar
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Andressa Eloisa Valengo
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil
| | - Roberto Rosati
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
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3
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Rao C, Tong J, Yang Y. Mechanistic insights into FEN1-mediated drug sensitivity and risk signature in colon cancer: An integrative bioinformatics study. Medicine (Baltimore) 2024; 103:e37517. [PMID: 38552056 PMCID: PMC10977573 DOI: 10.1097/md.0000000000037517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024] Open
Abstract
The overexpression of Flap endonuclease 1 (FEN1) has been implicated in drug resistance and prognosis across various cancer types. However, the precise role of FEN1 in colon cancer remains to be fully elucidated. In this study, we employed comprehensive datasets from The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas to examine FEN1 expression and assess its correlation with clinical pathology and prognosis in colon cancer. We utilized the pRRophetic algorithm to evaluate drug sensitivity and performed differential expression analysis to identify genes associated with FEN1-mediated drug sensitivity. Gene set enrichment analysis was conducted to further investigate these genes. Additionally, single-cell sequencing analysis was employed to explore the relationship between FEN1 expression and functional states. Cox regression analysis was implemented to construct a prognostic model, and a nomogram for prognosis was developed. Our analysis of The Cancer Genome Atlas and Gene Expression Omnibus datasets revealed a significant upregulation of FEN1 in colon cancer. However, while FEN1 expression showed no notable correlation with prognosis, it displayed associations with metastasis. Single-cell sequencing analysis further confirmed a positive correlation between FEN1 expression and colon cancer metastasis. Furthermore, we detected marked discrepancies in drug responsiveness between the High_FEN1 and Low_FEN1 groups, identifying 342 differentially expressed genes. Enrichment analysis showed significant suppression in processes related to DNA replication, spliceosome, and cell cycle pathways in the Low_FEN1 group, while the calcium signaling pathway, cAMP signaling pathway, and other pathways were activated. Of the 197 genes differentially expressed and strongly linked to FEN1 expression, 39 were significantly implicated in colon cancer prognosis. Finally, we constructed a risk signature consisting of 5 genes, which, when combined with drug treatment and pathological staging, significantly improved the prediction of colon cancer prognosis. This study offers novel insights into the interplay among FEN1 expression levels, colon cancer metastatic potential, and sensitivity to therapeutic agents. Furthermore, we successfully developed a multi-gene prognostic risk signature derived from FEN1.
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Affiliation(s)
- Chunhui Rao
- Department of Proctology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jingfei Tong
- Department of Proctology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yan Yang
- Department of Otolaryngology, Banshan Community Health Service Center, Gongshu District, Hangzhou, Zhejiang, China
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4
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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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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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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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Zhang L, Zhou S, Zhou T, Li X, Tang J. Targeting the lncRNA DUXAP8/miR-29a/ PIK3CA Network Restores Doxorubicin Chemosensitivity via PI3K-AKT-mTOR Signaling and Synergizes With Inotuzumab Ozogamicin in Chemotherapy-Resistant B-Cell Acute Lymphoblastic Leukemia. Front Oncol 2022; 12:773601. [PMID: 35311115 PMCID: PMC8924619 DOI: 10.3389/fonc.2022.773601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Purpose This study aimed to determine the expression profiles of long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA in chemotherapy-resistant B-cell acute lymphoblastic leukemia (B-ALL). Methods LncRNA, miRNA, and mRNA profiles were assessed by RNA-seq in diagnostic bone marrow samples from 6 chemotherapy-resistant and 6 chemotherapy-sensitive B-ALL patients. The lncRNA DUXAP8/miR-29a/PIK3CA signaling network was identified as the most dysregulated in chemoresistant patient samples, and its effect on cellular phenotypes, PI3K-AKT-mTOR signaling, and chemosensitivity of doxorubicin (Dox)-resistant Nalm-6 (N6/ADR), and Dox-resistant 697 (697/ADR) cells were assessed. Furthermore, its synergy with inotuzumab ozogamicin treatment was investigated. Results 1,338 lncRNAs, 75 miRNAs, and 1620 mRNAs were found to be dysregulated in chemotherapy-resistant B-ALL in comparison to chemotherapy-sensitive B-ALL patient samples. Through bioinformatics analyses and RT-qPCR validation, the lncRNA DUXAP8/miR-29a/PIK3CA network and PI3K-AKT-mTOR signaling were identified as significantly associated with B-ALL chemotherapy resistance. In N6/ADR and 697/ADR cells, LncRNA DUXAP8 overexpression and PIK3CA overexpression induced proliferation and inhibited apoptosis, and their respective knockdowns inhibited proliferation, facilitated apoptosis, and restored Dox chemosensitivity. MiR-29a was shown to affect the lncRNA DUXAP8/PIK3CA network, and luciferase reporter gene assay showed direct binding between lncRNA DUXAP8 and miR-29a, as well as between miR-29a and PIK3CA. Targeting lncRNA DUXAP8/miR-29a/PIK3CA network synergized with inotuzumab ozogamicin's effect on N6/ADR and 697/ADR cells. Conclusion Targeting the lncRNA DUXAP8/miR-29a/PIK3CA network not only induced an apoptotic effect on Dox-resistant B-ALL and restored Dox chemosensitivity via PI3K-AKT-mTOR signaling but also showed synergism with inotuzumab ozogamicin treatment.
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Affiliation(s)
- Li Zhang
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, China.,Orofacial Reconstruction and Regeneration Laboratory, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, China.,Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shixia Zhou
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tiejun Zhou
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaoming Li
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Junling Tang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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9
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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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10
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Wang H, Shen G, Liu M, Mao L, Mao H. Expression and clinical significance of lncRNA TCL6 in serum of patients with preeclampsia. Exp Ther Med 2021; 23:41. [PMID: 34849156 PMCID: PMC8613530 DOI: 10.3892/etm.2021.10963] [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: 11/25/2020] [Accepted: 05/07/2021] [Indexed: 11/06/2022] Open
Abstract
Preeclampsia is a common syndrome in pregnancy and a leading cause of mortality of pregnant females and their infants. To investigate the diagnostic and prognostic utility of lncRNA T-cell leukemia/lymphoma 6 (TCL6) in patients with preeclampsia, 120 singleton pregnant females with preeclampsia and another 100 healthy pregnant control subjects were analyzed in the present study. The expression of lncRNA TCL6 in the serum of the included patients was detected. Receiver operating characteristic curve analysis was applied to evaluate the efficiency of lncRNA TCL6 in terms of preeclampsia diagnosis and grading. Kaplan-Meier analysis was adopted to assess the effect of lncRNA TCL6 expression on the rate of adverse pregnancy. Multivariate logistic regression was used to determine high-risk factors of adverse pregnancy. The results indicated that lncRNA TCL6 was significantly increased in the serum of patients with preeclampsia. Furthermore, TCL6 was elevated in subgroups of patients with early-onset or severe preeclampsia and with Haemolysis, Elevated Liver enzymes and Low Platelet count syndrome in comparison with other patients with preeclampsia. High expression of TCL6 in pregnant females corresponded to a higher rate of adverse pregnancy outcomes. Severe preeclampsia, early-onset preeclampsia and high TCL6 expression were identified as independent risk factors for adverse pregnancy outcomes. For each unit increase in TCL6 expression, a 9.5-fold increase of the risk of adverse maternal and fetal outcomes was determined. Collectively, high expression of lncRNA TCL6 may assist the diagnosis and grading of preeclampsia and may be adopted as an independent risk factor for adverse pregnancy outcomes.
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Affiliation(s)
- Hong Wang
- Department of Obstetrics and Reproductive Center, The Affiliated Hospital of Yunnan University, Kunming, Yunnan 650000, P.R. China
| | - Guimei Shen
- Department of Obstetrics and Reproductive Center, The Affiliated Hospital of Yunnan University, Kunming, Yunnan 650000, P.R. China
| | - Mengsi Liu
- Department of Obstetrics and Reproductive Center, The Affiliated Hospital of Yunnan University, Kunming, Yunnan 650000, P.R. China
| | - Linjuan Mao
- Department of Obstetrics and Reproductive Center, The Affiliated Hospital of Yunnan University, Kunming, Yunnan 650000, P.R. China
| | - Hui Mao
- Department of Obstetrics and Reproductive Center, The Affiliated Hospital of Yunnan University, Kunming, Yunnan 650000, P.R. China
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11
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Zhao D, Xing Q, Song H, Zhao Y, Guo G. LINC00265/miR-4500 Axis Accelerates Acute Lymphoblastic Leukemia Progression by Enhancing STAT3 Signals. Cancer Manag Res 2021; 13:8147-8156. [PMID: 34737643 PMCID: PMC8560060 DOI: 10.2147/cmar.s274590] [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: 07/29/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022] Open
Abstract
Background Long noncoding RNA LINC00265 or miR-4500 is involved in the pathogenesis of many cancers. However, their functions in acute lymphoblastic leukemia (ALL) remain unknown. In this study, we investigated how LINC00265 and miR-4500 regulate the malignant characteristics of ALL. Methods Real-time PCR was used in examining the expression of LINC00265 in ALL cell lines and blood of patients with ALL. Cell proliferation, cell migration, and xenograft tumor assays were performed to verify the function of LINC00265 subjected to overexpressing and silencing experiments. The ceRNA mechanism with LINC00265/miR-4500/STAT3 was investigated through luciferase and RNA pull-down assays. Finally, the function of the LINC00265/miR-4500/STAT3 axis subjected to overexpressing and silencing assays was determined through cell proliferation, cell migration, and xenograft tumor assays. Results LINC00265 was highly expressed in ALL cell lines and blood of patients with ALL and facilitated the proliferation, migration, invasion, and growth of xenograft tumors of ALL cells. The silencing of LINC00265 expression with LINC00265 siRNA significantly inhibited the malignancy of the ALL cells. RNA pull-down and luciferase assays demonstrated that LINC00265 competitively targeted miR-4500 and enhanced STAT3 expression. Furthermore, miR-4500 inhibitors or overexpressed LINC00265 up-regulated STAT3 expression, and miR-4500 mimics or STAT3 shRNAs eliminated the LINC00265-induced malignancy of the ALL cells. Conclusion Mechanistically, LncRNA LINC00265 can competitively interact with miR-4500 and thereby up-regulates STAT3 signaling and enhances the malignancy of tumors.
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Affiliation(s)
- Donglu Zhao
- No. 4 Ward of Hematology Department, Institute of Hematology and Oncology, Harbin First Hospital, Harbin 150010, Heilongjiang Province, People's Republic of China
| | - Qi Xing
- No. 4 Ward of Hematology Department, Institute of Hematology and Oncology, Harbin First Hospital, Harbin 150010, Heilongjiang Province, People's Republic of China
| | - Hang Song
- No. 4 Ward of Hematology Department, Institute of Hematology and Oncology, Harbin First Hospital, Harbin 150010, Heilongjiang Province, People's Republic of China
| | - Yan Zhao
- No. 4 Ward of Hematology Department, Institute of Hematology and Oncology, Harbin First Hospital, Harbin 150010, Heilongjiang Province, People's Republic of China
| | - Guiying Guo
- No. 4 Ward of Hematology Department, Institute of Hematology and Oncology, Harbin First Hospital, Harbin 150010, Heilongjiang Province, People's Republic of China
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12
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Fu R, Qin P, Zou X, Hu Z, Hong N, Wang Y, Jin W. A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:702897. [PMID: 34722498 PMCID: PMC8548578 DOI: 10.3389/fcell.2021.702897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is becoming a powerful tool to investigate monoallelic expression (MAE) in various developmental and pathological processes. However, our knowledge of MAE during hematopoiesis and leukemogenesis is limited. In this study, we conducted a systematic interrogation of MAEs in bone marrow mononuclear cells (BMMCs) at single-cell resolution to construct a MAE atlas of BMMCs. We identified 1,020 constitutive MAEs in BMMCs, which included imprinted genes such as MEG8, NAP1L5, and IRAIN. We classified the BMMCs into six cell types and identified 74 cell type specific MAEs including MTSS1, MOB1A, and TCF12. We further identified 114 random MAEs (rMAEs) at single-cell level, with 78.1% single-allele rMAE and 21.9% biallelic mosaic rMAE. Many MAEs identified in BMMCs have not been reported and are potentially hematopoietic specific, supporting MAEs are functional relevance. Comparison of BMMC samples from a leukemia patient with multiple clinical stages showed the fractions of constitutive MAE were correlated with fractions of leukemia cells in BMMCs. Further separation of the BMMCs into leukemia cells and normal cells showed that leukemia cells have much higher constitutive MAE and rMAEs than normal cells. We identified the leukemia cell-specific MAEs and relapsed leukemia cell-specific MAEs, which were enriched in immune-related functions. These results indicate MAE is prevalent and is an important gene regulation mechanism during hematopoiesis and leukemogenesis. As the first systematical interrogation of constitutive MAEs, cell type specific MAEs, and rMAEs during hematopoiesis and leukemogenesis, the study significantly increased our knowledge about the features and functions of MAEs.
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Affiliation(s)
- Ruiqing Fu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Pengfei Qin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xianghui Zou
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yun Wang
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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13
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Fantini S, Rontauroli S, Sartini S, Mirabile M, Bianchi E, Badii F, Maccaferri M, Guglielmelli P, Ottone T, Palmieri R, Genovese E, Carretta C, Parenti S, Mallia S, Tavernari L, Salvadori C, Gesullo F, Maccari C, Zizza M, Grande A, Salmoiraghi S, Mora B, Potenza L, Rosti V, Passamonti F, Rambaldi A, Voso MT, Mecucci C, Tagliafico E, Luppi M, Vannucchi AM, Manfredini R. Increased Plasma Levels of lncRNAs LINC01268, GAS5 and MALAT1 Correlate with Negative Prognostic Factors in Myelofibrosis. Cancers (Basel) 2021; 13:cancers13194744. [PMID: 34638230 PMCID: PMC8507546 DOI: 10.3390/cancers13194744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 01/31/2023] Open
Abstract
Simple Summary Myelofibrosis (MF) displays the worst prognosis among Philadelphia-negative chronic myeloproliferative neoplasms. There is no curative therapy for MF, except for bone marrow transplantation, which however has a consistent percentage of failure. There is thus an urgent need of novel biomarkers to complement current stratification models and to enable better management of patients. To address this issue, we herein measured the plasma levels of several long noncoding RNAs (lncRNAs). Circulating lncRNAs has been already largely described as potential non-invasive biomarkers in cancers. In our study we unveiled that LINC01268, MALAT1 (both p < 0.0001) and GAS5 (p = 0.0003) plasma levels are significantly higher in MF patients if compared with healthy donors, and their increased plasma levels correlate with several detrimental features in MF. Among them, LINC01268 is an independent variable for both OS (p = 0.0297) and LFS (p = 0.0479), thus representing a putative new biomarker suitable for integrate contemporary prognostic models. Abstract Long non-coding RNAs (lncRNAs) have been recently described as key mediators in the development of hematological malignancies. In the last years, circulating lncRNAs have been proposed as a new class of non-invasive biomarkers for cancer diagnosis and prognosis and to predict treatment response. The present study is aimed to investigate the potential of circulating lncRNAs as non-invasive prognostic biomarkers in myelofibrosis (MF), the most severe among Philadelphia-negative myeloproliferative neoplasms. We detected increased levels of seven circulating lncRNAs in plasma samples of MF patients (n = 143), compared to healthy controls (n = 65). Among these, high levels of LINC01268, MALAT1 or GAS5 correlate with detrimental clinical variables, such as high count of leukocytes and CD34+ cells, severe grade of bone marrow fibrosis and presence of splenomegaly. Strikingly, high plasma levels of LINC01268 (p = 0.0018), GAS5 (p = 0.0008) or MALAT1 (p = 0.0348) are also associated with a poor overall-survival while high levels of LINC01268 correlate with a shorter leukemia-free-survival. Finally, multivariate analysis demonstrated that the plasma level of LINC01268 is an independent prognostic variable, suggesting that, if confirmed in future in an independent patients’ cohort, it could be used for further studies to design an updated classification model for MF patients.
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Affiliation(s)
- Sebastian Fantini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Sebastiano Rontauroli
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Stefano Sartini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Margherita Mirabile
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Elisa Bianchi
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Filippo Badii
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Monica Maccaferri
- Department of Laboratory Medicine and Pathology, Diagnostic Hematology and Clinical Genomics, AUSL/AOU Policlinico, 41124 Modena, Italy;
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
- Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), Neuro-Oncohematology, 00179 Rome, Italy
| | - Raffaele Palmieri
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
| | - Elena Genovese
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Chiara Carretta
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Sandra Parenti
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Selene Mallia
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Lara Tavernari
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
| | - Costanza Salvadori
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Francesca Gesullo
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Chiara Maccari
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Michela Zizza
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Alexis Grande
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Silvia Salmoiraghi
- Hematology, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (S.S.); (A.R.)
| | - Barbara Mora
- Division of Hematology, Ospedale ASST Sette Laghi, University of Insubria, 21100 Varese, Italy; (B.M.); (F.P.)
| | - Leonardo Potenza
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
| | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Foundation Policlinico San Matteo, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), 27100 Pavia, Italy;
| | - Francesco Passamonti
- Division of Hematology, Ospedale ASST Sette Laghi, University of Insubria, 21100 Varese, Italy; (B.M.); (F.P.)
| | | | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Tor Vergata, 00133 Rome, Italy; (T.O.); (R.P.); (M.T.V.)
- Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.), Neuro-Oncohematology, 00179 Rome, Italy
| | - Cristina Mecucci
- Department of Medicine and Surgery, Section of Hematology and Clinical Immunology, University of Perugia, 06129 Perugia, Italy;
| | - Enrico Tagliafico
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
- Center for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Mario Luppi
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, 41124 Modena, Italy; (L.P.); (E.T.); (M.L.)
| | - Alessandro Maria Vannucchi
- Department of Experimental and Clinical Medicine, and Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), University of Florence, Careggi University Hospital, 50134 Florence, Italy; (P.G.); (C.S.); (F.G.); (C.M.); (M.Z.); (A.M.V.)
| | - Rossella Manfredini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.F.); (S.R.); (S.S.); (M.M.); (E.B.); (F.B.); (E.G.); (C.C.); (S.P.); (S.M.); (L.T.)
- Correspondence:
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14
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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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15
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Zheng J, Guo J, Zhang H, Cao B, Xu G, Zhang Z, Tong J. Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer. Front Genet 2021; 12:672674. [PMID: 34367239 PMCID: PMC8336869 DOI: 10.3389/fgene.2021.672674] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in ovarian cancer (OC) development. However, prognosis-associated lncRNAs (PALs) for OC have not been completely elucidated. Our study aimed to identify the PAL signature of OC. A total of 663 differentially expressed lncRNAs were identified in the databases. According to the weighted gene coexpression analysis, the highly correlated genes were clustered into seven modules related to the clinical phenotype of OC. A total of 25 lncRNAs that were significantly related to overall survival were screened based on univariate Cox regression analysis. The prognostic risk model constructed contained seven PALs based on the parameter λmin, which could stratify OC patients into two risk groups. The results showed that the risk groups had different overall survival rates in both The Cancer Genome Atlas (TCGA) and two verified Gene Expression Omnibus (GEO) databases. Univariate and multivariate Cox regression analyses confirmed that the risk model was an independent risk factor for OC. Gene enrichment analysis revealed that the identified genes were involved in some pathways of malignancy. The competitive endogenous RNA (ceRNA) network included five PALs, of which four were selected for cell function assays. The four PALs were downregulated in 33 collected OC tissues and 3 OC cell lines relative to the control. They were shown to regulate the proliferative, migratory, and invasive potential of OC cells via Cell Counting Kit-8 (CCK-8) and transwell assays. Our study fills the gaps of the four PALs in OC, which are worthy of further study.
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Affiliation(s)
- Jianfeng Zheng
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
| | - Jialu Guo
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Huizhi Zhang
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Benben Cao
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Guomin Xu
- Department of Obstetrics and Gynecology, Haining Second People's Hospital, Haining, China
| | - Zhifen Zhang
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
| | - Jinyi Tong
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
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16
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Huang X, Huang L, Xie Q, Zhang L, Huang S, Hong M, Li J, Huang Z, Zhang H. LncRNAs serve as novel biomarkers for diagnosis and prognosis of childhood ALL. Biomark Res 2021; 9:45. [PMID: 34112247 PMCID: PMC8193891 DOI: 10.1186/s40364-021-00303-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 02/12/2023] Open
Abstract
Background Although some studies have demonstrated that lncRNAs are dysregulated in hematopoietic malignancies and may regulate the progression of leukemia, the detailed mechanism underlying tumorigenesis is still unclear. This study aimed to investigate lncRNAs that are differentially expressed in childhood B-cell acute lymphoblastic leukemia (B-ALL) and T-cell acute lymphoblastic leukemia (T-ALL) and their potential roles in the progression of childhood ALL. Methods Microarrays were used to detect differentially expressed lncRNAs and mRNAs. Several aberrantly expressed lncRNAs were validated by qRT-PCR. Leukemia-free survival was analyzed using the Kaplan–Meier method with a log-rank test. The co-expression correlations of lncRNAs and mRNAs were determined by Spearman’s correlation coefficient. CCK-8 assays and flow cytometry were performed to measure cell proliferation and apoptosis. Results We revealed that many lncRNAs were abnormally expressed in B-ALL and T-ALL. LncRNA/mRNA co-expression and the gene locus network showed that dysregulated lncRNAs are involved in diverse cellular processes. We also assessed the diagnostic value of the differentially expressed lncRNAs and confirmed the optimal combination of TCONS_00026679, uc002ubt.1, ENST00000411904, and ENST00000547644 with an area under the curve of 0.9686 [95 % CI: 0.9369–1.000, P < 0.001], with 90.7 % sensitivity and 92.19 % specificity, at a cut-off point of -0.5700 to distinguish childhood B-ALL patients from T-ALL patients, implying that these specific lncRNAs may have potential to detect subsets of childhood ALL. Notably, we found that the 8-year leukemia-free survival of patients with high TCONS_00026679 (p = 0.0081), ENST00000522339 (p = 0.0484), ENST00000499583 (p = 0.0381), ENST00000457217 (p = 0.0464), and ENST00000451368 (p = 0.0298) expression levels was significantly higher than that of patients with low expression levels of these lncRNAs, while patients with high uc002ubt.1 (p = 0.0499) and ENST00000547644 (p = 0.0451) expression levels exhibited markedly shorter 8-year leukemia-free survival. In addition, some lncRNAs were found to play different roles in cell proliferation and apoptosis in T-ALL and B-ALL. Conclusions Dysregulated lncRNAs involved in different regulatory mechanisms underlying the progression of childhood T-ALL and B-ALL might serve as novel biomarkers to distinguish ALL subsets and indicate poor outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-021-00303-x.
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Affiliation(s)
- Xuanmei Huang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Libin Huang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhong shan Er Lu, 510080, Guangzhou, China
| | - Qing Xie
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Ling Zhang
- Health Science Center, The University of Texas, 77030, Houston, USA
| | - Shaohui Huang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Mingye Hong
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Jiangbin Li
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Zunnan Huang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China
| | - Hua Zhang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Key Laboratory of Big Data Mining and Precision Drug Design, School of Medical Technology, Guangdong Medical University, Guangdong Medical University, 523808, Dongguan, China.
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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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18
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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: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
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Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
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20
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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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21
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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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