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Chen CY. Chromothripsis in myeloid malignancies. Ann Hematol 2024; 103:3955-3962. [PMID: 38814446 DOI: 10.1007/s00277-024-05814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Chromothripsis refers to massive genomic rearrangements developed during a catastrophic event. In total acute myeloid leukemia (AML), the incidence of chromothripsis ranges from 0 to 6.6%, in cases of complex karyotype AML, the incidence of chromothripsis ranges from 27.3 to 100%, whereas in cases of AML with TP53 mutations, the incidence ranges from 11.1 to 90%. For other types of malignancies, the incidence of chromothripsis also varies, from 0 to 10.5% in myelodysplastic syndrome to up to 61.5% in cases of myelodysplastic syndrome with TP53 mutations.Chromothripsis is typically associated with complex karyotypes and TP53 mutations, and monosomal karyotypes are associated with the condition. ERG amplifications are frequently noted in cases of chromothripsis, whereas MYC amplifications are not. Moreover, FLT3 and NPM1 mutations are negatively associated with chromothripsis. Chromothripsis typically occurs in older patients with AML with low leukocyte counts and bone marrow blast counts. Rare cases of patients with chromothripsis who received intensive induction chemotherapy revealed low response rates and poor overall prognosis. Signal pathways in chromothripsis typically involve copy number gain and upregulation of oncogene gene sets that promote cancer growth and a concomitant copy number loss and downregulation of gene sets associated with tumor suppression functions.Patients with chromothripsis showed a trend of lower complete remission rate and worse overall survival in myeloid malignancy. Large-scale studies are required to further elucidate the causes and treatments of the condition.
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Affiliation(s)
- Chien-Yuan Chen
- Department of Internal Medicine, Division of Hematology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan.
- Department of Pathology, Cytogenetic laboratory, National Taiwan University Hospital, Taipei, Taiwan.
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2
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Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024; 56:101025. [PMID: 38996538 PMCID: PMC11301242 DOI: 10.1016/j.neo.2024.101025] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
The study of extrachromosomal DNA (ecDNA), an element existing beyond classical chromosomes, contributes to creating a more comprehensive map of the cancer genome. In hematological malignancies, research on ecDNA has lacked comprehensive investigation into its frequency, structure, function, and mechanisms of formation. We re-analyzed WGS data from 208 hematological cancer samples across 11 types, focusing on ecDNA characteristics. Amplification of ecDNA was observed in 7 of these cancer types, with no instances found in normal blood cells. Patients with leukemia carrying ecDNA showed a low induction therapy remission rate (<30 %), a high relapse rate (75 %) among those who achieved complete remission, and a significantly lower survival rate compared to the general leukemia population, even those with complex chromosomal karyotypes. Among the 55 identified ecDNA amplicons, 268 genes were detected, of which 38 are known cancer-related genes exhibiting significantly increased copy numbers. By integrating RNA-Seq data, we discovered that the increased copy number, resulting in a higher amount of available DNA templates, indeed leads to the elevated expression of genes encoded on ecDNA. Additionally, through the integration of H3K4me3/H3K27ac chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin with sequencing, and high-throughput chromosome conformation capture data, we identified that ecDNA amplifications can also facilitate efficient, copy number-independent amplification of oncogenes. This process is linked to active histone modifications, improved chromatin accessibility, and enhancer hijacking, all of which are effects of ecDNA amplification. Mechanistically, chromothripsis and dysfunction of the DNA repair pathway can, to some extent, explain the origin of ecDNA.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Mingfeng Jia
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ming Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Long Zhao
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lina Wang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
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3
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Arthur NBJ, Christensen KA, Mannino K, Ruzinova MB, Kumar A, Gruszczynska A, Day RB, Erdmann-Gilmore P, Mi Y, Sprung R, York CR, Townsend RR, Spencer DH, Sykes SM, Ferraro F. Missense Mutations in Myc Box I Influence Nucleocytoplasmic Transport to Promote Leukemogenesis. Clin Cancer Res 2024; 30:3622-3639. [PMID: 38848040 PMCID: PMC11326984 DOI: 10.1158/1078-0432.ccr-24-0926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
PURPOSE Somatic missense mutations in the phosphodegron domain of the MYC gene (MYC Box I or MBI) are detected in the dominant clones of a subset of patients with acute myeloid leukemia (AML), but the mechanisms by which they contribute to AML are unknown. EXPERIMENTAL DESIGN To investigate the effects of MBI MYC mutations on hematopoietic cells, we employed a multi-omic approach to systematically compare the cellular and molecular consequences of expressing oncogenic doses of wild type, threonine-58 and proline-59 mutant MYC proteins in hematopoietic cells, and we developed a knockin mouse harboring the germline MBI mutation p.T58N in the Myc gene. RESULTS Both wild-type and MBI mutant MYC proteins promote self-renewal programs and expand highly selected subpopulations of progenitor cells in the bone marrow. Compared with their wild-type counterparts, mutant cells display decreased cell death and accelerated leukemogenesis in vivo, changes that are recapitulated in the transcriptomes of human AML-bearing MYC mutations. The mutant phenotypes feature decreased stability and translation of mRNAs encoding proapoptotic and immune-regulatory genes, increased translation of RNA binding proteins and nuclear export machinery, and distinct nucleocytoplasmic RNA profiles. MBI MYC mutant proteins also show a higher propensity to aggregate in perinuclear regions and cytoplasm. Like the overexpression model, heterozygous p.T58N knockin mice displayed similar changes in subcellular MYC localization, progenitor expansion, transcriptional signatures, and develop hematopoietic tumors. CONCLUSIONS This study uncovers that MBI MYC mutations alter RNA nucleocytoplasmic transport mechanisms to contribute to the development of hematopoietic malignancies.
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Affiliation(s)
- Nancy BJ Arthur
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Keegan A Christensen
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Kathleen Mannino
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Marianna B. Ruzinova
- Department of Pathology and Immunology, at Washington University School of Medicine, St. Louis, MO
| | - Ashutosh Kumar
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Agata Gruszczynska
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Ryan B. Day
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Petra Erdmann-Gilmore
- Department of Internal Medicine, Division of Endocrinology, Metabolism, and Lipid Research, at Washington University School of Medicine, St. Louis, MO
| | - Yiling Mi
- Department of Internal Medicine, Division of Endocrinology, Metabolism, and Lipid Research, at Washington University School of Medicine, St. Louis, MO
| | - Robert Sprung
- Department of Internal Medicine, Division of Endocrinology, Metabolism, and Lipid Research, at Washington University School of Medicine, St. Louis, MO
| | - Conner R. York
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
| | - R Reid Townsend
- Department of Internal Medicine, Division of Endocrinology, Metabolism, and Lipid Research, at Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, at Washington University School of Medicine, St. Louis, MO
| | - Stephen M. Sykes
- Department of Pediatrics, Division of Hematology-Oncology, at Washington University School of Medicine, St. Louis, MO
| | - Francesca Ferraro
- Department of Internal Medicine, Division of Oncology, at Washington University School of Medicine, St. Louis, MO
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [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: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Arthur NB, Christensen KA, Mannino K, Ruzinova MB, Kumar A, Gruszczynska A, Day RB, Erdmann-Gilmore P, Mi Y, Sprung R, York CR, Reid Townsend R, Spencer DH, Sykes SM, Ferraro F. Missense mutations in Myc Box I influence MYC cellular localization, mRNA partitioning and turnover to promote leukemogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563493. [PMID: 37961226 PMCID: PMC10634725 DOI: 10.1101/2023.10.22.563493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Somatic missense mutations in the phosphodegron domain of the MYC gene ( M YC Box I) are detected in the dominant clones of a subset of acute myeloid leukemia (AML) patients, but the mechanisms by which they contribute to AML are unknown. To unveil unique proprieties of MBI MYC mutant proteins, we systematically compared the cellular and molecular consequences of expressing similar oncogenic levels of wild type and MBI mutant MYC. We found that MBI MYC mutants can accelerate leukemia by driving unique transcriptional signatures in highly selected, myeloid progenitor subpopulations. Although these mutations increase MYC stability, they overall dampen MYC chromatin localization and lead to a cytoplasmic accumulation of the mutant proteins. This phenotype is coupled with increased translation of RNA binding proteins and nuclear export machinery, which results in altered RNA partitioning and accelerated decay of select transcripts encoding proapoptotic and proinflammatory genes. Heterozygous knockin mice harboring the germline MBI mutation Myc p.T73N exhibit cytoplasmic MYC localization, myeloid progenitors' expansion with similar transcriptional signatures to the overexpression model, and eventually develop hematological malignancies. This study uncovers that MBI MYC mutations alter MYC localization and disrupt mRNA subcellular distribution and turnover of select transcripts to accelerate tumor initiation and growth.
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Boscaro E, Urbino I, Catania FM, Arrigo G, Secreto C, Olivi M, D'Ardia S, Frairia C, Giai V, Freilone R, Ferrero D, Audisio E, Cerrano M. Modern Risk Stratification of Acute Myeloid Leukemia in 2023: Integrating Established and Emerging Prognostic Factors. Cancers (Basel) 2023; 15:3512. [PMID: 37444622 DOI: 10.3390/cancers15133512] [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: 06/06/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
An accurate estimation of AML prognosis is complex since it depends on patient-related factors, AML manifestations at diagnosis, and disease genetics. Furthermore, the depth of response, evaluated using the level of MRD, has been established as a strong prognostic factor in several AML subgroups. In recent years, this rapidly evolving field has made the prognostic evaluation of AML more challenging. Traditional prognostic factors, established in cohorts of patients treated with standard intensive chemotherapy, are becoming less accurate as new effective therapies are emerging. The widespread availability of next-generation sequencing platforms has improved our knowledge of AML biology and, consequently, the recent ELN 2022 recommendations significantly expanded the role of new gene mutations. However, the impact of rare co-mutational patterns remains to be fully disclosed, and large international consortia such as the HARMONY project will hopefully be instrumental to this aim. Moreover, accumulating evidence suggests that clonal architecture plays a significant prognostic role. The integration of clinical, cytogenetic, and molecular factors is essential, but hierarchical methods are reaching their limit. Thus, innovative approaches are being extensively explored, including those based on "knowledge banks". Indeed, more robust prognostic estimations can be obtained by matching each patient's genomic and clinical data with the ones derived from very large cohorts, but further improvements are needed.
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Affiliation(s)
- Eleonora Boscaro
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Irene Urbino
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Federica Maria Catania
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Giulia Arrigo
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Carolina Secreto
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Matteo Olivi
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Stefano D'Ardia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Chiara Frairia
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Valentina Giai
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Roberto Freilone
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Dario Ferrero
- Division of Hematology, Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Turin, Italy
| | - Ernesta Audisio
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Cerrano
- Division of Hematology, Department of Oncology, Presidio Molinette, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [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: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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9
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Camargo-Forero N, Orozco-Arias S, Perez Agudelo JM, Guyot R. HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Arch Virol 2023; 168:125. [PMID: 36988711 DOI: 10.1007/s00705-023-05747-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/03/2023] [Indexed: 03/30/2023]
Abstract
Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ2 test with p-values < 0.05.
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Affiliation(s)
- Nicolás Camargo-Forero
- School of Biology, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.
- Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia.
| | | | - Romain Guyot
- UMR DIADE, Université de Montpellier, Institut de recherche pour le développement, CIRAD, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
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10
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Tolomeo D, Traversa D, Venuto S, Ebbesen KK, García Rodríguez JL, Tamma G, Ranieri M, Simonetti G, Ghetti M, Paganelli M, Visci G, Liso A, Kok K, Muscarella LA, Fabrizio FP, Frassanito MA, Lamanuzzi A, Saltarella I, Solimando AG, Fatica A, Ianniello Z, Marsano RM, Palazzo A, Azzariti A, Longo V, Tommasi S, Galetta D, Catino A, Zito A, Mazza T, Napoli A, Martinelli G, Kjems J, Kristensen LS, Vacca A, Storlazzi CT. circPVT1 and PVT1/AKT3 show a role in cell proliferation, apoptosis, and tumor subtype-definition in small cell lung cancer. Genes Chromosomes Cancer 2022; 62:377-391. [PMID: 36562080 DOI: 10.1002/gcc.23121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Small cell lung cancer (SCLC) is treated as a homogeneous disease, although the expression of NEUROD1, ASCL1, POU2F3, and YAP1 identifies distinct molecular subtypes. The MYC oncogene, amplified in SCLC, was recently shown to act as a lineage-specific factor to associate subtypes with histological classes. Indeed, MYC-driven SCLCs show a distinct metabolic profile and drug sensitivity. To disentangle their molecular features, we focused on the co-amplified PVT1, frequently overexpressed and originating circular (circRNA) and chimeric RNAs. We analyzed hsa_circ_0001821 (circPVT1) and PVT1/AKT3 (chimPVT1) as examples of such transcripts, respectively, to unveil their tumorigenic contribution to SCLC. In detail, circPVT1 activated a pro-proliferative and anti-apoptotic program when over-expressed in lung cells, and knockdown of chimPVT1 induced a decrease in cell growth and an increase of apoptosis in SCLC in vitro. Moreover, the investigated PVT1 transcripts underlined a functional connection between MYC and YAP1/POU2F3, suggesting that they contribute to the transcriptional landscape associated with MYC amplification. In conclusion, we have uncovered a functional role of circular and chimeric PVT1 transcripts in SCLC; these entities may prove useful as novel biomarkers in MYC-amplified tumors.
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Affiliation(s)
- Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Debora Traversa
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Santina Venuto
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Karoline K Ebbesen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Grazia Tamma
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Marianna Ranieri
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Matteo Paganelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Grazia Visci
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Maria Antonia Frassanito
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Aurelia Lamanuzzi
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Ilaria Saltarella
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Antonio Palazzo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Amalia Azzariti
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Vito Longo
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Domenico Galetta
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Annamaria Catino
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Alfredo Zito
- Pathology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Alessandro Napoli
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Angelo Vacca
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
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11
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Yi E, Chamorro González R, Henssen AG, Verhaak RGW. Extrachromosomal DNA amplifications in cancer. Nat Rev Genet 2022; 23:760-771. [PMID: 35953594 PMCID: PMC9671848 DOI: 10.1038/s41576-022-00521-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/19/2022]
Abstract
Extrachromosomal DNA (ecDNA) amplification is an important driver alteration in cancer. It has been observed in most cancer types and is associated with worse patient outcome. The functional impact of ecDNA has been linked to its unique properties, such as its circular structure that is associated with altered chromatinization and epigenetic regulatory landscape, as well as its ability to randomly segregate during cell division, which fuels intercellular copy number heterogeneity. Recent investigations suggest that ecDNA is structurally more complex than previously anticipated and that it localizes to specialized nuclear bodies (hubs) and can act in trans as an enhancer for genes on other ecDNAs or chromosomes. In this Review, we synthesize what is currently known about how ecDNA is generated and how its genetic and epigenetic architecture affects proto-oncogene deregulation in cancer. We discuss how recently identified ecDNA functions may impact oncogenesis but also serve as new therapeutic vulnerabilities in cancer.
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Affiliation(s)
- Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rocío Chamorro González
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Anton G Henssen
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Neurosurgery, Amsterdam UMC, Amsterdam, the Netherlands.
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12
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Zhou M, Gao X, Zheng X, Luo J. Functions and clinical significance of circular RNAs in acute myeloid leukemia. Front Pharmacol 2022; 13:1010579. [PMID: 36506538 PMCID: PMC9729264 DOI: 10.3389/fphar.2022.1010579] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNA molecules. Four types of circRNAs have been reported in animal cells, and they have typical characteristics in their biogenesis, nuclear export and degradation. Advances in our understanding of the molecular functions of circRNAs in sponging microRNAs, modulating transcription, regulating RNA-binding proteins, as well as encoding proteins have been made very recently. Dysregulated circRNAs are associated with human diseases such as acute myeloid leukemia (AML). In this review, we focus on the recently described mechanisms, role and clinical significance of circRNAs in AML. Although great progress of circRNAs in AML has been achieved, substantial efforts are still required to explore whether circRNAs exert their biological function by other mechanisms such as regulation of gene transcription or serving as translation template in AML. It is also urgent that researchers study the machineries regulating circRNAs fate, the downstream effectors of circRNAs modulatory networks, and the clinical application of circRNAs in AML.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China,*Correspondence: Min Zhou, ; Jing Luo,
| | - Xianling Gao
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xin Zheng
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Luo
- Department of Anesthesiology, The First People’s Hospital of Yunnan Province, Kunming, China,Department of Anesthesiology, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China,*Correspondence: Min Zhou, ; Jing Luo,
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13
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Ilić M, Zaalberg IC, Raaijmakers JA, Medema RH. Life of double minutes: generation, maintenance, and elimination. Chromosoma 2022; 131:107-125. [PMID: 35487993 PMCID: PMC9470669 DOI: 10.1007/s00412-022-00773-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/20/2022]
Abstract
Advances in genome sequencing have revealed a type of extrachromosomal DNA, historically named double minutes (also referred to as ecDNA), to be common in a wide range of cancer types, but not in healthy tissues. These cancer-associated circular DNA molecules contain one or a few genes that are amplified when double minutes accumulate. Double minutes harbor oncogenes or drug resistance genes that contribute to tumor aggressiveness through copy number amplification in combination with favorable epigenetic properties. Unequal distribution of double minutes over daughter cells contributes to intratumoral heterogeneity, thereby increasing tumor adaptability. In this review, we discuss various models delineating the mechanism of generation of double minutes. Furthermore, we highlight how double minutes are maintained, how they evolve, and discuss possible mechanisms driving their elimination.
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Affiliation(s)
- Mila Ilić
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Irene C Zaalberg
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg, 100, 3584, CG Utrecht, The Netherlands
| | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - René H Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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14
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Zhu Y, Gong L, Wei CL. Guilt by association: EcDNA as a mobile transactivator in cancer. Trends Cancer 2022; 8:747-758. [PMID: 35753910 PMCID: PMC9388558 DOI: 10.1016/j.trecan.2022.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/10/2022] [Accepted: 04/28/2022] [Indexed: 10/17/2022]
Abstract
Extrachromosomal DNA (ecDNA), first described in the 1960s, is emerging as a prevalent but poorly characterized oncogenic alteration in cancer. ecDNA is a reservoir for oncogene amplification and is associated with an aggressive tumor phenotype and poor patient outcome. Despite the long-held knowledge of its existence, little is known about how ecDNA affects tumor cell behavior. Recent data reveal that ecDNA hubs are mobile transcriptional enhancers which can transactivate gene expression through chromatin interactions. Given its prevalence, structural complexity, and unequal segregation into daughter cells, ecDNA can offer selective growth advantages, contribute to intratumor heterogeneity (ITH), and accelerate tumor evolution. Future technology development is expected to transform the current paradigm for studying ecDNA and lead to therapeutic strategies targeting ecDNA vulnerabilities.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang 311121, China
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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15
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Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, Goodman MH, Moriceau G, Krijgsman O, Dharanipragada P, Ridgley T, Crosson WP, Salazar J, Pazol E, Karin G, Jayaraman R, Balanis NG, Alhani S, Sheu K, Hoeve JT, Palermo A, Motika SE, Senaratne TN, Paraiso KH, Hergenrother PJ, Rao PN, Multani AS, Peeper DS, Bafna V, Lo RS, Graeber TG. Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges. Cancer Discov 2022; 12:1046-1069. [PMID: 34930786 PMCID: PMC9192483 DOI: 10.1158/2159-8290.cd-20-0936] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/06/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022]
Abstract
Focal amplifications (FA) can mediate targeted therapy resistance in cancer. Understanding the structure and dynamics of FAs is critical for designing treatments that overcome plasticity-mediated resistance. We developed a melanoma model of dual MAPK inhibitor (MAPKi) resistance that bears BRAFV600 amplifications through either extrachromosomal DNA (ecDNA)/double minutes (DM) or intrachromosomal homogenously staining regions (HSR). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs exhibit drug addiction-driven structural loss of BRAF amplicons upon dose reduction. FA mechanisms can couple with kinase domain duplications and alternative splicing to enhance resistance. Drug-responsive amplicon plasticity is observed in the clinic and can involve other MAPK pathway genes, such as RAF1 and NRAS. BRAF FA-mediated dual MAPKi-resistant cells are more sensitive to proferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi resistance beyond cases of dedifferentiation. SIGNIFICANCE Understanding the structure and dynamics of oncogene amplifications is critical for overcoming tumor relapse. BRAF amplifications are highly plastic under MAPKi dosage challenges in melanoma, through involvement of de novo genomic alterations, even in the HSR mode. Moreover, BRAF FA-driven, dual MAPKi-resistant cells extend the spectrum of resistance-linked ferroptosis sensitivity. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Kai Song
- Department of Bioengineering, UCLA, Los Angeles, CA 90095, USA
| | - Jenna K. Minami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Arthur Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Siavash R. Dehkordi
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mark H. Goodman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Oscar Krijgsman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trevor Ridgley
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - William P. Crosson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jesus Salazar
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eli Pazol
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Gabriel Karin
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Rachana Jayaraman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nikolas G. Balanis
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Salwan Alhani
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kyle Sheu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Johanna ten Hoeve
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
| | - Amelia Palermo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
| | - Stephen E. Motika
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA
| | - T. Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kim H. Paraiso
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Paul J. Hergenrother
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA
| | - P. Nagesh Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Asha S. Multani
- Department of Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Daniel S. Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Roger S. Lo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Thomas G. Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
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16
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Traversa D, Simonetti G, Tolomeo D, Visci G, Macchia G, Ghetti M, Martinelli G, Kristensen LS, Storlazzi CT. Unravelling similarities and differences in the role of circular and linear PVT1 in cancer and human disease. Br J Cancer 2022; 126:835-850. [PMID: 34754096 PMCID: PMC8927338 DOI: 10.1038/s41416-021-01584-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
The plasmacytoma variant translocation 1 (PVT1) is a long non-coding RNA gene involved in human disease, mainly in cancer onset/progression. Although widely analysed, its biological roles need to be further clarified. Notably, functional studies on PVT1 are complicated by the occurrence of multiple transcript variants, linear and circular, which generate technical issues in the experimental procedures used to evaluate its impact on human disease. Among the many PVT1 transcripts, the linear PVT1 (lncPVT1) and the circular hsa_circ_0001821 (circPVT1) are frequently reported to perform similar pathologic and pro-tumorigenic functions when overexpressed. The stimulation of cell proliferation, invasion and drug resistance, cell metabolism regulation, and apoptosis inhibition is controlled through multiple targets, including MYC, p21, STAT3, vimentin, cadherins, the PI3K/AKT, HK2, BCL2, and CASP3. However, some of this evidence may originate from an incorrect evaluation of these transcripts as two separate molecules, as they share the lncPVT1 exon-2 sequence. We here summarise lncPVT1/circPVT1 functions by mainly focusing on shared pathways, pointing out the potential bias that may exist when the biological role of each transcript is analysed. These considerations may improve the knowledge about lncPVT1/circPVT1 and their specific targets, which deserve further studies due to their diagnostic, prognostic, and therapeutic potential.
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Affiliation(s)
- Debora Traversa
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Doron Tolomeo
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Grazia Visci
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Gemma Macchia
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Martina Ghetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
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Role and Mechanism of lncRNA-pvt1 in the Pathogenesis of Acute Lymphoblastic Leukemia in Children. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8955322. [PMID: 35281949 PMCID: PMC8916858 DOI: 10.1155/2022/8955322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 12/05/2022]
Abstract
Objective To investigate the role and mechanism of lncRNA-pvt1 in the pathogenesis of childhood acute lymphoblastic leukemia (ALL). Methods The expression of lncRNA-pvt1 in bone marrow tissues of ALL patients after initial diagnosis and complete remission was detected by RT-PCR to explore its possible involvement in the pathogenesis of ALL. The proliferation and apoptosis of Jurkat cells transfected with lncRNA-pvt1 were observed by MTT and flow cytometry. Results lncRNA-pvt1 expression was upregulated in bone marrow of ALL patients. Knockdown of lncRNA-pvt1 inhibited Jurkat cell proliferation and increased its apoptosis rate. Conclusion Silencing lncRNA-pvt1 expression can inhibit the development of ALL.
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18
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Halprin C, Kitahara S, Vail E, Eno CC. Detecting the "Undetectable" Alterations: Use of NGS to uncover high-risk alterations. Cancer Genet 2022; 264-265:5-7. [DOI: 10.1016/j.cancergen.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022]
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Li P, Qiao G, Lu J, Ji W, Gao C, Qi F. PVT1 is a prognostic marker associated with immune invasion of bladder urothelial carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:169-190. [PMID: 34902986 DOI: 10.3934/mbe.2022009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plasmacytoma variant translocation 1 (PVT1) is involved in multiple signaling pathways and plays an important regulatory role in a variety of malignant tumors. However, its role in the prognosis and immune invasion of bladder urothelial carcinoma (BLCA) remains unclear. This study investigated the expression of PVT1 in tumor tissue and its relationship with immune invasion, and determined its prognostic role in patients with BLCA. Patients were identified from the cancer genome atlas (TCGA). The enrichment pathway and function of PVT1 were explained by gene ontology (GO) term analysis, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA), and the degree of immune cell infiltration was quantified. Kaplan-Meier analysis and Cox regression were used to analyze the correlation between PVT1 and survival rate. PVT1-high BLCA patients had a lower 10-year disease-specific survival (DSS P < 0.05) and overall survival (OS P < 0.05). Multivariate Cox regression analysis showed that PVT1 (high vs. low) (P = 0.004) was an independent prognostic factor. A nomogram was used to predict the effect of PVT1 on the prognosis. PVT1 plays an important role in the progression and prognosis of BLCA and can be used as a medium biomarker to predict survival after cystectomy.
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Affiliation(s)
- Peiyuan Li
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Gangjie Qiao
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Jian Lu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei 230022, China
| | - Wenbin Ji
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Chao Gao
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
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20
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Chen T, Chen F. The role of circular RNA plasmacytoma variant translocation 1 as a biomarker for prognostication of acute myeloid leukemia. Hematology 2021; 26:1018-1024. [PMID: 34871521 DOI: 10.1080/16078454.2021.1987649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Circular RNA plasmacytoma variant translocation 1 (circ-PVT1) has been reported to be an oncogene and serves as a prognostic biomarker in several solid cancers and hematological malignancies. However, no study has been performed on the tumorigenesis role of circ-PVT1 in acute myeloid leukemia (AML). Thus, this study aimed to evaluate the correlation of circ-PVT1 with disease risk, clinical characteristics, cytogenetics/molecular genetics, and prognosis of AML. METHODS A total of 68 de novo AML patients, 30 disease controls and 30 health donors were enrolled in this study. Circ-PVT1 expression in bone marrow (BM) was determined. Complete remission (CR) status after induction therapy, event-free survival (EFS) and overall survival (OS) were evaluated in AML patients. RESULTS Circ-PVT1 expression was different among AML patients, disease controls and health donors, which was highest in AML patients, followed by disease controls and lowest in health donors. Meanwhile, circ-PVT1 could distinguish AML patients from health donors and disease controls by receiver operating characteristic curve analysis. Furthermore, circ-PVT1 was correlated with BM blasts and FLT3-ITD mutation, but not other clinical features, such as French-American-Britain subtypes in AML patients. Moreover, circ-PVT1 expression was lower in AML patients with CR compared with those without CR. Besides, high circ-PVT1 expression was correlated with shorter EFS and OS in AML patients. After adjustment by multivariate Cox's regression analysis, higher circ-PVT1 expression was an independent factor in predicting shorter EFS and OS for AML patients. CONCLUSION Circ-PVT1 potentially serves as a biomarker for evaluating the prognosis of AML patients.
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Affiliation(s)
- Tao Chen
- Department of Hematology, Baoji Central Hospital, Baoji, Shaanxi Province, China
| | - Fengyun Chen
- Department of Hematology, Baoji Central Hospital, Baoji, Shaanxi Province, China
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21
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Rosswog C, Bartenhagen C, Welte A, Kahlert Y, Hemstedt N, Lorenz W, Cartolano M, Ackermann S, Perner S, Vogel W, Altmüller J, Nürnberg P, Hertwig F, Göhring G, Lilienweiss E, Stütz AM, Korbel JO, Thomas RK, Peifer M, Fischer M. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer. Nat Genet 2021; 53:1673-1685. [PMID: 34782764 DOI: 10.1038/s41588-021-00951-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/10/2021] [Indexed: 12/24/2022]
Abstract
The mechanisms behind the evolution of complex genomic amplifications in cancer have remained largely unclear. Using whole-genome sequencing data of the pediatric tumor neuroblastoma, we here identified a type of amplification, termed 'seismic amplification', that is characterized by multiple rearrangements and discontinuous copy number levels. Overall, seismic amplifications occurred in 9.9% (274 of 2,756) of cases across 38 cancer types, and were associated with massively increased copy numbers and elevated oncogene expression. Reconstruction of the development of seismic amplification showed a stepwise evolution, starting with a chromothripsis event, followed by formation of circular extrachromosomal DNA that subsequently underwent repetitive rounds of circular recombination. The resulting amplicons persisted as extrachromosomal DNA circles or had reintegrated into the genome in overt tumors. Together, our data indicate that the sequential occurrence of chromothripsis and circular recombination drives oncogene amplification and overexpression in a substantial fraction of human malignancies.
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Affiliation(s)
- Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Else Kröner Forschungskolleg Clonal Evolution in Cancer, University Hospital Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Nadine Hemstedt
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Witali Lorenz
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Pathology Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Wenzel Vogel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Pathology Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Esther Lilienweiss
- Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Adrian M Stütz
- European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
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22
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Issah MA, Wu D, Zhang F, Zheng W, Liu Y, Fu H, Zhou H, Chen R, Shen J. Epigenetic modifications in acute myeloid leukemia: The emerging role of circular RNAs (Review). Int J Oncol 2021; 59:107. [PMID: 34792180 PMCID: PMC8651224 DOI: 10.3892/ijo.2021.5287] [Citation(s) in RCA: 3] [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: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 11/06/2022] Open
Abstract
Canonical epigenetic modifications, which include histone modification, chromatin remodeling and DNA methylation, play key roles in numerous cellular processes. Epigenetics underlies how cells that posses DNA with similar sequences develop into different cell types with different functions in an organism. Earlier epigenetic research has primarily been focused at the chromatin level. However, the number of studies on epigenetic modifications of RNA, such as N1‑methyladenosine, 2'‑O‑ribosemethylation, inosine, 5‑methylcytidine, N6‑methyladenosine (m6A) and pseudouridine, has seen an increase. Circular RNAs (circRNAs), a type of RNA species that lacks a 5' cap or 3' poly(A) tail, are abundantly expressed in acute myeloid leukemia (AML) and may regulate disease progression. circRNAs possess various functions, including microRNA sponging, gene transcription regulation and RNA‑binding protein interaction. Furthermore, circRNAs are m6A methylated in other types of cancer, such as colorectal and hypopharyngeal squamous cell cancers. Therefore, the critical roles of circRNA epigenetic modifications, particularly m6A, and their possible involvement in AML are discussed in the present review. Epigenetic modification of circRNAs may become a diagnostic and therapeutic target for AML in the future.
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Affiliation(s)
- Mohammed Awal Issah
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dansen Wu
- Medical Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Feng Zhang
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Weili Zheng
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanquan Liu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Haiying Fu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Huarong Zhou
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Rong Chen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jianzhen Shen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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23
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Zhou H, Liu W, Zhou Y, Hong Z, Ni J, Zhang X, Li Z, Li M, He W, Zhang D, Chen X, Zhu J. Therapeutic inhibition of GAS6-AS1/YBX1/MYC axis suppresses cell propagation and disease progression of acute myeloid leukemia. J Exp Clin Cancer Res 2021; 40:353. [PMID: 34753494 PMCID: PMC8576903 DOI: 10.1186/s13046-021-02145-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common type of leukemia in adults. Its therapy has not significantly improved during the past four decades despite intense research efforts. New molecularly targeted therapies are in great need. The proto-oncogene c-Myc (MYC) is an attractive target due to its transactivation role in multiple signaling cascades. Deregulation of the MYC is considered one of a series of oncogenic events required for tumorigenesis. However, limited knowledge is available on which mechanism underlie MYC dysregulation and how long non-coding RNAs (lncRNAs) are involved in MYC dysregulation in AML. METHODS AML microarray chips and public datasets were screened to identify novel lncRNA GAS6-AS1 was dysregulated in AML. Gain or loss of functional leukemia cell models were produced, and in vitro and in vivo experiments were applied to demonstrate its leukemogenic phenotypes. Interactive network analyses were performed to define intrinsic mechanism. RESULTS We identified GAS6-AS1 was overexpressed in AML, and its aberrant function lead to more aggressive leukemia phenotypes and poorer survival outcomes. We revealed that GAS6-AS1 directly binds Y-box binding protein 1 (YBX1) to facilitate its interaction with MYC, leading to MYC transactivation and upregulation of IL1R1, RAB27B and other MYC target genes associated with leukemia progression. Further, lentiviral-based GAS6-AS1 silencing inhibited leukemia progression in vivo. CONCLUSIONS Our findings revealed a previously unappreciated role of GAS6-AS1 as an oncogenic lncRNA in AML progression and prognostic prediction. Importantly, we demonstrated that therapeutic targeting of the GAS6-AS1/YBX1/MYC axis inhibits AML cellular propagation and disease progression. Our insight in lncRNA associated MYC-driven leukemogenesis may contribute to develop new anti-leukemia treatment strategies.
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Affiliation(s)
- Hao Zhou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Liu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yongming Zhou
- Department of Hematology, The Affiliated Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, 430064, China
| | - Zhenya Hong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jian Ni
- Department of Oncology Clinical Pharmacy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaoping Zhang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ziping Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenjuan He
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xuexing Chen
- Department of Hematology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441000, China.
| | - Jianhua Zhu
- Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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24
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Singh VK, Thakral D, Gupta R. Regulatory noncoding RNAs: potential biomarkers and therapeutic targets in acute myeloid leukemia. AMERICAN JOURNAL OF BLOOD RESEARCH 2021; 11:504-519. [PMID: 34824883 PMCID: PMC8610797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
The noncoding RNAs (ncRNA) comprise a substantial segment of the human transcriptome and have emerged as key elements of cellular homeostasis and disease pathogenesis. Dysregulation of these ncRNAs by alterations in the primary RNA motifs and/or aberrant expression levels is relevant in various diseases, especially cancer. The recent research advances indicate that ncRNAs regulate vital oncogenic processes, including hematopoietic cell differentiation, proliferation, apoptosis, migration, and angiogenesis. The ever-expanding role of ncRNAs in cancer progression and metastasis has sparked interest as potential diagnostic and prognostic biomarkers in acute myeloid leukemia. Moreover, advances in antisense oligonucleotide technologies and pharmacologic discoveries of small molecule inhibitors in targeting RNA structures and RNA-protein complexes have opened newer avenues that may help develop the next generation anti-cancer therapeutics. In this review, we have discussed the role of ncRNA in acute myeloid leukemia and their utility as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Vivek Kumar Singh
- Laboratory Oncology, Dr B.R.A, IRCH, All India Institute of Medical Sciences New Delhi 110029, India
| | - Deepshi Thakral
- Laboratory Oncology, Dr B.R.A, IRCH, All India Institute of Medical Sciences New Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology, Dr B.R.A, IRCH, All India Institute of Medical Sciences New Delhi 110029, India
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25
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Lin G, Fei Y, Zhang Y. Hsa-circ_0003420 induces apoptosis in acute myeloid leukemia stem cells and impairs stem cell properties. Immunopharmacol Immunotoxicol 2021; 43:622-631. [PMID: 34477035 DOI: 10.1080/08923973.2021.1963272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To explore the effect of circular RNA-0003420 (circ_0003420) in acute myeloid leukemia (AML) relapse and leukemia stem cells (LSCs) properties. MATERIALS AND METHODS TRIzol reagent was used to extract total RNA from AML tissues or cells. Cell viability was assessed by Cell Counting Kit-8 and EdU staining assays. Cell apoptosis was determined by flow cytometry. RESULTS Compared with normal hematopoietic stem cells, circular RNA hsa-circ_0003420 expression was considerably decreased in non-m3 AML stem cells. Furthermore, the lack of hsa-circ_0003420 is correlated with poor clinical results and impaired therapeutic effects in AML. Overexpression of hsa-circ_0003420 via transfection caused LSC death and inhibited the characteristics of leukemia tumor stem cells, including expression of Homeobox B4 (HOXB4), MYB, and aldehyde dehydrogenase 1 family member A1 (ALDH1A1) axis. Furthermore, hsa-circ_0003420 targets the mRNA of insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and hsa-circ_0003420 expression markedly repressed IGF2BP1 levels in LSCs. Restoration of IGF2BP1 eliminated the effect of hsa-circ_0003420 on the replication, apoptosis, and LSC phenotype of KG-1a cells. DISCUSSION AND CONCLUSIONS Up-regulation of hsa-circ_0003420 expression in LSCs caused redox disorder, inflammation and apoptosis, suggesting that this protein could be used as a target for the treatment AML.
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Affiliation(s)
- Guoqiang Lin
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, China
| | - Yingying Fei
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, China
| | - Yanming Zhang
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, China
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26
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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27
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Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K, Rubtsov N. New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis. Cells 2021; 10:cells10071819. [PMID: 34359988 PMCID: PMC8305704 DOI: 10.3390/cells10071819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.
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Affiliation(s)
- Tatyana Karamysheva
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1332)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
| | | | - Marija Rajičić
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Alexey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Jelena Blagojević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Mladen Vujošević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Konstantin Orishchenko
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay Rubtsov
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
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28
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Jia Y, Gu W. Up-regulation of circPVT1 in T cell acute lymphoblastic leukemia promoted cell proliferation via miR-30e/DLL4 induced activating NOTCH signaling. Pathol Res Pract 2021; 224:153536. [PMID: 34237615 DOI: 10.1016/j.prp.2021.153536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022]
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic cancer with dismal prognosis. Recent studies disclosed that circPVT1 played an oncogene role in various cancers. But its role in T-ALL is still unclear. In this study, we found the expression levels of circPVT1 in bone marrows and cell lines of T-ALL were significantly up regulated and knock-down of circPVT1 in T-ALL cell lines could inhibit the cell proliferation and increase the cell apoptosis. Further analysis showed that circPVT1 could bind directly to miR-30e and contributed to the activate the Notch signaling by regulating miR-30e/DLL4 pathway. The levels of circPVT1 were obviously related to cumulative relapse rate and 5-year survival rate. In conclusion, our study reveals that circPVT1 participates in the progression of T-ALL through the miR-30e/DLL4 pathway and might represent a potential therapeutic target for T-ALL treatment.
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Affiliation(s)
- Yongqing Jia
- Departrment of Hematology, The Third Affiliated Hospital of Soochow University, Changzhou, China; Departrment of Hematology, Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Weiying Gu
- Departrment of Hematology, The Third Affiliated Hospital of Soochow University, Changzhou, China.
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29
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Papuc SM, Erbescu A, Cisleanu D, Ozunu D, Enache C, Dumitru I, Lupoaia Andrus E, Gaman M, Popov VM, Dobre M, Stanca O, Angelescu S, Berbec N, Colita A, Vladareanu AM, Bumbea H, Arghir A. Delineation of Molecular Lesions in Acute Myeloid Leukemia Patients at Diagnosis: Integrated Next Generation Sequencing and Cytogenomic Studies. Genes (Basel) 2021; 12:genes12060846. [PMID: 34070898 PMCID: PMC8229708 DOI: 10.3390/genes12060846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disorder characterized by a wide range of genetic defects. Cytogenetics, molecular and genomic technologies have proved to be helpful for deciphering the mutational landscape of AML and impacted clinical practice. Forty-eight new AML patients were investigated with an integrated approach, including classical and molecular cytogenetics, array-based comparative genomic hybridization and targeted next generation sequencing (NGS). Various genetic defects were identified in all the patients using our strategy. Targeted NGS revealed known pathogenic mutations as well as rare or unreported variants with deleterious predictions. The mutational screening of the normal karyotype (NK) group identified clinically relevant variants in 86.2% of the patients; in the abnormal cytogenetics group, the mutation detection rate was 87.5%. Overall, the highest mutation prevalence was observed for the NPM1 gene, followed by DNMT3A, FLT3 and NRAS. An unexpected co-occurrence of KMT2A translocation and DNMT3A-R882 was identified; alterations of these genes, which are involved in epigenetic regulation, are considered to be mutually exclusive. A microarray analysis detected CNVs in 25% of the NK AML patients. In patients with complex karyotypes, the microarray analysis made a significant contribution toward the accurate characterization of chromosomal defects. In summary, our results show that the integration of multiple investigative strategies increases the detection yield of genetic defects with potential clinical relevance.
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Affiliation(s)
- Sorina Mihaela Papuc
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Alina Erbescu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Diana Cisleanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Diana Ozunu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Cristina Enache
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Ion Dumitru
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Elena Lupoaia Andrus
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Mihaela Gaman
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | | | - Maria Dobre
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Oana Stanca
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Silvana Angelescu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Nicoleta Berbec
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Andrei Colita
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Ana-Maria Vladareanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Horia Bumbea
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
- Correspondence: ; Tel.: +40-2-1319-2732-207; Fax: +40-2-1319-4528
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de Oliveira Lisboa M, Brofman PRS, Schmid-Braz AT, Rangel-Pozzo A, Mai S. Chromosomal Instability in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13112655. [PMID: 34071283 PMCID: PMC8198625 DOI: 10.3390/cancers13112655] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Chromosomal instability (CIN), the increasing rate in which cells acquire new chromosomal alterations, is one of the hallmarks of cancer. Many studies highlighted CIN as an important mechanism in the origin, progression, and relapse of acute myeloid leukemia (AML). The ambivalent feature of CIN as a cancer-promoting or cancer-suppressing mechanism might explain the prognostic variability. The latter, however, is described in very few studies. This review highlights the important CIN mechanisms in AML, showing that CIN signatures can occur largely in all the three major AML types (de novo AML, secondary-AML, and therapy-related-AML). CIN features in AML could also be age-related and reflect the heterogeneity of the disease. Although most of these abnormalities show an adverse prognostic value, they also offer a strong new perspective on personalized therapy approaches, which goes beyond assessing CIN in vitro in patient tumor samples to predict prognosis. Current and emerging AML therapies are exploring CIN to improve AML treatment, which includes blocking CIN or increasing CIN beyond the limit threshold to induce cell death. We argue that the characterization of CIN features, not included yet in the routine diagnostic of AML patients, might provide a better stratification of patients and be extended to a more personalized therapeutic approach.
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Affiliation(s)
- Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Paulo Roberto Slud Brofman
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Ana Teresa Schmid-Braz
- Hospital das Clínicas, Universidade Federal do Paraná, Curitiba 80060-240, Paraná, Brazil;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
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31
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Xiao Q, Fu Y, Yang Y, Dai J, Luo J. NSL2CD: identifying potential circRNA-disease associations based on network embedding and subspace learning. Brief Bioinform 2021; 22:6265177. [PMID: 33954582 DOI: 10.1093/bib/bbab177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/29/2021] [Accepted: 04/14/2021] [Indexed: 12/28/2022] Open
Abstract
Many studies have evidenced that circular RNAs (circRNAs) are important regulators in various pathological processes and play vital roles in many human diseases, which could serve as promising biomarkers for disease diagnosis, treatment and prognosis. However, the functions of most of circRNAs remain to be unraveled, and it is time-consuming and costly to uncover those relationships between circRNAs and diseases by conventional experimental methods. Thus, identifying candidate circRNAs for human diseases offers new opportunities to understand the functional properties of circRNAs and the pathogenesis of diseases. In this study, we propose a novel network embedding-based adaptive subspace learning method (NSL2CD) for predicting potential circRNA-disease associations and discovering those disease-related circRNA candidates. The proposed method first calculates disease similarities and circRNA similarities by fully utilizing different data sources and learns low-dimensional node representations with network embedding methods. Then, we adopt an adaptive subspace learning model to discover potential associations between circRNAs and diseases. Meanwhile, an integrated weighted graph regularization term is imposed to preserve local geometric structures of data spaces, and L1,2-norm constraint is also incorporated into the model to realize the smoothness and sparsity of projection matrices. The experiment results show that NSL2CD achieves comparable performance under different evaluation metrics, and case studies further confirm its ability to discover potential candidate circRNAs for human diseases.
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Affiliation(s)
- Qiu Xiao
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, China
| | - Yu Fu
- Hunan Normal University, China
| | - Yide Yang
- School of Medicine, Hunan Normal University, China
| | - Jianhua Dai
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, China
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32
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Wang N, Yuan L, Jing Y, Fan K, Jin H, Lv C, Wang L, Yu L. Double minute chromosomes in acute myeloid leukemia and myelodysplastic syndromes are associated with complex karyotype, monosomal karyotype, TP53 deletion, and TP53 mutations. Leuk Lymphoma 2021; 62:2466-2474. [PMID: 33904352 DOI: 10.1080/10428194.2021.1919663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Double minute chromosomes (DMs) are rare in hematologic malignancies. We presented the cytogenetic characteristics and clinical features of the largest single-center cohort of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) patients with DMs. A total of 2576 AML patients and 1642 MDS patients were investigated, and 30 patients (AML = 19; MDS = 11) who had DMs were followed up. DMs were more common in primary AML (94.7%) and MDS (90.9%). Monosomal karyotypes (MK) were also the main cytogenetic characteristics, like complex karyotypes (CK). AML with myelodysplasia-related changes (AML-MRC) and MDS-refractory anemia with excess blasts (MDS-RAEB) was common in this cohort. We conclude that DMs-positive AML and DMs-positive MDS are associated with older age, complex karyotypes, monosomal karyotypes, TP53 deletion and TP53 mutations. DMs are a type of chromothripsis, which can be observed by the karyotype analysis. MYC and KMT2A were the most commonly amplified genes in DMs. Most patients with DMs presented an extremely poor prognosis.
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Affiliation(s)
- Nan Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Lijun Yuan
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Keke Fan
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Hongshi Jin
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Chao Lv
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.,Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
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33
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Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. Int J Biol Sci 2021; 17:1010-1025. [PMID: 33867825 PMCID: PMC8040306 DOI: 10.7150/ijbs.54614] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of cellular DNAs in eukaryotes are organized into linear chromosomes. In addition to chromosome DNAs, genes also reside on extrachromosomal elements. The extrachromosomal DNAs are commonly found to be circular, and they are referred to as extrachromosomal circular DNAs (eccDNAs). Recent technological advances have enriched our knowledge of eccDNA biology. There is currently increasing concern about the connection between eccDNA and cancer. Gene amplification on eccDNAs is prevalent in cancer. Moreover, eccDNAs commonly harbor oncogenes or drug resistance genes, hence providing a growth or survival advantage to cancer cells. eccDNAs play an important role in tumor heterogeneity and evolution, facilitating tumor adaptation to challenging circumstances. In addition, eccDNAs have recently been identified as cell-free DNAs in circulating system. The altered level of eccDNAs is observed in cancer patients relative to healthy controls. Particularly, eccDNAs are associated with cancer progression and poor outcomes. Thus, eccDNAs could be useful as novel biomarkers for the diagnosis and prognosis of cancer. In this review, we summarize current knowledge regarding the formation, characteristics and biological importance of eccDNAs, with a focus on the molecular mechanisms associated with their roles in cancer progression. We also discuss their potential applications in the detection and treatment of cancer. A better understanding of the functional role of eccDNAs in cancer would facilitate the comprehensive analysis of molecular mechanisms involved in cancer pathogenesis.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xinzhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Fei Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Han Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
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Tolomeo D, Agostini A, Visci G, Traversa D, Storlazzi CT. PVT1: A long non-coding RNA recurrently involved in neoplasia-associated fusion transcripts. Gene 2021; 779:145497. [PMID: 33600954 DOI: 10.1016/j.gene.2021.145497] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]
Abstract
NGS technologies and bioinformatics tools allow the rapid identification of chimeric transcripts in cancer. More than 40,000 fusions are so far reported in the literature; however, for most of them, the role in oncogenesis is still not fully understood. This is the case for fusions involving the long non-coding RNA (lncRNA) Plasmacytoma variant translocation 1 (PVT1) (8q24.21). This lncRNA displays oncogenic functions in several cancer types interacting with microRNAs and proteins, but the role of PVT1 fusion transcripts is more obscure. These chimeras have been identified in both hematological malignancies and solid tumors, mainly arising from rearrangements and/or amplification of the 8q24 chromosomal region. In this review, we detail the full spectrum of PVT1 fusions in cancer, summarizing current knowledge about their genesis, function, and role as biomarkers.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Antonio Agostini
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Grazia Visci
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
| | - Debora Traversa
- Department of Biology, University of Bari, Via Orabona no.4, 70125 Bari, Italy.
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Wilson C, Kanhere A. 8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer. Int J Mol Sci 2021; 22:1094. [PMID: 33499210 PMCID: PMC7865353 DOI: 10.3390/ijms22031094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation. While the clinical importance of the majority of lncRNAs have yet to be identified, it is puzzling that a large number of disease-associated genetic variations are seen in lncRNA genes. The 8q24.21 locus is rich in lncRNAs and very few protein-coding genes are located in this region. Interestingly, the 8q24.21 region is also a hot spot for genetic variants associated with an increased risk of cancer. Research focusing on the lncRNAs in this area of the genome has indicated clinical relevance of lncRNAs in different cancers. In this review, we summarise the lncRNAs in the 8q24.21 region with respect to their role in cancer and discuss the potential impact of cancer-associated genetic polymorphisms on the function of lncRNAs in initiation and progression of cancer.
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Affiliation(s)
| | - Aditi Kanhere
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
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汪 雨, 叶 凡, 张 霄, 邹 睿, 王 明, 俞 锴, 崔 诗. [Amplification of Extrachromosomal Oncogene and Tumorigenesis and Development]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:1101-1107. [PMID: 33357318 PMCID: PMC7786228 DOI: 10.3779/j.issn.1009-3419.2020.101.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 11/05/2022]
Abstract
Extrachromosomal DNA (ecDNA) is a small segment of circular DNA located outside the chromosome, which has the function of self-replication. Recently, amplification of oncogenes on ecDNA has been proved to be a common phenomenon in tumor cells, and has some characteristics worth studying, such as correlation with patients' poor prognosis. Multiple chromosomal events are involved in the formation of ecDNA, and its amplification can directly increase the number of DNA copies of extra-chromosomal oncogenes and accelerate the generation and development of tumors. Moreover, the segregation pattern of unequal transmission of parental ecDNA cells to offspring not only increases tumor heterogeneity, but also enhances tumor adaptation to environment and response to therapy. This article reviews the current status and potential significance of ecDNA in tumor cells.
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Affiliation(s)
- 雨彤 汪
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 凡 叶
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 霄 张
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 睿涵 邹
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 明远 王
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 锴 俞
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 诗允 崔
- 210029 南京,南京医科大学第一附属医院肿瘤科Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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37
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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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Xiao Q, Zhong J, Tang X, Luo J. iCDA-CMG: identifying circRNA-disease associations by federating multi-similarity fusion and collective matrix completion. Mol Genet Genomics 2020; 296:223-233. [PMID: 33159254 DOI: 10.1007/s00438-020-01741-2] [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: 06/11/2020] [Accepted: 10/23/2020] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are a special class of non-coding RNAs with covalently closed-loop structures. Studies prove that circRNAs perform critical roles in various biological processes, and the aberrant expression of circRNAs is closely related to tumorigenesis. Therefore, identifying potential circRNA-disease associations is beneficial to understand the pathogenesis of complex diseases at the circRNA level and helps biomedical researchers and practitioners to discover diagnostic biomarkers accurately. However, it is tremendously laborious and time-consuming to discover disease-related circRNAs with conventional biological experiments. In this study, we develop an integrative framework, called iCDA-CMG, to predict potential associations between circRNAs and diseases. By incorporating multi-source prior knowledge, including known circRNA-disease associations, disease similarities and circRNA similarities, we adopt a collective matrix completion-based graph learning model to prioritize the most promising disease-related circRNAs for guiding laborious clinical trials. The results show that iCDA-CMG outperforms other state-of-the-art models in terms of cross-validation and independent prediction. Moreover, the case studies for several representative cancers suggest the effectiveness of iCDA-CMG in screening circRNA candidates for human diseases, which will contribute to elucidating the pathogenesis mechanisms and unveiling new opportunities for disease diagnosis and targeted therapy.
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Affiliation(s)
- Qiu Xiao
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, College of Information Science and Engineering, Hunan Normal University, Changsha, 410081, China.,Hunan Xiangjiang Artificial Intelligence Academy, Changsha, 410000, China
| | - Jiancheng Zhong
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, College of Information Science and Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Xiwei Tang
- School of Information Science and Engineering, Hunan First Normal University, Changsha, 410205, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
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39
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CircRNAs and Fusion-circRNAs in cancer: New players in an old game. Cell Signal 2020; 75:109747. [DOI: 10.1016/j.cellsig.2020.109747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
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40
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Zhou X, Zhan L, Huang K, Wang X. The functions and clinical significance of circRNAs in hematological malignancies. J Hematol Oncol 2020; 13:138. [PMID: 33069241 PMCID: PMC7568356 DOI: 10.1186/s13045-020-00976-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
With covalently closed circular structures, circular RNAs (circRNAs) were once misinterpreted as by-products of mRNA splicing. Being abundant, stable, highly conserved, and tissue-specific, circRNAs are recently identified as a type of regulatory RNAs. CircRNAs bind to certain miRNAs or proteins to participate in gene transcription and translation. Emerging evidence has indicated that the dysregulation of circRNAs is closely linked to the tumorigenesis and treatment response of hematological malignancies. CircRNAs play critical roles in various biological processes, including tumorigenesis, drug resistance, tumor metabolism, autophagy, pyroptosis, and ferroptosis. The N6-methyladenosine modification of circRNAs and discovery of fusion-circRNAs provide novel insights into the functions of circRNAs. Targeting circRNAs in hematological malignancies will be an attractive treatment strategy. In this review, we systematically summarize recent advances toward the novel functions and molecular mechanisms of circRNAs in hematological malignancies, and highlight the potential clinical applications of circRNAs as novel biomarkers and therapeutic targets for future exploration.
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Affiliation(s)
- Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China. .,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China. .,School of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, People's Republic of China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, People's Republic of China. .,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 251006, People's Republic of China.
| | - Linquan Zhan
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China
| | - Kai Huang
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China. .,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China. .,School of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, People's Republic of China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, People's Republic of China. .,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 251006, People's Republic of China.
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41
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Yan Y, Guo G, Huang J, Gao M, Zhu Q, Zeng S, Gong Z, Xu Z. Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance. J Hematol Oncol 2020; 13:124. [PMID: 32928268 PMCID: PMC7491193 DOI: 10.1186/s13045-020-00960-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/03/2020] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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42
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Fu L, Tang D, Sun A, Zhu D, Zhang G, Wang Y. Recent progress in study of circRNAs and its role in leukemia. J Leukoc Biol 2020; 109:731-739. [PMID: 32911578 DOI: 10.1002/jlb.2ru0619-213r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/13/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of newly identified noncoding RNA and are considered as a new feature of eukaryotic gene expression. Hundreds of thousands of endogenous circRNAs have been found in mammalian cells, which we knew little before. CircRNAs are covalently closed, circular RNA molecules that typically comprise exonic sequences and are spliced at canonical splice sites. Researchers with RNA-Seq technology have identified that the expression of circRNAs is developmentally regulated, tissue- and cell-type specific. Like long noncoding RNAs (lncRNAs), circRNAs are becoming a new research hotspot in the RNA field, and aberrant expression of circRNAs could contribute to carcinogenesis. Recent studies have demonstrated that circRNAs play important roles in the development, maintenance, and progression of leukemia. Herein, we describe the biologic characteristics and functions of circRNAs, with a focus on circRNAs that play essential roles in leukemia.
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Affiliation(s)
- Lei Fu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Doudou Tang
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Hunan Centre for Evidence-Based Medicine, Central South University, Changsha, Hunan, China
| | - Ailian Sun
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dengqin Zhu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guangsen Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yewei Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
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43
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Xiao Q, Yu H, Zhong J, Liang C, Li G, Ding P, Luo J. An in-silico method with graph-based multi-label learning for large-scale prediction of circRNA-disease associations. Genomics 2020; 112:3407-3415. [DOI: 10.1016/j.ygeno.2020.06.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/03/2023]
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44
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Wu Z, Sun H, Li J, Jin H. Circular RNAs in leukemia. Aging (Albany NY) 2020; 11:4757-4771. [PMID: 31306100 PMCID: PMC6660040 DOI: 10.18632/aging.102091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022]
Abstract
In pace with the development of gene sequencing technology and transcriptome research, it has been found that 70 to 90% of the human genome is transcribed into RNAs, while only 2% of RNAs encode proteins. This implies that non-coding RNAs (ncRNAs) may exert vital biological functions and a full analysis of non-coding transcriptomes is needed. Over the past decade, the advance in high-throughput sequencing and transcriptome profiling has enabled the identification of circular RNAs (circRNAs) involved in many biological processes and the occurrence and development of diseases. Accumulating evidence has revealed that circRNAs may serve as new biomarkers for diagnosis as well as provide promising therapeutic approaches and novel drug screening strategies for leukemia. A comprehensive understanding of circRNAs in leukemia is a prerequisite for the development of clinical translational research. In this review, we will discuss the general information of circRNAs and focus on the current advances in understanding the association between dysregulated circRNAs and leukemia.
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Affiliation(s)
- Zijuan Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
| | - Handong Sun
- The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
| | - Hui Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
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45
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Montoro MJ, Rivero E, Teixidó M, Rodriguez Y, Chávez C, Salamero O, Navarrete M, Talavera E, Ortega M, Valcárcel D. Micronuclei, dmin chromosomes and MYC amplifications as a singular presentation of myeloid malignancies. Br J Haematol 2020; 191:e19-e22. [PMID: 32627175 DOI: 10.1111/bjh.16942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/12/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Julia Montoro
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Eugenia Rivero
- Department of Hematology, Arnau de Vilanova University Hospital, Lleida, Spain
| | - Montserrat Teixidó
- Department of Hematology, Arnau de Vilanova University Hospital, Lleida, Spain
| | - Yva Rodriguez
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carlos Chávez
- Department of Hematology, Arnau de Vilanova University Hospital, Lleida, Spain
| | - Olga Salamero
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mayda Navarrete
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Elisabet Talavera
- Department of Hematology, Arnau de Vilanova University Hospital, Lleida, Spain
| | - Margarita Ortega
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - David Valcárcel
- Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Experimental Hematology Unit, Valld'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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46
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Benetatos L, Benetatou A, Vartholomatos G. Long non-coding RNAs and MYC association in hematological malignancies. Ann Hematol 2020; 99:2231-2242. [PMID: 32621182 DOI: 10.1007/s00277-020-04166-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) have an established role in cell biology. Among their functions is the regulation of hematopoiesis. They characterize the different stages of hematopoiesis in a more lineage-restricted expression pattern than coding mRNAs. They affect hematopoietic stem cell renewal, proliferation, and differentiation of committed progenitors by interacting with master regulators transcription factors. Among these transcription factors, MYC has a prominent role. Similar to MYC's transcriptional activation/amplification of protein coding genes, MYC also regulates lncRNAs' expression profile, while it is also regulated by lncRNAs. Both myeloid and lymphoid malignancies are prone to the association of MYC with lncRNAs. Such interaction inhibits apoptosis, enhances cell proliferation, deregulates metabolism, and promotes genomic instability and resistance to treatment. In this review, we discuss the recent findings that encompass the crosstalk between lncRNAs and describe the pathways that very probably have a pathogenetic role in both acute and chronic hematologic malignancies.
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Affiliation(s)
| | - Agapi Benetatou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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47
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Li Y, Shi H, Yuan J, Qiao L, Dong L, Wang Y. Downregulation of circular RNA circPVT1 restricts cell growth of hepatocellular carcinoma through downregulation of Sirtuin 7 via microRNA-3666. Clin Exp Pharmacol Physiol 2020; 47:1291-1300. [PMID: 32017171 DOI: 10.1111/1440-1681.13273] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/20/2019] [Accepted: 02/01/2020] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) have been identified recently as pivotal regulators in the development and progression of cancers, generally by acting as competing endogenous RNAs of microRNAs (miRNAs) to regulate gene expression. The dysregulation of circRNAs in hepatocellular carcinoma (HCC) has attracted much attention, but the precise role of circRNAs in HCC remains largely unknown. In this study, we aimed to investigate the potential role of circular RNA PVT1 (circPVT1), a newly identified cancer-related circRNA, in HCC. Herein, we found that circPVT1 expression was significantly upregulated in HCC tissues and cell lines. Knockdown of circPVT1 significantly reduced the growth and colony formation, and increased cell apoptosis, of HCC cells. Our results further identified circPVT1 as a sponge for miR-3666. Knockdown of circPVT1 significantly increased miR-3666 expression in HCC cells. Moreover, miR-3666 expression was significantly downregulated in HCC tissues and was inversely correlated with circPVT1 expression. In addition, the overexpression of miR-3666 inhibited the growth of HCC cells by targeting Sirtuin 7 (SIRT7). Notably, miR-3666 inhibition or SIRT7 overexpression partially reversed the circPVT1 knockdown-mediated inhibitory effect on HCC cell growth. Overall, these results demonstrate that downregulation of circPVT1 represses HCC cell growth by upregulating miR-3666 to inhibit SIRT7, suggesting circPVT1 as a potential therapeutic target for HCC. Our study highlights the involvement of circPVT1/miR-3666/SIRT7 in regulating HCC cell growth.
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Affiliation(s)
- Yong Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Yuan
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lu Qiao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lei Dong
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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48
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Mansoor A, Mansoor MO, Patel JL, Zhao S, Natkunam Y, Bieker JJ. KLF1/EKLF expression in acute leukemia is correlated with chromosomal abnormalities. Blood Cells Mol Dis 2020; 83:102434. [PMID: 32311573 DOI: 10.1016/j.bcmd.2020.102434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 12/15/2022]
Abstract
KLF1 (EKLF) is a master regulator of erythropoiesis and controls expression of a wide array of target genes. We interrogated human tissue microarray samples via immunohistological analysis to address whether levels of KLF1 protein are associated with leukemia. We have made the unexpected findings that higher KLF1 levels are correlated with cells containing abnormal chromosomes, and that high KLF1 expression is not limited to acute myeloid leukemia (AML) associated with erythroid/megakaryoblastic differentiation. Expression of KLF1 is associated with poor survival. Further analyses reveal that KLF1 directly regulates a number of genes that play a role in chromosomal integrity. Together these results suggest that monitoring KLF1 levels may provide a new marker for risk stratification and prognosis in patients with AML.
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Affiliation(s)
- Adnan Mansoor
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Mohammad Omer Mansoor
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Jay L Patel
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Shuchun Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James J Bieker
- Department of Cell, Developmental, & Regenerative Biology, Black Family Stem Cell Institute, Tisch Cancer Institute, Mount Sinai School of Medicine, New York, NY, USA.
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49
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Bailey C, Shoura MJ, Mischel PS, Swanton C. Extrachromosomal DNA-relieving heredity constraints, accelerating tumour evolution. Ann Oncol 2020; 31:884-893. [PMID: 32275948 DOI: 10.1016/j.annonc.2020.03.303] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) provides a mechanism by which cancer cells can rapidly adapt to changes in the tumour microenvironment. These circular structures contain oncogenes and their regulatory elements, and, lacking centromeres, they are subject to unequal segregation during mitosis. This non-Mendelian mechanism of inheritance results in increased tumour heterogeneity with daughter cells that can contain increasingly amplified oncogene copy number. These structures also contain favourable epigenetic modifications including transcriptionally active chromatin, further fuelling positive selection. ecDNA drives aggressive tumour behaviour, is related to poorer survival outcomes and provides mechanisms of drug resistance. Recent evidence suggests one in four solid tumours contain cells with ecDNA structures. The concept of tumour evolution is one in which cancer cells compete to survive in a diverse tumour microenvironment under the Darwinian principles of variation and fitness heritability. Unconstrained by conventional segregation constraints, ecDNA can accelerate intratumoral heterogeneity and cellular fitness. In this review, we highlight some of the recent discoveries underpinning this process.
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Affiliation(s)
- C Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - M J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - P S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, San Diego, USA; San Diego Moores Cancer Center, University of California, La Jolla, USA; Department of Pathology, University of California San Diego, La Jolla, USA
| | - C Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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50
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Bhat AA, Younes SN, Raza SS, Zarif L, Nisar S, Ahmed I, Mir R, Kumar S, Sharawat SK, Hashem S, Elfaki I, Kulinski M, Kuttikrishnan S, Prabhu KS, Khan AQ, Yadav SK, El-Rifai W, Zargar MA, Zayed H, Haris M, Uddin S. Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. Mol Cancer 2020; 19:57. [PMID: 32164715 PMCID: PMC7069174 DOI: 10.1186/s12943-020-01175-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Early-stage detection of leukemia is a critical determinant for successful treatment of the disease and can increase the survival rate of leukemia patients. The factors limiting the current screening approaches to leukemia include low sensitivity and specificity, high costs, and a low participation rate. An approach based on novel and innovative biomarkers with high accuracy from peripheral blood offers a comfortable and appealing alternative to patients, potentially leading to a higher participation rate. Recently, non-coding RNAs due to their involvement in vital oncogenic processes such as differentiation, proliferation, migration, angiogenesis and apoptosis have attracted much attention as potential diagnostic and prognostic biomarkers in leukemia. Emerging lines of evidence have shown that the mutational spectrum and dysregulated expression of non-coding RNA genes are closely associated with the development and progression of various cancers, including leukemia. In this review, we highlight the expression and functional roles of different types of non-coding RNAs in leukemia and discuss their potential clinical applications as diagnostic or prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Ajaz A Bhat
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Salma N Younes
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Lucknow, Uttar Pradesh, India
| | - Lubna Zarif
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Sabah Nisar
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ikhlak Ahmed
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Rashid Mir
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Sachin Kumar
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Santosh K Yadav
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami, Miami, Florida, USA
| | - Mohammad A Zargar
- Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India
| | - Hatem Zayed
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
| | - Mohammad Haris
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory Animal Research Center, Qatar University, Doha, Qatar.
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar.
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