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Chatzidavid S, Kontandreopoulou CN, Giannakopoulou N, Diamantopoulos PT, Stafylidis C, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Role of Methylation in Chronic Lymphocytic Leukemia and Its Prognostic and Therapeutic Impacts in the Disease: A Systematic Review. Adv Hematol 2024; 2024:1370364. [PMID: 38435839 PMCID: PMC10907108 DOI: 10.1155/2024/1370364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Epigenetic regulation has been thoroughly investigated in recent years and has emerged as an important aspect of chronic lymphocytic leukemia (CLL) biology. Characteristic aberrant features such as methylation patterns and global DNA hypomethylation were the early findings of the research during the last decades. The investigation in this field led to the identification of a large number of genes where methylation features correlated with important clinical and laboratory parameters. Gene-specific analyses investigated methylation in the gene body enhancer regions as well as promoter regions. The findings included genes and proteins involved in key pathways that play central roles in the pathophysiology of the disease. Τhe application of these findings beyond the theoretical understanding can not only lead to the creation of prognostic and predictive models and scores but also to the design of novel therapeutic agents. The following is a review focusing on the present knowledge about single gene/gene promoter methylation or mRNA expression in CLL cases as well as records of older data that have been published in past papers.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Thalassemia and Sickle Cell Disease Center, Laikon General Hospital, Athens, Greece
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Panagiotis T. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Hematology Department, Iatriko Kentro Palaiou Falirou, Athens, Greece
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Hansen MH, Cédile O, Kjeldsen MLG, Thomassen M, Preiss B, von Neuhoff N, Abildgaard N, Nyvold CG. Toward Cytogenomics: Technical Assessment of Long-Read Nanopore Whole-Genome Sequencing for Detecting Large Chromosomal Alterations in Mantle Cell Lymphoma. J Mol Diagn 2023; 25:796-805. [PMID: 37683892 DOI: 10.1016/j.jmoldx.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
The current advances and success of next-generation sequencing hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional use of short reads impedes the resolution of chromosomal aberrations. Thus, this study evaluated the detection and reproducibility of extensive copy number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies whole-genome sequencing compared with short-read Illumina sequencing. Using the mantle cell lymphoma cell line Granta-519, almost 99% copy-number reproducibility at the 100-kilobase resolution between replicates was demonstrated, with 98% concordance to Illumina. Collectively, the performance of copy number calling from 1.5 million to 7.5 million long reads was comparable to 1 billion Illumina-based reads (50× coverage). Expectedly, the long-read resolution of canonical translocation t(11;14)(q13;q32) was superior, with a sequence similarity of 89% to the already published CCND1/IGH junction (9× coverage), spanning up to 69 kilobases. The cytogenetic profile of Granta-519 was in general agreement with the literature and karyotype, although several differences remained unresolved. In conclusion, contemporary long-read sequencing is primed for future cytogenomics or sequencing-guided cytogenetics. The combined strength of long- and short-read sequencing is apparent, where the high-precision junctional mapping complements and splits paired-end reads. The potential is emphasized by the flexible single-sample genomic data acquisition of Oxford Nanopore Technologies with the high resolution of allelic imbalances using Illumina short-read sequencing.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Marie L G Kjeldsen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Birgitte Preiss
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Nils von Neuhoff
- Department of Pediatric Hematology and Oncology, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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Li Q, Huang L, Ding Y, Sherchan P, Peng W, Zhang JH. Recombinant Slit2 suppresses neuroinflammation and Cdc42-mediated brain infiltration of peripheral immune cells via Robo1-srGAP1 pathway in a rat model of germinal matrix hemorrhage. J Neuroinflammation 2023; 20:249. [PMID: 37899442 PMCID: PMC10613398 DOI: 10.1186/s12974-023-02935-2] [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: 03/22/2023] [Accepted: 10/17/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND Germinal matrix hemorrhage (GMH) is a devastating neonatal stroke, in which neuroinflammation is a critical pathological contributor. Slit2, a secreted extracellular matrix protein, plays a repulsive role in axon guidance and leukocyte chemotaxis via the roundabout1 (Robo1) receptor. This study aimed to explore effects of recombinant Slit2 on neuroinflammation and the underlying mechanism in a rat model of GMH. METHODS GMH was induced by stereotactically infusing 0.3 U of bacterial collagenase into the germinal matrix of 7-day-old Sprague Dawley rats. Recombinant Slit2 or its vehicle was administered intranasally at 1 h after GMH and daily for 3 consecutive days. A decoy receptor recombinant Robo1 was co-administered with recombinant Slit2 after GMH. Slit2 siRNA, srGAP1 siRNA or the scrambled sequences were administered intracerebroventricularly 24 h before GMH. Neurobehavior, brain water content, Western blotting, immunofluorescence staining and Cdc42 activity assays were performed. RESULTS The endogenous brain Slit2 and Robo1 expressions were increased after GMH. Robo1 was expressed on neuron, astrocytes and infiltrated peripheral immune cells in the brain. Endogenous Slit2 knockdown by Slit2 siRNA exacerbated brain edema and neurological deficits following GMH. Recombinant Slit2 (rSlit2) reduced neurological deficits, proinflammatory cytokines, intercellular adhesion molecules, peripheral immune cell markers, neuronal apoptosis and Cdc42 activity in the brain tissue after GMH. The anti-neuroinflammation effects were reversed by recombinant Robo1 co-administration or srGAP1 siRNA. CONCLUSIONS Recombinant Slit2 reduced neuroinflammation and neuron apoptosis after GMH. Its anti-neuroinflammation effects by suppressing onCdc42-mediated brain peripheral immune cells infiltration was at least in part via Robo1-srGAP1 pathway. These results imply that recombinant Slit2 may have potentials as a therapeutic option for neonatal brain injuries.
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Affiliation(s)
- Qian Li
- Department of Pediatrics, Army Medical Center, Army Medical University, 10 Changjiang Access Rd, Yuzhong District, Chongqing, 400042, China
- Women and Children's Hospital of Chongqing Medical University, 120 Longshan Access Rd, Yubei District, Chongqing, 400010, China
| | - Lei Huang
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, 92354, USA
- Department of Neurosurgery, School of Medicine, Loma Linda University, 11234 Anderson Street, Loma Linda, CA, 92354, USA
| | - Yan Ding
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, 92354, USA
| | - Prativa Sherchan
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, 92354, USA
| | - Wenjie Peng
- Department of Pediatrics, Army Medical Center, Army Medical University, 10 Changjiang Access Rd, Yuzhong District, Chongqing, 400042, China
| | - John H Zhang
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, 92354, USA.
- Department of Neurosurgery, School of Medicine, Loma Linda University, 11234 Anderson Street, Loma Linda, CA, 92354, USA.
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Li C, Wang Z, Wei B, Liu Z, Li B, Kang H, Wang J, Liu J, Wang Q, Guo H, Wu X, Liu N, Luo J. Upregulation of ROBO3 promotes proliferation, migration and adhesion of AML cells and affects the survival of AML patients. Biochem Biophys Res Commun 2023; 661:1-9. [PMID: 37084487 DOI: 10.1016/j.bbrc.2023.04.030] [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: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy, which is the most common and severe acute leukemia in adults. Its occurrence, development and prognosis are affected by many factors, and more research is still needed to further guide its treatment. Here, we found that roundabout3 (ROBO3) was associated with poor prognosis in AML through bioinformatics analysis. We then found that overexpression of ROBO3 promoted AML cell proliferation, adhesion and migration while knockdown of ROBO3 had opposite effects. We subsequently found that ROBO3 regulated CD34 expression in AML cells, and this regulatory effect may be achieved through the Hippo-YAP pathway. The inhibitors of this pathway, K-975 and verteporfin, showed an inhibitory effect on AML cells with high ROBO3 expression. ROBO3 was also found to be significantly increased in bone marrow samples from AML patients. Our research indicates that ROBO3 plays an important role in the development of AML, which suggests that ROBO3 can be a prognostic biomarker and potential therapeutic target for AML.
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Affiliation(s)
- Chaonan Li
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China; Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Zhen Wang
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Binghui Wei
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Zechen Liu
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Bei Li
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Hening Kang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Jue Wang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Junle Liu
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Qingyu Wang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Hongming Guo
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Xiaoli Wu
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Na Liu
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Jianmin Luo
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
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Low Expression and Promoter Hypermethylation of the Tumour Suppressor SLIT2, are Associated with Adverse Patient Outcomes in Diffuse Large B Cell Lymphoma. Pathol Oncol Res 2019; 25:1223-1231. [DOI: 10.1007/s12253-019-00600-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
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Integrative bioinformatics analysis identifies ROBO1 as a potential therapeutic target modified by miR-218 in hepatocellular carcinoma. Oncotarget 2017; 8:61327-61337. [PMID: 28977866 PMCID: PMC5617426 DOI: 10.18632/oncotarget.18099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/11/2017] [Indexed: 02/07/2023] Open
Abstract
Patients diagnosed with advanced hepatocellular carcinoma (HCC) presented poor prognosis and short survival time. Althouth accumulating contribution of continuous research has gradually revealed complex tumorigenesis mechanism of HCC with numerous and jumbled biomarkers, those specific ones for HCC diagnose and therapeutic treatment are required illustration. Multiple genes over-expressed in HCC specimens with at least 1.5 fold change were cohorted, compared with the non-cancerous tissues through integrative bioinformatics analysis from Gene Expression Omnibus (GEO) datasets GSE14520 and GSE6764, including 445 and 45 cases of samples spearatly, along with intensive exploration on the Cancer Genome Altas (TCGA) dataset of liver cancer. Thirteen genes significantly highly expressed, overlapping in the datasets above. The Database for Annotation Visualization and Integrated Discovery (DAVID) program was utilized for functional pathway enrichment analysis. Protein-protein Interaction (PPI) analysis was conducted through the Search Tool for the Retrieval of Interacting Genes (STRING) database. ROBO1 was highlighted as one of the most probable molecules among the 13 candidates participating in cancer process. Cancer Cell Line Encycolopedia (CCLE) database was utilized exploring ROBO1 expression in cell lines. Immunochemistry analysis and qRT-PCR assay were performed in our medical center, which indicates significant over-expression status in either HCC tumor specimens and 3 HCC cell lines. Furtherly, we recognized that miR-218, a tumor suppressor, might be an upstream regulator for ROBO1 directly binding to the mRNA 3’UTR and potentially modifying the expression and function of ROBO1. Herein, we conclude that ROBO1 is a mighty therapeutic targets modified by miR-218 in HCC deserving further investigation.
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