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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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Characterization of bone marrow heterogeneity in NK-AML (M4/M5) based on single-cell RNA sequencing. Exp Hematol Oncol 2023; 12:25. [PMID: 36879313 PMCID: PMC9987113 DOI: 10.1186/s40164-023-00391-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
Normal karyotype acute myeloid leukemia (NK-AML) is a heterogeneous hematological malignancy that contains a minor population of self-renewing leukemia stem cells (LSCs), which complicate efforts to achieve long-term survival. We performed single-cell RNA sequencing to profile 39,288 cells from 6 bone marrow (BM) aspirates including 5 NK-AML (M4/M5) patients and 1 healthy donor. The single-cell transcriptome atlas and gene expression characteristics of each cell population in NK-AML (M4/M5) and healthy BM were obtained. In addition, we identified a distinct LSC-like cluster with possible biomarkers in NK-AML (M4/M5) and verified 6 genes using qRT‒PCR and bioinformatic analyses. In conclusion, we utilized single-cell technologies to provide an atlas of NK-AML (M4/M5) cell heterogeneity, composition, and biomarkers with implications for precision medicine and targeted therapies.
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Lymph Node Metastasis-Related Gene ITGA4 Promotes the Proliferation, Migration, and Invasion of Gastric Cancer Cells by Regulating Tumor Immune Microenvironment. JOURNAL OF ONCOLOGY 2022; 2022:1315677. [PMID: 36254221 PMCID: PMC9569201 DOI: 10.1155/2022/1315677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
Abstract
The Integrin Subunit Alpha 4 (ITGA4) plays important roles in cancers pathogenesis. However, the expression and association with clinicopathological and survival probability have not been previously assessed in gastric cancer (GC). Protein expression of ITGA4 was assessed in TMA using immunohistochemistry and correlated with clinicopathological factors and survival. The mRNA expression of ITGA4 was also assessed in the HMU-GC cohort. Bioinformatics function analysis was conducted through GSEA. The “CIBERSORT” package was used for immune infiltration analysis. “SvyNom” package is used to construct prognosis model. ITGA4 knock down using shRNA. The evaluation of cell function was performed by CCK-8 and Transwell invasion and migration experiments. ITGA4 was significantly associated with N classification (
), tumor location (
), WHO classification (
), and poor prognosis in mRNA level. GSEA analysis of the validation cohort suggested that ITGA4 was associated with macrophage infiltration. Immunohistochemistry showed that ITGA4 was associated with poor prognosis. Multivariate Cox regression analysis found that ITGA4 (
) and lymph node metastasis rate (
) were independent prognostic factors and could construct a prognosis model. ITGA4 knockdown cell line significantly reduced the ability of proliferation, invasion, and metastasis. ITGA4 is associated with patient survival in GC and may be an important prognostic biomarker.
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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Jafarpour S, Saberi F, Yazdi M, Nedaeinia R, Amini G, Ferns GA, Salehi R. Association between colorectal cancer and the degree of ITGA4 promoter methylation in peripheral blood mononuclear cells. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Bai Y, Li X, Chen Z, Li J, Tian H, Ma Y, Raza SHA, Shi B, Han X, Luo Y, Hu J, Wang J, Liu X, Li S, Zhao Z. Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis. Front Vet Sci 2022; 8:788316. [PMID: 34977220 PMCID: PMC8716587 DOI: 10.3389/fvets.2021.788316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
The enzyme long-chain acyl-CoA synthetase 1 (ACSL1) is essential for lipid metabolism. The ACSL1 gene controls unsaturated fatty acid (UFA) synthesis as well as the formation of lipid droplets in bovine adipocytes. Here, we used RNA-Seq to determine lncRNA and mRNA that regulate UFA synthesis in bovine adipocytes using RNA interference and non-interference with ACSL1. The corresponding target genes of differentially expressed (DE) lncRNAs and the DE mRNAs were found to be enriched in lipid and FA metabolism-related pathways, according to GO and KEGG analyses. The differentially expressed lncRNA- differentially expressed mRNA (DEL-DEM) interaction network indicated that some DELs, such as TCONS_00069661, TCONS_00040771, TCONS_ 00035606, TCONS_00048301, TCONS_001309018, and TCONS_00122946, were critical for UFA synthesis. These findings assist our understanding of the regulation of UFA synthesis by lncRNAs and mRNAs in bovine adipocytes.
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Affiliation(s)
- Yanbin Bai
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Xupeng Li
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Zongchang Chen
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jingsheng Li
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Hongshan Tian
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Yong Ma
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | | | - Bingang Shi
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Xiangmin Han
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Zhidong Zhao
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
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Faleiro I, Roberto VP, Demirkol Canli S, Fraunhoffer NA, Iovanna J, Gure AO, Link W, Castelo-Branco P. DNA Methylation of PI3K/AKT Pathway-Related Genes Predicts Outcome in Patients with Pancreatic Cancer: A Comprehensive Bioinformatics-Based Study. Cancers (Basel) 2021; 13:cancers13246354. [PMID: 34944974 PMCID: PMC8699150 DOI: 10.3390/cancers13246354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
Simple Summary Pancreatic cancer is a highly lethal malignancy. Dysregulation of epigenetic mechanisms leads to abnormal patterns of gene expression contributing to the development and progression of cancer. We explored the ability of DNA methylation of PI3K-related genes to differentiate between malignant and healthy pancreatic tissue using distinct pancreatic cancer cohorts, and found that the methylation levels of the ITGA4, SFN, ITGA2, and PIK3R1 genes are altered in tumour samples since the early stages of malignant transformation and could serve as new diagnostic tools. We also demonstrate that these alterations correlate with overall survival and recurrence-free survival of the patients suggesting that its assessment can serve as independent prognostic indicators of patients’ survival with higher sensitivity and specificity than the currently implemented biomarkers. Therefore, the methylation profile of genes involved in this pathway may be an alternative method for predicting cell malignancy and help doctors’ decisions on patient care. Abstract Pancreatic cancer (PCA) is one of the most lethal malignancies worldwide with a 5-year survival rate of 9%. Despite the advances in the field, the need for an earlier detection and effective therapies is paramount. PCA high heterogeneity suggests that epigenetic alterations play a key role in tumour development. However, only few epigenetic biomarkers or therapeutic targets have been identified so far. Here we explored the potential of distinct DNA methylation signatures as biomarkers for early detection and prognosis of PCA. PI3K/AKT-related genes differentially expressed in PCA were identified using the Pancreatic Expression Database (n = 153). Methylation data from PCA patients was obtained from The Cancer Genome Atlas (n = 183), crossed with clinical data to evaluate the biomarker potential of the epigenetic signatures identified and validated in independent cohorts. The majority of selected genes presented higher expression and hypomethylation in tumour tissue. The methylation signatures of specific genes in the PI3K/AKT pathway could distinguish normal from malignant tissue at initial disease stages with AUC > 0.8, revealing their potential as PCA diagnostic tools. ITGA4, SFN, ITGA2, and PIK3R1 methylation levels could be independent prognostic indicators of patients’ survival. Methylation status of SFN and PIK3R1 were also associated with disease recurrence. Our study reveals that the methylation levels of PIK3/AKT genes involved in PCA could be used to diagnose and predict patients’ clinical outcome with high sensitivity and specificity. These results provide new evidence of the potential of epigenetic alterations as biomarkers for disease screening and management and highlight possible therapeutic targets.
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Affiliation(s)
- Inês Faleiro
- Faculty of Medicine and Biomedical Sciences (FMCB), Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal;
- Algarve Biomedical Center Research Institute (ABC-RI), 8005-139 Faro, Portugal
- Instituto de Medicina Molecular João Lobo Antunes (IMM), Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Vânia Palma Roberto
- Faculty of Medicine and Biomedical Sciences (FMCB), Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal;
- Algarve Biomedical Center Research Institute (ABC-RI), 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
- Correspondence: (V.P.R.); (P.C.-B.)
| | - Secil Demirkol Canli
- Molecular Pathology Application and Research Center, Hacettepe University, 06100 Ankara, Turkey;
| | - Nicolas A. Fraunhoffer
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France; (N.A.F.); (J.I.)
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France; (N.A.F.); (J.I.)
| | - Ali Osmay Gure
- Department of Medical Biology, Acibadem University, 34684 Istanbul, Turkey;
| | - Wolfgang Link
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain;
| | - Pedro Castelo-Branco
- Faculty of Medicine and Biomedical Sciences (FMCB), Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal;
- Algarve Biomedical Center Research Institute (ABC-RI), 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
- Correspondence: (V.P.R.); (P.C.-B.)
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Chitosan oligosaccharides packaged into rat adipose mesenchymal stem cells-derived extracellular vesicles facilitating cartilage injury repair and alleviating osteoarthritis. J Nanobiotechnology 2021; 19:343. [PMID: 34702302 PMCID: PMC8549296 DOI: 10.1186/s12951-021-01086-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023] Open
Abstract
Objectives This study aimed to investigate the roles of adipose mesenchymal stem cell (AMSC)-derived extracellular vesicles (EVs) binding with chitosan oligosaccharides (COS) in cartilage injury, as well as the related mechanisms. Results IL-1β treatment significantly inhibited the viability and migration of chondrocytes and enhanced cell apoptosis (P < 0.05), while chitosan oligosaccharides and extracellular vesicles-chitosan oligosaccharide conjugates (EVs-COS/EVs-COS conjugates) reversed the changes induced by IL-1β (P < 0.05), and the effects of extracellular vesicles-chitosan oligosaccharide conjugates were better than those of chitosan oligosaccharides (P < 0.05). After cartilage damage, IL-1β, OPN, and p53 were significantly upregulated, COL1A1, COL2A1, OCN, RUNX2, p-Akt/Akt, PI3K, c-Myc, and Bcl2 were markedly downregulated, and extracellular vesicles-chitosan oligosaccharide conjugates reversed the expression induced by cartilage injury. Through sequencing, 760 differentially expressed genes (DEGs) clustered into four expression patterns were associated with negative regulation of the canonical Wnt, PI3K-Akt, AMPK, and MAPK signaling pathways. Conclusion Extracellular vesicles-chitosan oligosaccharide conjugates may serve as a new cell-free biomaterial to facilitate cartilage injury repair and improve osteoarthritis. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-01086-x.
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Jin H, Pang L, Li H, Xu M, Yan H, Li R. [Value of combined detection of ITGA4 and SFRP2 gene methylation in stool DNA in diagnosis and prognostic evaluation of colorectal tumors]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:891-897. [PMID: 34238742 DOI: 10.12122/j.issn.1673-4254.2021.06.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the value of quantitative detection of ITGA4 and SFRP2 gene methylation in stool DNA for the early diagnosis and prognostic evaluation of colorectal tumors. OBJECTIVE Real-time PCR was used for quantitative assessment of ITGA4 and SFRP2 gene methylation levels in stool samples of 85 patients with colorectal cancer, 65 patients with colorectal adenoma and 40 healthy subjects. OBJECTIVE The 3 groups were comparable for age and gender composition. Methylated ITGA4 and SFRP2 promoters were detected in 48.2% and 62.4% of patients with colorectal cancer, respectively, with a combined positivity of 81.2%. ITGA4 and SFRP2 promoter methylation was detected in 23.1% and 43.1% of patients with colorectal adenoma, respectively, with a combined positivity of 69.2%. The positivity rates of ITGA4 and SFRP2 methylation were significantly higher in patients with colorectal cancer than in those with colorectal adenoma (P < 0.001; P= 0.001) and healthy subjects (P < 0.001; P < 0.001). In colorectal cancer group, ITGA4 and SFRP2 promoter methylation levels were correlated with postoperative tumor recurrence in colorectal cancer group, and the relapse-free survival rate was significantly lower in positive patients for ITGA4 and SFRP2 promoter methylation than in the negative patients (P=0.0002; P=0.007). Multivariate analysis with the COX proportional hazard regression model showed that methylation of ITGA4 and SFRP2 gene promoters (P=0.01) and the degree of tumor differentiation (P=0.03) were associated with the recurrence of colorectal cancer, and were independent risk factors for the recurrence of colorectal cancer. OBJECTIVE Combined detection of ITGA4 and SFRP2 gene methylation levels in stool DNA can improve the early diagnosis rate of colorectal tumor. ITGA4 and SFRP2 promoter methylation and the degree of tumor differentiation are independent risk factors for colorectal cancer recurrence.
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Affiliation(s)
- H Jin
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - L Pang
- First School of Clinical Medicine, Mudanjiang Medical University, Mudanjiang 157011, China
| | - H Li
- Department of Quality Control, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - M Xu
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - H Yan
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - R Li
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
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