1
|
Pham DAT, Le SD, Doan TM, Luu PT, Nguyen UQ, Ho SV, Vo LTT. Standardization of DNA amount for bisulfite conversion for analyzing the methylation status of LINE-1 in lung cancer. PLoS One 2021; 16:e0256254. [PMID: 34403448 PMCID: PMC8370637 DOI: 10.1371/journal.pone.0256254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
Highly methylated Long Interspersed Nucleotide Elements 1 (LINE-1) constitute approximately 20% of the human genome, thus serving as a surrogate marker of global genomic DNA methylation. To date, there is still lacking a consensus about the precise location in LINE-1 promoter and its methylation threshold value, making challenging the use of LINE-1 methylation as a diagnostic, prognostic markers in cancer. This study reports on a technical standardization of bisulfite-based DNA methylation analysis, which ensures the complete bisulfite conversion of repeated LINE-1 sequences, thus allowing accurate LINE-1 methylation value. In addition, the study also indicated the precise location in LINE-1 promoter of which significant variance in methylation level makes LINE-1 methylation as a potential diagnostic biomarker for lung cancer. A serial concentration of 5-50-500 ng of DNA from 275 formalin-fixed paraffin-embedded lung tissues were converted by bisulfite; methylation level of two local regions (at nucleotide position 300–368 as LINE-1.1 and 368–460 as LINE-1.2) in LINE-1 promoter was measured by real time PCR. The use of 5 ng of genomic DNA but no more allowed to detect LINE-1 hypomethylation in lung cancer tissue (14.34% versus 16.69% in non-cancerous lung diseases for LINE-1.1, p < 0.0001, and 30.28% versus 32.35% for LINE-1.2, p < 0.05). Our study thus highlighted the optimal and primordial concentration less than 5 ng of genomic DNA guarantees the complete LINE-1 bisulfite conversion, and significant variance in methylation level of the LINE-1 sequence position from 300 to 368 allowed to discriminate lung cancer from non-cancer samples.
Collapse
Affiliation(s)
| | - Son Duc Le
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Trang Mai Doan
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Phuong Thu Luu
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Uyen Quynh Nguyen
- Department of Biology, VNU Institute of Microbiology and Biotechnology, Hanoi, Vietnam
| | - Son Van Ho
- Department of Biochemistry, 175 Hospital, Ho Chi Minh City, Vietnam
| | - Lan Thi Thuong Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
- * E-mail:
| |
Collapse
|
2
|
DNA Methylation Is Correlated with Oxidative Stress in Myelodysplastic Syndrome-Relevance as Complementary Prognostic Biomarkers. Cancers (Basel) 2021; 13:cancers13133138. [PMID: 34201739 PMCID: PMC8268426 DOI: 10.3390/cancers13133138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Myelodysplastic syndrome (MDS) is a hematological malignancy with a high propensity to evolve to acute myeloid leukemia. Oxidative stress and abnormal DNA methylation are important in this neoplasia’s development and progression. We investigate whether oxidative stress parameters were correlated with localized and global DNA methylations in the peripheral blood of patients with MDS. We found that oxidative stress was positively correlated with DNA methylation and associated with worse overall survival. Biologically, these facts suggest a relationship between oxidative stress and DNA methylation, two common pathogenic mechanisms involved in MDS. Clinically, our findings can improve an MDS patient’s management if used as complementary prognostic biomarkers. Abstract Oxidative stress and abnormal DNA methylation have been implicated in cancer, including myelodysplastic syndromes (MDSs). This fact leads us to investigate whether oxidative stress is correlated with localized and global DNA methylations in the peripheral blood of MDS patients. Sixty-six MDS patients and 26 healthy individuals were analyzed. Several oxidative stress and macromolecule damage parameters were analyzed. Localized (gene promotor) and global DNA methylations (5-mC and 5-hmC levels; LINE-1 methylation) were assessed. MDS patients had lower levels of reduced glutathione and total antioxidant status (TAS) and higher levels of peroxides, nitric oxide, peroxides/TAS, and 8-hydroxy-2-deoxyguanosine compared with controls. These patients had higher 5-mC levels and lower 5-hmC/5-mC ratio and LINE-1 methylation and increased methylation frequency of at least one methylated gene. Peroxide levels and peroxide/TAS ratio were higher in patients with methylated genes than those without methylation and negatively correlated with LINE-1 methylation and positively with 5-mC levels. The 5-hmC/5-mC ratio was significantly associated with progression to acute leukemia and peroxide/TAS ratio with overall survival. This study points to a relationship between oxidative stress and DNA methylation, two common pathogenic mechanisms involved in MDS, and suggests the relevance of 5-hmC/5-mC and peroxide/TAS ratios as complementary prognostic biomarkers.
Collapse
|
3
|
Impact of Tumor LINE-1 Methylation Level and Neoadjuvant Treatment and Its Association with Colorectal Cancer Survival. J Pers Med 2020; 10:jpm10040219. [PMID: 33187096 PMCID: PMC7712476 DOI: 10.3390/jpm10040219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Recent studies suggest that long-interspersed nucleotide element-1 (LINE-1) hypomethylation is commonly found in colorectal cancer (CRC), and is associated with worse prognosis. However, the utility of LINE-1 methylation on the prognosis of CRC is still controversial, and may be due to the fact that some clinical and pathological features may affect LINE-1 methylation. Thus, the aim of this study was to assess the prognostic value of tumor LINE-1 methylation in CRC, through their association with the CRC clinical and pathological characteristics. Survival of sixty-seven CRC patients was evaluated according to the median of tumor LINE-1 methylation, as well as pathological and oncological variables. We also studied the association between LINE-1 methylation and pathological features, and finally, we assessed the overall and disease-free survival of LINE1 methylation, stratified by neoadjuvant treatment and further checked by multivariate Cox regression to assess the statistical interactions. LINE-1 was hypomethylated in the CRC tumor with respect to the tumor adjacent-free area (p < 0.05), without association with any other clinical and oncological features, nor with overall and disease-free survival rates for CRC. Relevantly, in neoadjuvant treatment, LINE-1 methylation was associated with survival rates. Thus, disease-free and overall survival rates of treated CRC patients were worse in the hypomethylated LINE-1 tumors than those with normal LINE-1 methylation (p = 0.004 and 0.0049, respectively). Indeed, LINE-1 was hypermethylated more in the treated patients than in the non-treated patients (p < 0.05). The present study showed that tumor LINE-1 hypomethylation was associated with worse survival rates in only treated patients. Our data suggest an interactive effect of neoadjuvant treatment and tumor LINE-1 methylation, which could be a specific-tissue biomarker to predict survival of the treated patients, and help to personalize treatment in CRC.
Collapse
|
4
|
Zeggar HR, How-Kit A, Daunay A, Bettaieb I, Sahbatou M, Rahal K, Adouni O, Gammoudi A, Douik H, Deleuze JF, Kharrat M. Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. Oncol Lett 2020; 20:1999-2006. [PMID: 32724446 PMCID: PMC7377197 DOI: 10.3892/ol.2020.11745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P<0.03). DNA hypomethylation of LINE-1 was also indicated to be associated with low grade (P=0.023). To the best of our knowledge, the current study is the first study regarding DNA methylation of LINE-1 and Alu repeats element in breast cancer of the Tunisian population. The results of the current study suggest that, since hypomethylation of LINE-1 is associated with low grade, it could be used as a biomarker for prognosis for patients with breast cancer.
Collapse
Affiliation(s)
- Hayet Radia Zeggar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Ilhem Bettaieb
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Khaled Rahal
- Service de Chirurgie Carcinologique, Institut Salah Azaiz de Tunis, 1006 Tunis, Tunisia
| | - Olfa Adouni
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Amor Gammoudi
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Hayet Douik
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Le Commissariat à l'énergie atomique et aux énergies alternatives-Institut François Jacob, 92265 Evry, France
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| |
Collapse
|
5
|
Binetti M, Lauro A, Vaccari S, Cervellera M, Tonini V. Proteogenomic biomarkers in colorectal cancers: clinical applications. Expert Rev Proteomics 2020; 17:355-363. [PMID: 32536221 DOI: 10.1080/14789450.2020.1782202] [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: 02/06/2023]
Abstract
INTRODUCTION Colorectal cancer (CRC) is one of the leading cancers in terms of incidence and mortality, rate requiring a multidisciplinary approach. The discovery of specific CRC biomarkers has caused a paradigm shift in its clinical management. AREAS COVERED The aim is to illustrate the possible clinical applications of CRC biomarkers through an updated literature review (from 2015 to 2020) based on the PubMed database. A relationship between cancer localization and genetic profile has been identified. Nowadays, the tumor markers are largely used to select patients that could really benefit from a specific type of adjuvant therapy, in order to optimize treatment programs, especially in metastatic patients. This review highlights both CRC biomarkers' advantages and critical issues. EXPERT OPINION New biomarker discoveries allow to set noninvasive tests that could increase patient's compliance with therapy. They also permit a cost-effective early diagnosis, as well as patient-tailored treatments, improving the overall survival. The CRC biomarkers could also have a prognostic value, and usually, they are included in follow-up programs. However, despite the continuous progression of new technologies, their clinical validation is still debated. In this context, additional clinical studies are still necessary to identify, among potential markers, the most effective ones.
Collapse
Affiliation(s)
| | - Augusto Lauro
- Emergency Surgery Unit, St. Orsola University Hospital , Bologna, Italy
| | - Samuele Vaccari
- Department of Surgical Sciences, Umberto I University Hospital , Rome, Italy
| | | | - Valeria Tonini
- Emergency Surgery Unit, St. Orsola University Hospital , Bologna, Italy
| |
Collapse
|
6
|
Kerachian MA, Kerachian M. Long interspersed nucleotide element-1 (LINE-1) methylation in colorectal cancer. Clin Chim Acta 2018; 488:209-214. [PMID: 30445031 DOI: 10.1016/j.cca.2018.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) represents a group of molecularly heterogeneous diseases characterized by genetic and epigenetic alterations. Long interspersed nuclear elements (LINEs) are a form of retrotransposable element found in many eukaryotic genomes. These LINEs, when active, can mobilize in the cell and steadily cause genomic rearrangement. Active LINE reorganization is a source of endogenous mutagenesis and polymorphism in the cell that brings about individual genomic variation. In normal somatic cells, these elements are heavily methylated and thus mostly suppressed, in turn, preventing their potential for bringing about genomic instability. When LINEs are inadequately controlled, they can play a role in the pathogenesis of several genetic diseases, such as cancer. In tumor cells, LINE hypomethylation can reactivate the mobilization of these elements and is associated with both an advanced stage and a poor prognosis. In this article, we summarize the current knowledge surrounding LINE methylation, its correlation to CRC and its application as a diagnostic, prognostic and predictive biomarker in colon cancer.
Collapse
Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Matin Kerachian
- Faculty of Medicine, McGill University, Montreal, Canada; Research Institute at McGill University Health Center, Montreal, Canada
| |
Collapse
|