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Ahuja P, Yadav R, Goyal S, Yadav C, Ranga S, Kadian L. Targeting epigenetic deregulations for the management of esophageal carcinoma: recent advances and emerging approaches. Cell Biol Toxicol 2023; 39:2437-2465. [PMID: 37338772 DOI: 10.1007/s10565-023-09818-5] [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: 03/16/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Ranking from seventh in incidence to sixth in mortality, esophageal carcinoma is considered a severe malignancy of food pipe. Later-stage diagnosis, drug resistance, and a high mortality rate contribute to its lethality. Esophageal squamous cell carcinoma and esophageal adenocarcinoma are the two main histological subtypes of esophageal carcinoma, with squamous cell carcinoma alone accounting for more than eighty percent of its cases. While genetic anomalies are well known in esophageal cancer, accountability of epigenetic deregulations is also being explored for the recent two decades. DNA methylation, histone modifications, and functional non-coding RNAs are the crucial epigenetic players involved in the modulation of different malignancies, including esophageal carcinoma. Targeting these epigenetic aberrations will provide new insights into the development of biomarker tools for risk stratification, early diagnosis, and effective therapeutic intervention. This review discusses different epigenetic alterations, emphasizing the most significant developments in esophageal cancer epigenetics and their potential implication for the detection, prognosis, and treatment of esophageal carcinoma. Further, the preclinical and clinical status of various epigenetic drugs has also been reviewed.
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Affiliation(s)
- Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India.
| | - Sandeep Goyal
- Department of Internal Medicine, Pt. B.D, Sharma University of Health Sciences, (Haryana), Rohtak, 124001, India
| | - Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, (Haryana), Rohtak, 124001, India
| | - Lokesh Kadian
- Department of Dermatology, School of Medicine, Indiana University, Indianapolis, Indiana, 46202, USA
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Sato H, Watanabe KI, Kobayashi Y, Tomihari M, Uemura A, Tagawa M. LINE-1 Methylation Status in Canine Splenic Hemangiosarcoma Tissue and Cell-Free DNA. Animals (Basel) 2023; 13:2987. [PMID: 37760387 PMCID: PMC10525518 DOI: 10.3390/ani13182987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Splenic hemangiosarcoma is one of the most common malignant tumors in dogs, and early diagnosis is of great importance for achieving a good prognosis. DNA methylation plays an important role in cancer development. Long interspersed nuclear element 1 (LINE-1) is the most abundant repetitive element in the genome. LINE-1 hypomethylation has been shown to be related to carcinogenesis in humans, and it has been used as a novel cancer biomarker. This study aimed to evaluate the methylation status of LINE-1 in tumor tissue and circulating cell-free DNA and assess its clinical significance in canine splenic hemangiosarcoma. Genomic DNA was isolated from splenic masses of 13 dogs with hemangiosarcoma, 11 with other malignant tumors, and 15 with benign lesions. LINE-1 methylation was quantified using methylation-sensitive and -insensitive restriction enzyme digestion followed by real-time polymerase chain reaction. Additionally, blood samples were collected from eight patients to isolate cell-free DNA to determine LINE-1 methylation status changes during the treatment course. LINE-1 methylation in tumor samples was significantly lower in patients with hemangiosarcoma than in those with other malignant tumors and benign lesions. Non-significant but similar results were observed for the cell-free DNA samples. Our results demonstrate that LINE-1 methylation status is a potential biomarker for splenic hemangiosarcoma.
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Affiliation(s)
- Hiroki Sato
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Ken-Ichi Watanabe
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Yoshiyasu Kobayashi
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Mizuki Tomihari
- Department of Veterinary Science, Osaka Metropolitan University, Izumisano 545-8585, Japan
| | - Akiko Uemura
- Department of Veterinary Clinical Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Michihito Tagawa
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
- Department of Veterinary Associated Science, Okayama University of Science, Imabari 794-8555, Japan
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Geng Z, Chen M, Yu Q, Guo S, Chen T, Liu D. Histone Modification of Colorectal Cancer by Natural Products. Pharmaceuticals (Basel) 2023; 16:1095. [PMID: 37631010 PMCID: PMC10458348 DOI: 10.3390/ph16081095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Natural products play important roles in the pathogenesis of many human malignancies, including colorectal cancer, and can act as a gene regulator in many cancers. They regulate malignant cell growth through many cellular signal pathways, including Rac family small GTPase 1 (RAC1)/PI3K/AKT (α-serine/threonine-protein kinase), mitogen-activated protein kinase (MAPK), Wnt/β-catenin pathway, transforming growth factor-β (TGF-β), Janus kinase and signal transducer and activator of transcription (JAK-STAT), nuclear factor kappa-B (NF-κB), the Notch pathway, Hippo pathway, and Hedgehog pathway. In this review, we describe the epigenetic roles of several natural products, e.g., platycodin D (PD), ginsenoside Rd, tretinoin, Rutin, curcumin, clove extract, betulinic acid, resveratrol, and curcumin, in colorectal cancer, including their impact on colorectal cancer cell proliferation, apoptosis, invasion, migration, and anti-chemotherapeutic resistance. The aim is to illustrate the epigenetic mechanisms of action of natural products in cancer prevention and treatment, and to provide (1) a theoretical basis for the study of the role of epigenetics in influencing colorectal cancer; (2) new directions for studying the occurrence, development, and prognosis of colorectal cancer; and (3) new targets for treating and preventing colorectal cancer.
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Affiliation(s)
| | | | | | | | - Tianli Chen
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (Z.G.); (M.C.); (Q.Y.); (S.G.)
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (Z.G.); (M.C.); (Q.Y.); (S.G.)
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Potential health risks of mRNA-based vaccine therapy: A hypothesis. Med Hypotheses 2023; 171:111015. [PMID: 36718314 PMCID: PMC9876036 DOI: 10.1016/j.mehy.2023.111015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/08/2022] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
Therapeutic applications of synthetic mRNA were proposed more than 30 years ago, and are currently the basis of one of the vaccine platforms used at a massive scale as part of the public health strategy to get COVID-19 under control. To date, there are no published studies on the biodistribution, cellular uptake, endosomal escape, translation rates, functional half-life and inactivation kinetics of synthetic mRNA, rates and duration of vaccine-induced antigen expression in different cell types. Furthermore, despite the assumption that there is no possibility of genomic integration of therapeutic synthetic mRNA, only one recent study has examined interactions between vaccine mRNA and the genome of transfected cells, and reported that an endogenous retrotransposon, LINE-1 is unsilenced following mRNA entry to the cell, leading to reverse transcription of full length vaccine mRNA sequences, and nuclear entry. This finding should be a major safety concern, given the possibility of synthetic mRNA-driven epigenetic and genomic modifications arising. We propose that in susceptible individuals, cytosolic clearance of nucleotide modified synthetic (nms-mRNAs) is impeded. Sustained presence of nms-mRNA in the cytoplasm deregulates and activates endogenous transposable elements (TEs), causing some of the mRNA copies to be reverse transcribed. The cytosolic accumulation of the nms-mRNA and the reverse transcribed cDNA molecules activates RNA and DNA sensory pathways. Their concurrent activation initiates a synchronized innate response against non-self nucleic acids, prompting type-I interferon and pro-inflammatory cytokine production which, if unregulated, leads to autoinflammatory and autoimmune conditions, while activated TEs increase the risk of insertional mutagenesis of the reverse transcribed molecules, which can disrupt coding regions, enhance the risk of mutations in tumour suppressor genes, and lead to sustained DNA damage. Susceptible individuals would then expectedly have an increased risk of DNA damage, chronic autoinflammation, autoimmunity and cancer. In light of the current mass administration of nms-mRNA vaccines, it is essential and urgent to fully understand the intracellular cascades initiated by cellular uptake of synthetic mRNA and the consequences of these molecular events.
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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Cui H, Rong W, Ma J, Zhu Q, Jiang B, Zhang L, Li C, Zhuo Z, Chen M. DNA N6-Adenine methylation in HBV-related hepatocellular carcinoma. Gene 2022; 822:146353. [PMID: 35189250 DOI: 10.1016/j.gene.2022.146353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/26/2022] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
DNA methylation on N6-adenine (6mA) has recently been found to be a potential epigenetic marker in prokaryotes and eukaryotes. However, its distribution patterns and potential functions in human tumorigenesis remain largely unknown. Here, we reported global profiling of 6mA sites in the genome of hepatocellular carcinoma at single-nucleotide resolution using Nanopore sequencing. 6mA was widely distributed throughout the human genome. The 6mA sites were related to the porphyrin and chlorophyll metabolism in autosomes and were related to oxidative phosphorylation and ATP metabolism in mitochondria. AGG was the most significant motif associated with 6mA modification and the prevalent motifs in tumors were mainly distributed in mitochondria. The density of 6mA was related to the activation of gene transcription and 6mA density in repetitive sequences decreased in hepatocellular carcinoma. DNA 6mA methylation modification may also be a potential biomarker for cancer diagnosis and treatment.
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Affiliation(s)
- Hongyuan Cui
- Department of General Surgery, Department of Hepato-bilio-pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, China; Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai 810001, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai 810001, China
| | - Qing Zhu
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Qinghai University, Qinghai 810001, China
| | - Boyue Jiang
- Department of General Surgery, Department of Hepato-bilio-pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chang Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhongling Zhuo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Meng Chen
- National Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Lead (Pb) and neurodevelopment: A review on exposure and biomarkers of effect (BDNF, HDL) and susceptibility. Int J Hyg Environ Health 2021; 238:113855. [PMID: 34655857 DOI: 10.1016/j.ijheh.2021.113855] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Lead (Pb) is a ubiquitous environmental pollutant and a potent toxic compound. Humans are exposed to Pb through inhalation, ingestion, and skin contact via food, water, tobacco smoke, air, dust, and soil. Pb accumulates in bones, brain, liver and kidney. Fetal exposure occurs via transplacental transmission. The most critical health effects are developmental neurotoxicity in infants and cardiovascular effects and nephrotoxicity in adults. Pb exposure has been steadily decreasing over the past decades, but there are few recent exposure data from the general European population; moreover, no safe Pb limit has been set. Sensitive biomarkers of exposure, effect and susceptibility, that reliably and timely indicate Pb-associated toxicity are required to assess human exposure-health relationships in a situation of low to moderate exposure. Therefore, a systematic literature review based on PubMed entries published before July 2019 that addressed Pb exposure and biomarkers of effect and susceptibility, neurodevelopmental toxicity, epigenetic modifications, and transcriptomics was conducted. Finally included were 58 original papers on Pb exposure and 17 studies on biomarkers. The biomarkers that are linked to Pb exposure and neurodevelopment were grouped into effect biomarkers (serum brain-derived neurotrophic factor (BDNF) and serum/saliva cortisol), susceptibility markers (epigenetic markers and gene sequence variants) and other biomarkers (serum high-density lipoprotein (HDL), maternal iron (Fe) and calcium (Ca) status). Serum BDNF and plasma HDL are potential candidates to be further validated as effect markers for routine use in HBM studies of Pb, complemented by markers of Fe and Ca status to also address nutritional interactions related to neurodevelopmental disorders. For several markers, a causal relationship with Pb-induced neurodevelopmental toxicity is likely. Results on BDNF are discussed in relation to Adverse Outcome Pathway (AOP) 13 ("Chronic binding of antagonist to N-methyl-D-aspartate receptors (NMDARs) during brain development induces impairment of learning and memory abilities") of the AOP-Wiki. Further studies are needed to validate sensitive, reliable, and timely effect biomarkers, especially for low to moderate Pb exposure scenarios.
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Paredes-Céspedes DM, Rojas-García AE, Medina-Díaz IM, Ramos KS, Herrera-Moreno JF, Barrón-Vivanco BS, González-Arias CA, Bernal-Hernández YY. Environmental and socio-cultural impacts on global DNA methylation in the indigenous Huichol population of Nayarit, Mexico. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4472-4487. [PMID: 32940839 DOI: 10.1007/s11356-020-10804-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Alterations of global DNA methylation have been evaluated in several studies worldwide; however, Long Interspersed Nuclear Elements-1 (LINE-1) methylation in genetically conserved populations such as indigenous communities have not, to our knowledge, been reported. The aim of this study was to evaluate the relationship between LINE-1 methylation patterns and factors such as pesticide exposure and socio-cultural characteristics in the Indigenous Huichol Population of Nayarit, Mexico. A cross-sectional study was conducted in 140 Huichol indigenous individuals. A structured questionnaire was used to determine general and anthropometric characteristics, diet, harmful habits, and pesticide exposure. DNA methylation was determined by pyrosequencing of bisulfite-treated DNA. A lower level of LINE-1 methylation was found in the indigenous population when compared to a Mestizo population previously studied by our group. This difference might be due to the influence of the genetic admixture and differing dietary and lifestyle habits. The males in the indigenous population exhibited increased LINE-1 methylation in comparison to the females. Sex and alcohol consumption showed positive associations with LINE-1 methylation, while weight, current work in the field, current pesticide usage, and folate intake exhibited negative associations with LINE-1 methylation. The results suggest that ethnicity, as well as other internal and environmental factors, might influence LINE-1 methylation.
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Affiliation(s)
- Diana Marcela Paredes-Céspedes
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Km. 9 Carretera Tepic-Compostela, Xalisco, Nayarit, México
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Aurora Elizabeth Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Irma Martha Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, 121 W. Holcombe Blvd, Houston, TX, 77030 m EE,UU, USA
| | - José Francisco Herrera-Moreno
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Km. 9 Carretera Tepic-Compostela, Xalisco, Nayarit, México
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Briscia Socorro Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Cyndia Azucena González-Arias
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Yael Yvette Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México.
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Aberrant Methylation of LINE-1 Transposable Elements: A Search for Cancer Biomarkers. Cells 2020; 9:cells9092017. [PMID: 32887319 PMCID: PMC7563416 DOI: 10.3390/cells9092017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer remains one of the main causes of human mortality despite significant progress in its diagnostics and therapy achieved in the past decade. Massive hypomethylation of retrotransposons, in particular LINE-1, is considered a hallmark of most malignant transformations as it results in the reactivation of retroelements and subsequent genomic instability. Accumulating data on LINE-1 aberrant methylation in different tumor types indicates its significant role in cancer initiation and progression. However, direct evidence that LINE-1 activation can be used as a cancer biomarker is still limited. The objective of this review was to critically evaluate the published results regarding the diagnostic/prognostic potential of the LINE-1 methylation status in cancer. Our analysis indicates that LINE-1 hypomethylation is a promising candidate biomarker of cancer development, which, however, needs validation in both clinical and laboratory studies to confirm its applicability to different cancer types and/or stages. As LINE-1 is present in multiple cell-free copies in blood, it has advantages over single-copy genes regarding perspectives of using its methylation status as an epigenetic cancer biomarker for cell-free DNA liquid biopsy.
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Tumor Long-interspersed Nucleotide Element-1 Methylation Level and Immune Response to Esophageal Cancer. Ann Surg 2019; 272:1025-1034. [DOI: 10.1097/sla.0000000000003264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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.
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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
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Baba Y, Yagi T, Sawayama H, Hiyoshi Y, Ishimoto T, Iwatsuki M, Miyamoto Y, Yoshida N, Baba H. Long Interspersed Element-1 Methylation Level as a Prognostic Biomarker in Gastrointestinal Cancers. Digestion 2018; 97:26-30. [PMID: 29393154 DOI: 10.1159/000484104] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Epigenetic changes play a crucial role in human cancer development. DNA methylation is a central epigenetic process that regulates levels of gene expression. Changes in DNA methylation that occur in human tumors include global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Long interspersed element-1 (LINE-1) is a repetitive DNA retrotransposon that duplicates via a copy-and-paste genetic mechanism. As LINE-1 constitutes approximately 17% of the human genome, the extent of LINE-1 methylation is regarded as a surrogate marker of global DNA methylation. In a variety of gastrointestinal (GI) cancers, LINE-1 hypomethylation is strongly associated with a poor prognosis, supporting its potential role as a prognostic biomarker. In this article, we summarize current knowledge regarding LINE-1 methylation and its prognostic impact in GI cancers.
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Wong CC, Li W, Chan B, Yu J. Epigenomic biomarkers for prognostication and diagnosis of gastrointestinal cancers. Semin Cancer Biol 2018; 55:90-105. [PMID: 29665409 DOI: 10.1016/j.semcancer.2018.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development. As such, detection of aberrant DNA methylation is being developed as biomarkers for prognostic and diagnostic purposes in gastrointestinal cancers. Diverse tissue types are suitable for the analyses of methylated DNA, such as tumor tissues, blood, plasma, and stool, and some of these markers are already utilized in the clinical setting. Recent advances in the genome-wide epigenomic approaches are enabling the comprehensive mapping of the cancer methylome, thus providing new avenues for mining novel biomarkers for disease prognosis and diagnosis. Here, we review the current knowledge on DNA methylation biomarkers for the prognostication and non-invasive diagnosis of gastrointestinal cancers and highlight their clinical application.
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Affiliation(s)
- Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Bertina Chan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
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14
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LINE-1 hypomethylation status of circulating cell-free DNA in plasma as a biomarker for colorectal cancer. Oncotarget 2017; 8:11906-11916. [PMID: 28060757 PMCID: PMC5355314 DOI: 10.18632/oncotarget.14439] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer (CRC) is a serious public health problem and non-invasive biomarkers improving diagnosis or therapy are strongly required. Circulating cell-free DNA (cfDNA) has been a promising target for this purpose. In this study, we evaluated the potential of long interspersed nuclear element-1 (LINE-1) hypomethylation as a blood biomarker for CRC. LINE-1 hypomethylation level in plasma cfDNA in 114 CRC patients was retrospectively examined by absolute quantitative analysis of methylated alleles real-time PCR, and was expressed using LINE-1 hypomethylation index (LHI) [unmethylated copy number/ (methylated copy number + unmethylated copy number)]. Greater LHI values indicated enhanced hypomethylation. In our clinicopathological analysis, CRC patients with large tumors (≥6.0 cm), advanced N stage (≥2), and distant metastasis (M1) had statistically significantly higher cfDNA LHI than other CRC patients, suggesting cfDNA LHI as a disease progression biomarker for CRC. Furthermore, early stage I/II (n = 57) as well as advanced stage III/IV (n =57) CRC patients had significantly higher cfDNA LHI than healthy donors (n=53) [stage I/II: median 0.369 (95% confidence interval, 0.360–0.380) vs. 0.332 (0.325–0.339), P < 0.0001; stage III/IV: 0.372 (0.365–0.388) vs. 0.332 (0.325–0.339), P < 0.0001]. The receiver operating characteristic analysis showed that cfDNA LHI had the detection capacity of CRC with area under the curve(AUC) of 0.79 and 0.83 in stage I/II and stage III/IV CRC patients, respectively. The present study demonstrated for the first time the potential of plasma cfDNA LHI as a novel biomarker for CRC, particularly for early stage detection.
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15
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LINE-1 hypomethylation is not a common event in preneoplastic stages of gastric carcinogenesis. Sci Rep 2017; 7:4828. [PMID: 28684753 PMCID: PMC5500474 DOI: 10.1038/s41598-017-05143-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/16/2017] [Indexed: 02/07/2023] Open
Abstract
LINE-1 hypomethylation is widely accepted as marker for global genomic DNA hypomethylation, which is a frequent event in cancer. The aim of the study was to evaluate LINE-1 methylation status at different stages of gastric carcinogenesis and evaluate its prognostic potential in clinical settings. LINE-1 methylation was analyzed in 267 tissue samples by bisulfite pyrosequencing including primary colorectal cancer tissues (T-CRC) with corresponding adjacent colon mucosa (N-CRC), gastric cancer tissues (T-GC) with corresponding gastric mucosa (N-GC), normal gastric tissues (N), chronic non-atrophic and atrophic gastritis (CG). LINE-1 methylation level was lower in both T-GC and T-CRC when compared to paired adjacent tissues. No difference was observed for LINE-1 methylation status between patients with normal gastric mucosa, CG and N-GC. LINE-1 methylation in T-GC but not N-GC tended to correlate with age. Subgroup stratification analysis did not reveal significant differences in LINE-1 methylation status according to tumor stage, anatomical location, histological subtype, differentiation grade. We observed similar overall survival data between patients with high or low LINE-1 levels. In summary, LINE-1 hypomethylation is a characteristic feature in GC but not very common in early preneoplastic stages of gastric carcinogenesis. Prognostic role of LINE-1 hypomethylation in GC patients could not be confirmed in this cohort.
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16
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Min J, Choi B, Han TS, Lee HJ, Kong SH, Suh YS, Kim TH, Choe HN, Kim WH, Hur K, Yang HK. Methylation Levels of LINE-1 As a Useful Marker for Venous Invasion in Both FFPE and Frozen Tumor Tissues of Gastric Cancer. Mol Cells 2017; 40:346-354. [PMID: 28535662 PMCID: PMC5463043 DOI: 10.14348/molcells.2017.0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) is a retrotransposon that contains a CpG island in its 5'-untranslated region. The CpG island of LINE-1 is often heavily methylated in normal somatic cells, which is associated with poor prognosis in various cancers. DNA methylation can differ between formalin-fixed paraffin-embedded (FFPE) and frozen tissues. Therefore, this study aimed to compare the LINE-1 methylation status between the two tissue-storage conditions in gastric cancer (GC) clinical samples and to evaluate whether LINE-1 can be used as an independent prognostic marker for each tissue-storage type. We analyzed four CpG sites of LINE-1 and examined the methylation levels at these sites in 25 FFPE and 41 frozen GC tissues by quantitative bisulfite pyrosequencing. The LINE-1 methylation status was significantly different between the FFPE and frozen GC tissues (p < 0.001). We further analyzed the clinicopathological features in the two groups separately. In the frozen GC tissues, LINE-1 was significantly hypomethylated in GC tissues compared to their corresponding normal gastric mucosa tissues (p < 0.001), and its methylation status was associated with gender, differentiation state, and lymphatic and venous invasion of GC. In the FFPE GC tissues, the methylation levels of LINE-1 differed according to tumor location and venous invasion of GC. In conclusion, LINE-1 can be used as a useful methylation marker for venous invasion in both FFPE and frozen tumor tissues of GC.
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Affiliation(s)
- Jimin Min
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Boram Choi
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Tae-Su Han
- Biotherapeutics Translational Research Center, Division of Biomedical Science, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141,
Korea
| | - Hyuk-Joon Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Tae-Han Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Hwi-Nyeong Choe
- Department of Nursing, Seoul National University Hospital, Seoul 03080,
Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944,
Korea
| | - Han-Kwang Yang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
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17
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Furlan C, Polesel J, Barzan L, Franchin G, Sulfaro S, Romeo S, Colizzi F, Rizzo A, Baggio V, Giacomarra V, Dei Tos AP, Boscolo-Rizzo P, Vaccher E, Dolcetti R, Sigalotti L, Fratta E. Prognostic significance of LINE-1 hypomethylation in oropharyngeal squamous cell carcinoma. Clin Epigenetics 2017; 9:58. [PMID: 28572862 PMCID: PMC5450111 DOI: 10.1186/s13148-017-0357-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/18/2017] [Indexed: 01/13/2023] Open
Abstract
Background Inclusion of new biomarkers to improve a personalized treatment approach for oropharyngeal squamous cell carcinoma (OPSCC) is urgently needed. Hypomethylation of the Long interspersed nucleotide element-1 (LINE-1) repetitive elements, a widely accepted surrogate of overall genomic DNA methylation content, was found to be associated with a poor prognosis in several cancers. At present, no studies have investigated the influence of LINE-1 methylation levels on OPSCC relapse. The main goal of this study was the evaluation of the prognostic value of LINE-1 methylation status in predicting early tumor relapse in locally advanced OPSCC. Methods We retrospectively reviewed a cohort of 77 patients with stage III–IVB OPSCC. Methylation of LINE-1 repetitive sequences was evaluated by real-time quantitative methylation-specific PCR in formalin-fixed paraffin-embedded tissues. The prognostic relevance of LINE-1 methylation was assessed by comparing patients who relapsed within 2 years from the end of treatment (cases) with those who did not (controls). Results were validated in an independent cohort of 33 patients with OPSCC. Results With respect to early OPSCC relapse, the mean LINE-1 methylation level was significantly lower in relapsed cases than in control group (p < 0.01). Interestingly, LINE-1 methylation was lower in relapsed cases than in controls in both HPV16-negative and HPV16-positive OPSCC patients, even if statistical significance was reached only for the former group (p = 0.01). LINE-1 methylation levels were also significantly reduced in relapsed cases with respect to the controls in OPSCC current smokers (p = 0.02). Consistently, in HPV16-negative current smokers, OPSCC relapse was significantly associated with decreased levels of LINE-1 methylation (p = 0.02). Using logistic regression model, we found that patients with hypomethylated LINE-1 were associated with a 3.5 higher risk of early relapse than hypermethylated ones (OR = 3.51; 95% CI 1.03–12.00). Adjustment for potential confounders did not substantially change the risk magnitude. Results from the validation cohort confirmed the lower LINE-1 methylation in patients who early relapsed compared to relapse-free patients. Conclusions LINE-1 hypomethylation is associated with higher risk of early relapse in stage III–IVB OPSCC. Further validation in a prospective study is needed for its application in daily clinical practice.
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Affiliation(s)
- Carlo Furlan
- Division of Radiotherapy, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Jerry Polesel
- Unit of Cancer Epidemiology, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Luigi Barzan
- Department of Surgery, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Giovanni Franchin
- Division of Radiotherapy, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Sandro Sulfaro
- Division of Pathology, General Hospital "S. Maria degli Angeli", Pordenone, Italy
| | - Salvatore Romeo
- Department of Pathology, San Donà di Piave Hospital, San Donà di Piave, Italy
| | - Francesca Colizzi
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Aurora Rizzo
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Vittorio Baggio
- Department of Radiation Oncology, Treviso Regional Hospital, Treviso, Italy
| | - Vittorio Giacomarra
- Unit of Otolaryngology, General Hospital "S. Maria degli Angeli", Pordenone, Italy
| | | | - Paolo Boscolo-Rizzo
- Department of Neurosciences, ENT Clinic and Regional Center for Head and Neck Cancer, Treviso Regional Hospital, University of Padua, Treviso, Italy
| | - Emanuela Vaccher
- Division of Medical Oncology A, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Riccardo Dolcetti
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy.,Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, Australia
| | - Luca Sigalotti
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy.,Institute of Clinical Pathology, University Hospital of Udine, Udine, Italy
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
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18
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Nakamura K, Yoshida N, Baba Y, Kosumi K, Uchihara T, Kiyozumi Y, Ohuchi M, Ishimoto T, Iwatsuki M, Sakamoto Y, Watanabe M, Baba H. Elevated preoperative neutrophil-to-lymphocytes ratio predicts poor prognosis after esophagectomy in T1 esophageal cancer. Int J Clin Oncol 2017; 22:469-475. [PMID: 28097441 DOI: 10.1007/s10147-017-1090-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND The neutrophil-to-lymphocyte ratio (NLR) has been reported to predict the prognosis of various malignant tumors, including esophageal cancer. However, no previous reports have supported the use of the preoperative NLR as an independent prognostic marker focused on superficial (T1) esophageal cancer. The aim of this study was to elucidate the prognostic impact of the preoperative NLR in T1 esophageal cancer. METHODS This retrospective study recruited 245 consecutive patients with T1 esophageal cancer who underwent subtotal esophagectomy between 2005 and 2016. The relationship between the preoperative NLR and clinicopathological characteristics was analyzed. RESULTS The preoperative NLR was significantly higher in male patients (p = 0.029), patients with T1b esophageal cancer (p = 0.0274), and patients with venous vessel invasion (p = 0.0082). In the Kaplan-Meier analysis, the elevated preoperative NLR was significantly associated with a poorer disease-free survival (p < 0.0001) and overall survival (p = 0.0004). In the multivariate Cox model, the elevated preoperative NLR was an independent prognostic marker for both disease-free survival (p = 0.0013) and overall survival (p = 0.0027). CONCLUSION An elevated preoperative NLR predicts poor prognosis in T1 esophageal cancer, suggesting the utility of the NLR as an easily measurable and generally available independent prognostic marker.
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Affiliation(s)
- Kenichi Nakamura
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Keisuke Kosumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Tomoyuki Uchihara
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Yuki Kiyozumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Mayuko Ohuchi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Yasuo Sakamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Kumamoto, Kumamoto, 860-8556, Japan.
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19
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Wen X, Jeong S, Kim Y, Bae JM, Cho NY, Kim JH, Kang GH. Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process. Clin Epigenetics 2017; 9:1. [PMID: 28149329 PMCID: PMC5270344 DOI: 10.1186/s13148-016-0308-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation. To identify whether formalin fixation might impact the measured values of methylation in LINE-1 repetitive elements and whether prolonged heat-induced denaturation of DNA might reduce the artificial increases in measured values caused by formalin fixation, we analyzed paired fresh-frozen (FF) and FFPE xenograft tissue samples for their methylation levels in LINE-1 using a pyrosequencing assay. To further confirm the effect of a heating step in the measurement of LINE-1 or single gene methylation levels, we analyzed FFPE tissue samples of gastric cancer and colorectal cancer for their methylation status in LINE-1 and eight single genes, respectively. Results Formalin fixation led to an increase in the measured values of LINE-1 methylation regardless of the duration of fixation. Prolonged heating of the DNA at 95 °C for 30 min before bisulfite conversion was found (1) to decrease the discrepancy in the measured values between the paired FF and FFPE tissue samples, (2) to decrease the standard deviation of the measured value of LINE-1 methylation levels in FFPE tissue samples of gastric cancer, and (3) to improve the performance in the measurement of single gene methylation levels in FFPE tissue samples of colorectal cancer. Conclusions Formalin fixation leads to artificial increases in the measured values of LINE-1 methylation, and the application of prolonged heating of DNA samples decreases the discrepancy in the measured values of LINE-1 methylation between paired FF and FFPE tissue samples. The application of prolonged heating of DNA samples improves bisulfite conversion-based measurement of LINE-1 or single gene methylation levels in FFPE tissue samples. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0308-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianyu Wen
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Seorin Jeong
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong Mo Bae
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Nam Yun Cho
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jung Ho Kim
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
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20
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Kim EJ, Chung WC, Kim DB, Kim YJ, Lee JM, Jung JH, Lee YK. Long interspersed nuclear element (LINE)-1 methylation level as a molecular marker of early gastric cancer. Dig Liver Dis 2016; 48:1093-7. [PMID: 27375206 DOI: 10.1016/j.dld.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 04/14/2016] [Accepted: 06/06/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND/AIMS This study was performed to examine the state of long interspersed nuclear element (LINE)-1 methylation level in gastric epithelial dysplasias (GEDs) and evaluate as a molecular marker for gastric carcinogenesis when it was compared with RUNX3 expression. METHODS We examined 89 patients with GEDs subcategorized by the Vienna classification - 41 category 3 (low grade) and 48 category 4 (high grade/intramucosal carcinoma) lesion. All tissue samples were evaluated for RUNX3 immunohistochemical staining and the level of LINE-1 methylation. RESULTS The rate of negative expression of RUNX3 in category 4 lesion was significant higher than category 3 (P<0.01). LINE-1 methylation level was statistically different between category 3 and category 4 lesion (P<0.01). Between positive and negative expression of RUNX3 in GEDs, there was a significant difference of LINE-1 methylation level (P<0.01). The area under the ROC curve (AUC) of LINE-1 methylation level for diagnosis of category 4 lesion was 0.88 (95% CI, 0.76-1.00). CONCLUSIONS LINE-1 methylation level was well correlated with the Vienna classification of GED and it had a close relationship with the negative expression of RUNX3 in category 4 lesion. LINE-1 methylation level could be a good candidate for a molecular marker of early gastric cancer.
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Affiliation(s)
- Eun Jung Kim
- Department of Internal Medicine, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea
| | - Woo Chul Chung
- Department of Internal Medicine, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea.
| | - Dae Bum Kim
- Department of Internal Medicine, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea
| | - Yeon-Ji Kim
- Department of Internal Medicine, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea
| | - Ji Min Lee
- Department of Internal Medicine, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea
| | - Ji Han Jung
- Department of Pathology, St. Vincent's Hospital, the College of Medicine, the Catholic University of Korea, Seoul, South Korea
| | - Yun Kyung Lee
- Department of Pathology, Samsung Medical Center of Korea, Seoul, South Korea
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21
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Nishizawa Y, Nishida N, Konno M, Kawamoto K, Asai A, Koseki J, Takahashi H, Haraguchi N, Nishimura J, Hata T, Matsuda C, Mizushima T, Satoh T, Doki Y, Mori M, Ishii H. Clinical Significance of Histone Demethylase NO66 in Invasive Colorectal Cancer. Ann Surg Oncol 2016; 24:841-849. [DOI: 10.1245/s10434-016-5395-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 01/06/2023]
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22
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Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma. Hum Mutat 2016; 37:942-54. [PMID: 27319353 DOI: 10.1002/humu.23027] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/01/2016] [Indexed: 12/16/2022]
Abstract
Squamous cell carcinoma of the esophagus (SCC) is the most common form of esophageal cancer in the world and is typically diagnosed at an advanced stage when successful treatment is challenging. Understanding the mutational profile of this cancer may identify new treatment strategies. Because somatic retrotransposition has been shown in tumors of the gastrointestinal system, we focused on LINE-1 (L1) mobilization as a source of genetic instability in this cancer. We hypothesized that retrotransposition is ongoing in SCC patients. The expression of L1 encoded proteins is necessary for retrotransposition to occur; therefore, we evaluated the expression of L1 open reading frame 1 protein (ORF1p). Using immunohistochemistry, we detected ORF1p expression in all four SCC cases evaluated. Using L1-seq, we identified and validated 74 somatic insertions in eight tumors of the nine evaluated. Of these, 12 insertions appeared to be somatic, not genetically inherited, and sub-clonal (i.e., present in less than one copy per genome equivalent) in the adjacent normal esophagus (NE), while clonal in the tumor. Our results indicate that L1 retrotransposition is active in SCC of the esophagus and that insertion events are present in histologically NE that expands clonally in the subsequent tumor.
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Affiliation(s)
- Tara T Doucet-O'Hare
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland.,National Institutes of Health: National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Reema Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nemanja Rodić
- Dermatology Department, Yale School of Medicine, New Haven, Connecticut
| | - Robert A Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Haig H Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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23
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Ariumi Y. Guardian of the Human Genome: Host Defense Mechanisms against LINE-1 Retrotransposition. Front Chem 2016; 4:28. [PMID: 27446907 PMCID: PMC4924340 DOI: 10.3389/fchem.2016.00028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/14/2016] [Indexed: 11/13/2022] Open
Abstract
Long interspersed element type 1 (LINE-1, L1) is a mobile genetic element comprising about 17% of the human genome, encoding a newly identified ORF0 with unknown function, ORF1p with RNA-binding activity and ORF2p with endonuclease and reverse transcriptase activities required for L1 retrotransposition. L1 utilizes an endonuclease (EN) to insert L1 cDNA into target DNA, which induces DNA double-strand breaks (DSBs). The ataxia-telangiectasia mutated (ATM) is activated by DSBs and subsequently the ATM-signaling pathway plays a role in regulating L1 retrotransposition. In addition, the host DNA repair machinery such as non-homologous end-joining (NHEJ) repair pathway is also involved in L1 retrotransposition. On the other hand, L1 is an insertional mutagenic agent, which contributes to genetic change, genomic instability, and tumorigenesis. Indeed, high-throughput sequencing-based approaches identified numerous tumor-specific somatic L1 insertions in variety of cancers, such as colon cancer, breast cancer, and hepatocellular carcinoma (HCC). In fact, L1 retrotransposition seems to be a potential factor to reduce the tumor suppressive property in HCC. Furthermore, recent study demonstrated that a specific viral-human chimeric transcript, HBx-L1, contributes to hepatitis B virus (HBV)-associated HCC. In contrast, host cells have evolved several defense mechanisms protecting cells against retrotransposition including epigenetic regulation through DNA methylation and host defense factors, such as APOBEC3, MOV10, and SAMHD1, which restrict L1 mobility as a guardian of the human genome. In this review, I focus on somatic L1 insertions into the human genome in cancers and host defense mechanisms against deleterious L1 insertions.
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Affiliation(s)
- Yasuo Ariumi
- Ariumi Project Laboratory, Center for AIDS Research and International Research Center for Medical Sciences, Kumamoto University Kumamoto, Japan
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24
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Chen D, Wen X, Song YS, Rhee YY, Lee TH, Cho NY, Han SW, Kim TY, Kang GH. Associations and prognostic implications of Eastern Cooperative Oncology Group performance status and tumoral LINE-1 methylation status in stage III colon cancer patients. Clin Epigenetics 2016; 8:36. [PMID: 27051466 PMCID: PMC4820986 DOI: 10.1186/s13148-016-0203-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/31/2016] [Indexed: 12/16/2022] Open
Abstract
Background Low methylation status of LINE-1 in tumors is associated with poor survival in patients with colon cancer. Eastern Cooperative Oncology Group performance status (ECOG-PS) is a method to assess the functional status of a patient. We retrospectively evaluated the relationship between ECOG-PS and LINE-1 methylation in colorectal cancers (CRCs) and their prognostic impact in CRC or colon cancer patients receiving adjuvant 5-fluorouracil/leucovorin/oxaliplatin (FOLFOX). Results LINE-1 methylation and microsatellite instability were analyzed in stage III or high-risk stage II CRCs (n = 336). LINE-1 methylation levels were correlated with clinicopathological features, including PS and recurrence-free survival (RFS). The association between the tumoral LINE-1 methylation level and PS was observed (OR = 2.56, P < 0.001). Differences in LINE-1 methylation levels in cancer tissue between the PS 0 and 1 groups were significant in patients older than 60 years (P = 0.001), the overweight body mass index group (P = 0.005), and the stage III disease group (P = 0.008). Prognostic significances of LINE-1 methylation status or combined PS and LINE-1 methylation statuses were identified in stage III colon cancers, not in stage III and high-risk stage II CRCs. Low LINE-1 methylation status was closely associated with a shorter RFS time. The difference between PS(0)/LINE-1(high) and PS(≥1)/LINE-1(low) was significant, which suggests that colon cancer patients with concurrent PS(≥1)/LINE-1 (low) have a higher recurrence rate. Conclusions PS was associated with LINE-1 methylation in CRC tissue. LINE-1 methylation was associated with RFS in stage III colon cancer patients who were treated with adjuvant FOLFOX chemotherapy. Combined PS and LINE-1 methylation status might serve as a useful predictor of cancer recurrence. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0203-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Duo Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xianyu Wen
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Young Seok Song
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ye-Young Rhee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Tae Hun Lee
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Nam Yun Cho
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Won Han
- Division of Oncology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Division of Oncology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
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Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet's Disease Patients. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1393089. [PMID: 27123441 PMCID: PMC4829674 DOI: 10.1155/2016/1393089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/17/2016] [Accepted: 03/06/2016] [Indexed: 11/22/2022]
Abstract
Behcet's Disease (BD) is a multisystem chronic inflammatory disease. The pathology is believed to involve both genetic susceptibility and environmental factors. Hypomethylation leading to activation of interspersed repetitive sequences (IRSs) such as LINE-1 and Alu contributes to the pathologies of autoimmune diseases and cancer. Herein, the epigenetic changes of IRSs in BD were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences (COBRA-IRS). DNA from neutrophils and peripheral blood mononuclear cells (PBMCs) of BD patients with ocular involvement that were in active or inactive states and healthy controls were used to analyze LINE-1 and Alu methylation levels. For Alu sequences, significant differences were observed in the frequency of uCuC alleles between PBMCs of patients and controls (p = 0.03), and between inactive patients and controls (p = 0.03). For neutrophils, the frequency of uCuC was significantly higher between patients and controls (p = 0.006) and between inactive patients and controls (p = 0.002). The partial methylation (uCmC + mCuC) frequencies of Alu between inactive patients and control samples also differed (p = 0.02). No statistically significant differences for LINE-1 were detected. Thus, changes in the methylation level of IRS elements might contribute to the pathogenesis of BD. The role of Alu transcripts in BD should be investigated further.
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Baba Y, Ishimoto T, Kurashige J, Iwatsuki M, Sakamoto Y, Yoshida N, Watanabe M, Baba H. Epigenetic field cancerization in gastrointestinal cancers. Cancer Lett 2016; 375:360-366. [PMID: 26971491 DOI: 10.1016/j.canlet.2016.03.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 02/06/2023]
Abstract
Epigenetic alterations, including aberrant DNA methylation, play an important role in human cancer development. Importantly, epigenetic alterations are reversible and can be targets for therapy or chemoprevention for various types of human cancers. A field for cancerization, or a field defect, is formed by the accumulation of genetic and/or epigenetic alterations in normal-appearing tissues and can correlate with risk of cancer development. Thus, a better understanding of epigenetic field cancerization may represent a useful translational opportunity for cancer risk assessment, including previous history and exposure to carcinogenic factors, and for cancer prevention. In this article, we summarize current knowledge regarding epigenetic field cancerization and its clinical implications in gastrointestinal cancers, including colorectal cancer, gastric cancer and esophageal cancer.
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Affiliation(s)
- Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Junji Kurashige
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Yasuo Sakamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Japan.
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Baba H. Introduction of Surgical Case Reports: the second official journal of the Japanese Surgical Society. Surg Case Rep 2016; 1:2. [PMID: 26943370 PMCID: PMC4747963 DOI: 10.1186/s40792-014-0001-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/03/2014] [Indexed: 11/10/2022] Open
Affiliation(s)
- Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto-city, 860-8556, Japan.
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Song YS, Kim Y, Cho NY, Yang HK, Kim WH, Kang GH. Methylation status of long interspersed element-1 in advanced gastric cancer and its prognostic implication. Gastric Cancer 2016; 19:98-106. [PMID: 25609453 DOI: 10.1007/s10120-015-0463-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/29/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUNDS Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded archival tissue samples. In this study, we assayed the methylation levels at four individual CpG sites of L1 using pyrosequencing and found that the methylation levels at individual CpG sites were different but were closely correlated between paired snap-frozen and formalin-fixed paraffin-embedded tissue samples. We aimed to determine whether low methylation status of L1 is associated with gastric cancer patient prognosis. METHODS We analyzed 434 formalin-fixed paraffin-embedded tissue samples of advanced gastric cancer for their methylation status at four CpG sites of L1 [nucleotide positions 328, 321, 318, and 306 of X58075 (Genbank)] using pyrosequencing, and correlated the L1 methylation level with clinicopathological features. RESULTS Older age at onset, males, tumor location at antrum or lower body, intestinal type, and lymphatic or venous invasion were associated with a low average methylation level of L1 at the two CpG sites 1 and 4 combined. The average methylation level of L1 at CpG sites 1 and 4 combined was significantly lower in microsatellite-stable and EBV-negative gastric cancers than in EBV-positive or microsatellite-unstable gastric cancers. Low methylation status of L1 was independently correlated with shorter overall survival and disease-free survival time. CONCLUSION Our findings indicate that the discrepancy in the methylation level of L1 between fresh tissue and formalin-fixed paraffin-embedded tissue samples depends on the CpG sites considered, and that the methylation status of L1 at CpG sites 1 and 4 combined could be utilized as a prognostic parameter for advanced gastric cancers.
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Affiliation(s)
- Young Seok Song
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Nam Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Han Kwang Yang
- Department of General Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea
| | - Gyeong Hoon Kang
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. .,Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.
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Sahnane N, Magnoli F, Bernasconi B, Tibiletti MG, Romualdi C, Pedroni M, Ponz de Leon M, Magnani G, Reggiani-Bonetti L, Bertario L, Signoroni S, Capella C, Sessa F, Furlan D. Aberrant DNA methylation profiles of inherited and sporadic colorectal cancer. Clin Epigenetics 2015; 7:131. [PMID: 26697123 PMCID: PMC4687378 DOI: 10.1186/s13148-015-0165-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/16/2015] [Indexed: 12/11/2022] Open
Abstract
Background Aberrant DNA methylation has been widely investigated in sporadic colorectal carcinomas (CRCs), and extensive work has been performed to characterize different methylation profiles of CRC. Less information is available about the role of epigenetics in hereditary CRC and about the possible clinical use of epigenetic biomarkers in CRC, regardless of the etiopathogenesis. Long interspersed nucleotide element 1 (LINE-1) hypomethylation and gene-specific hypermethylation of 38 promoters were analyzed in multicenter series of 220 CRCs including 71 Lynch (Lynch colorectal cancer with microsatellite instability (LS-MSI)), 23 CRCs of patients under 40 years in which the main inherited CRC syndromes had been excluded (early-onset colorectal cancer with microsatellite stability (EO-MSS)), and 126 sporadic CRCs, comprising 28 cases with microsatellite instability (S-MSI) and 98 that were microsatellite stable (S-MSS). All tumor methylation patterns were integrated with clinico-pathological and genetic characteristics, namely chromosomal instability (CIN), TP53 loss, BRAF, and KRAS mutations. Results LS-MSI mainly showed absence of extensive DNA hypo- and hypermethylation. LINE-1 hypomethylation was observed in a subset of LS-MSI that were associated with the worse prognosis. Genetically, they commonly displayed G:A transition in the KRAS gene and absence of a CIN phenotype and of TP53 loss. S-MSI exhibited a specific epigenetic profile showing low rates of LINE-1 hypomethylation and extensive gene hypermethylation. S-MSI were mainly characterized by MLH1 methylation, BRAF mutation, and absence of a CIN phenotype and of TP53 loss. By contrast, S-MSS showed a high frequency of LINE-1 hypomethylation and of CIN, and they were associated with a worse prognosis. EO-MSS were a genetically and epigenetically heterogeneous group of CRCs. Like LS-MSI, some EO-MSS displayed low rates of DNA hypo- or hypermethylation and frequent G:A transitions in the KRAS gene, suggesting that a genetic syndrome might still be unrevealed in these patients. By contrast, some EO-MSS showed similar features to those observed in S-MSS, such as LINE-1 hypomethylation, CIN, and TP53 deletion. In all four classes, hypermethylation of ESR1, GATA5, and WT1 was very common. Conclusions Aberrant DNA methylation analysis allows the identification of different subsets of CRCs. This study confirms the potential utility of methylation tests for early detection of CRC and suggests that LINE-1 hypomethylation may be a useful prognostic marker in both sporadic and inherited CRCs. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0165-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Sahnane
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | - Francesca Magnoli
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | - Barbara Bernasconi
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | | | - Chiara Romualdi
- CRIBI Biotechnology Center, University of Padova, Padua, Italy
| | - Monica Pedroni
- Department of Diagnostic Medicine, Clinical and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Maurizio Ponz de Leon
- Department of Diagnostic Medicine, Clinical and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Magnani
- Department of Diagnostic Medicine, Clinical and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Lucio Bertario
- Unit of Hereditary Digestive Tract Tumours, Fondazione IRCCS-Istituto Nazionale dei Tumori Milan, Modena, Italy
| | - Stefano Signoroni
- Unit of Hereditary Digestive Tract Tumours, Fondazione IRCCS-Istituto Nazionale dei Tumori Milan, Modena, Italy
| | - Carlo Capella
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | - Fausto Sessa
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
| | - Daniela Furlan
- Department of Surgical and Morphological Sciences, Section of Anatomic Pathology, University of Insubria, Via O. Rossi, 9, 21100 Varese, Italy
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Kemp JR, Longworth MS. Crossing the LINE Toward Genomic Instability: LINE-1 Retrotransposition in Cancer. Front Chem 2015; 3:68. [PMID: 26734601 PMCID: PMC4679865 DOI: 10.3389/fchem.2015.00068] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/27/2015] [Indexed: 12/17/2022] Open
Abstract
Retrotransposons are repetitive DNA sequences that are positioned throughout the human genome. Retrotransposons are capable of copying themselves and mobilizing new copies to novel genomic locations in a process called retrotransposition. While most retrotransposon sequences in the human genome are incomplete and incapable of mobilization, the LINE-1 retrotransposon, which comprises~17% of the human genome, remains active. The disruption of cellular mechanisms that suppress retrotransposon activity is linked to the generation of aneuploidy, a potential driver of tumor development. When retrotransposons insert into a novel genomic region, they have the potential to disrupt the coding sequence of endogenous genes and alter gene expression, which can lead to deleterious consequences for the organism. Additionally, increased LINE-1 copy numbers provide more chances for recombination events to occur between retrotransposons, which can lead to chromosomal breaks and rearrangements. LINE-1 activity is increased in various cancer cell lines and in patient tissues resected from primary tumors. LINE-1 activity also correlates with increased cancer metastasis. This review aims to give a brief overview of the connections between LINE-1 retrotransposition and the loss of genome stability. We will also discuss the mechanisms that repress retrotransposition in human cells and their links to cancer.
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Affiliation(s)
- Jacqueline R Kemp
- Department of Cellular and Molecular Medicine, Lerner Research Institute of Cleveland Clinic Cleveland, OH, USA
| | - Michelle S Longworth
- Department of Cellular and Molecular Medicine, Lerner Research Institute of Cleveland Clinic Cleveland, OH, USA
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31
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Kosumi K, Baba Y, Ishimoto T, Harada K, Nakamura K, Ohuchi M, Kiyozumi Y, Izumi D, Tokunaga R, Taki K, Higashi T, Miyata T, Kurashige J, Hiyoshi Y, Iwagami S, Sakamoto Y, Miyamoto Y, Yoshida N, Watanabe M, Baba H. Neutrophil/lymphocyte ratio predicts the prognosis in esophageal squamous cell carcinoma patients. Surg Today 2015; 46:405-13. [PMID: 26036223 DOI: 10.1007/s00595-015-1197-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/28/2015] [Indexed: 01/10/2023]
Abstract
PURPOSE As cancer advances, changes in the systemic inflammatory response alter the relative levels of circulating white blood cell types and may contribute to the progression and outcomes of cancer. The aim of the current study is to clarify the impact of the preoperative neutrophil/lymphocyte ratio (NLR) on the prognosis and whether clinical and pathological features modify the influence of the NLR on the prognosis of esophageal squamous cell carcinoma (ESCC) patients. METHODS We retrospectively analyzed the mortality hazard ratios (HRs), including the preoperative NLR, obtained from data for 283 ESCC patients undergoing resection in the period from 2005 to 2011, adjusting for clinical and pathological features. RESULTS A high NLR was associated with a significantly shorter overall survival (p = 0.0018) and cancer-specific survival (p = 0.0097). In the multivariate Cox model, we confirmed that the NLR was an independent prognostic marker for both overall survival (p = 0.0081) and cancer-specific survival (p = 0.028). The outcomes were not significantly modified by other diagnostic factors, including the tumor stage, in the survival analysis. CONCLUSIONS The preoperative NLR is significantly associated with a poor prognosis in patients with ESCC, suggesting the utility of NLR as a cost-effective and broadly available independent prognostic marker of ESCC.
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Affiliation(s)
- Keisuke Kosumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Kazuto Harada
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Kenichi Nakamura
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Mayuko Ohuchi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yuki Kiyozumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Daisuke Izumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Ryuma Tokunaga
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Katsunobu Taki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Takaaki Higashi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Tatsunori Miyata
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Junji Kurashige
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yukiharu Hiyoshi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Shiro Iwagami
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yasuo Sakamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.
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Xu H, Yan Y, Deb S, Rangasamy D, Germann M, Malaterre J, Eder NC, Ward RL, Hawkins NJ, Tothill RW, Chen L, Mortensen NJ, Fox SB, McKay MJ, Ramsay RG. Cohesin Rad21 mediates loss of heterozygosity and is upregulated via Wnt promoting transcriptional dysregulation in gastrointestinal tumors. Cell Rep 2014; 9:1781-1797. [PMID: 25464844 DOI: 10.1016/j.celrep.2014.10.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 08/29/2014] [Accepted: 10/27/2014] [Indexed: 01/22/2023] Open
Abstract
Loss of heterozygosity (LOH) of the adenomatous polyposis coli (APC) gene triggers a series of molecular events leading to intestinal adenomagenesis. Haploinsufficiency of the cohesin Rad21 influences multiple initiating events in colorectal cancer (CRC). We identify Rad21 as a gatekeeper of LOH and a β-catenin target gene and provide evidence that Wnt pathway activation drives RAD21 expression in human CRC. Genome-wide analyses identified Rad21 as a key transcriptional regulator of critical CRC genes and long interspersed element (LINE-1 or L1) retrotransposons. Elevated RAD21 expression tracks with reactivation of L1 expression in human sporadic CRC, implicating cohesin-mediated L1 expression in global genomic instability and gene dysregulation in cancer.
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Affiliation(s)
- Huiling Xu
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Yuqian Yan
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia
| | - Siddhartha Deb
- Pathology Department, PMCC, East Melbourne, VIC 3002, Australia; Victorian Cancer Biobank, Carlton, VIC 3053, Australia
| | - Danny Rangasamy
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Markus Germann
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Jordane Malaterre
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Noreen C Eder
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia
| | - Robyn L Ward
- Prince of Wales Clinical School, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | | | - Richard W Tothill
- Cancer Therapeutics Program, Cancer Research Division, PMCC, East Melbourne, VIC 3002, Australia
| | - Long Chen
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Neil J Mortensen
- Department of Colorectal Surgery, Oxford University Hospitals, Oxford Cancer Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Stephen B Fox
- Department of Pathology, The University of Melbourne, Parkville, VIC 3000, Australia; Pathology Department, PMCC, East Melbourne, VIC 3002, Australia
| | - Michael J McKay
- University of Sydney and North Coast Cancer Institute, Lismore, NSW 2480, Australia
| | - Robert G Ramsay
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre (PMCC), East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia.
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Kim J, Lee Y, Yang M. Environmental exposure to lead (Pb) and variations in its susceptibility. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2014; 32:159-85. [PMID: 24875442 DOI: 10.1080/10590501.2014.907461] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Based on exposure frequency and intrinsic toxicity, lead (Pb) ranks one of the highest priority toxic materials. Continuous regulation of environmental Pb exposure has contributed to dramatically diminished exposure levels of Pb, for example, blood level of Pb. However, the safety level of Pb is not established, as low-level exposure to Pb still shows severe toxicity in high susceptible population and late onset of some diseases from early exposure. In the present study, we focused on food-borne Pb exposure and found broad variations in Pb exposure levels via food among countries. In addition, there are genetic or ethnical variations in Pb-targeted and protective genes. Moreover, various epigenetic alterations were induced by Pb poisoning. Therefore, we suggest a systemic approach including governmental (public) and individual prevention from Pb exposure with continuous biological monitoring and genetic or epigenetic consideration.
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Affiliation(s)
- Jina Kim
- a Research Center for Cell Fate Control, College of Pharmacy , Sookmyung Women's University , Seoul , Republic of Korea
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