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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Dynamic Changes in Circulating Methylated Markers in Response to Antitumor Therapy of Rectal Cancer. J Gastrointest Cancer 2024:10.1007/s12029-024-01066-y. [PMID: 38829580 DOI: 10.1007/s12029-024-01066-y] [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] [Accepted: 05/05/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Rectal cancer (RC) occupies a leading position in the structure of oncological morbidity and mortality. Aberrant methylation of tumor-suppressor genes and hypomethylation of retrotransposons were shown to be detectable in cell-free DNA, circulating in the blood (cfDNA) of cancer patients, indicating the possibility to use them as diagnostic and prognosis markers. PURPOSE Evaluation of the changes in the methylation level of LINE-1 elements and SEPTIN9 and IKZF1 genes in the cell-surface-bound cfDNA (csb-cfDNA) from the blood of RC patients after antitumor therapy at a long-term follow-up. METHODS Blood samples were obtained from RC patients (n = 25) before treatment, after preoperative chemotherapy (3 courses according to the XELOX scheme), 10-15 days after surgery, and every 3 months during 12 months of dynamic observation. The methylation level of LINE-1, SEPTIN9, and IKZF1 in the csb-cfDNA was evaluated by quantitative methyl-specific PCR. RESULTS The LINE-1 methylation level in the csb-cfDNA increased 1.6 times in RC patients after chemotherapy and 3 times after tumor resection versus methylation level before therapy. The SEPTIN9 gene methylation level in the csb-cfDNA decreased by 1.7 times in RC patients after chemotherapy and by 2.3 times after tumor resection compared with the values before the treatment. The IKZF1 gene methylation level decreased by 2 times in RC patients after combined therapy. Notably, all patients with relapses (n = 5) showed an increase in methylation level for the SEPTIN9 and IKZF1 genes and a decrease of methylation level for the LINE-1 elements by 2 times or more in comparison with the level 10-15 days after surgery. There were no changes in the circulating SEPTIN9, IKZF1, and LINE-1 methylation levels during the 12-month follow-up period after the combined therapy of RC patients (n = 20) without relapses. CONCLUSION The results indicate that SEPTIN9, IKZF1, and LINE-1 methylation levels in the csb-cfDNA are potential markers of the effectiveness of antitumor therapy and early detection of relapse in RC patients.
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Affiliation(s)
- Anastasia A Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia.
| | - Elena Yu Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087, Novosibirsk, Russia
| | - Anastasia I Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050, Tomsk, Russia
| | - Anna S Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Dmitry N Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Alexey Yu Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Sergey A Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Nadezhda V Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050, Tomsk, Russia
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Reddam A, Bollati V, Wu H, Favero C, Tarantini L, Hoxha M, Comfort N, Gold DR, Phipatanakul W, Baccarelli AA. Air pollution and human endogenous retrovirus methylation in the school inner-city asthma intervention study. Toxicol Sci 2023; 193:166-174. [PMID: 37042721 PMCID: PMC10230279 DOI: 10.1093/toxsci/kfad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are transposable genomic elements generally repressed through DNA methylation. HERVs can be demethylated and expressed in response to environmental stimuli. Therefore, more research is needed to understand the influence of environmental exposures on HERV methylation. Air pollutants are commonly linked with global hypomethylation, and as HERVs comprise of nearly 8% of repetitive elements in the human genome, our objective was to examine the association between air pollutant exposure and HERV methylation. We investigated 180 students with asthma participating in the School Inner-City Asthma Intervention Study, which evaluated the efficacy of classroom air filters and school-wide pest management on air pollutant/allergen exposure and asthma. Both air pollutants measured in classrooms and asthma outcomes assessed by surveys were collected pre- and post-intervention. Buccal swabs were also collected pre- and post-intervention, and methylation levels from 9 transposable genomic elements (HERV-E, -FRD, -K, -L, -R, -W, -9, and HRES and LINE1) were measured. Adjusting for relevant covariates, the overall air pollutant mixture was cross-sectionally associated with higher HERV-W and lower HERV-L and LINE1 methylation. Coarse PM was cross-sectionally associated with higher HERV-K methylation and CO2 with lower LINE1 methylation. These results suggest that exposure to air pollutants is associated with HERV-W and HERV-K hypermethylation and HERV-L and LINE1 hypomethylation in children with asthma. Future studies are needed to characterize the links between HERV methylation and possible adverse outcomes.
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Affiliation(s)
- Aalekhya Reddam
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Haotian Wu
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Chiara Favero
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Letizia Tarantini
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Mirjam Hoxha
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Nicole Comfort
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Wanda Phipatanakul
- Asthma Clinical Research Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
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Issah I, Arko-Mensah J, Rozek LS, Zarins KR, Agyekum TP, Dwomoh D, Basu N, Batterman S, Robins TG, Fobil JN. Global DNA (LINE-1) methylation is associated with lead exposure and certain job tasks performed by electronic waste workers. Int Arch Occup Environ Health 2021; 94:1931-1944. [PMID: 34148106 DOI: 10.1007/s00420-021-01733-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE This study assessed the associations between blood and urine levels of toxic metals; cadmium (Cd) and lead (Pb), and methylation levels of the LINE-1 gene among e-waste and control populations in Ghana. METHODS The study enrolled 100 male e-waste workers and 51 all-male non-e-waste workers or controls. The concentrations of Cd and Pb were measured in blood and urine using inductively coupled plasma mass spectrometry, while LINE1 methylation levels were assessed by pyrosequencing of bisulfite-converted DNA extracted from whole blood. Single and multiple metals linear regression models were used to determine the associations between metals and LINE1 DNA methylation. RESULTS Blood lead (BPb) and urine lead (UPb) showed higher median concentrations among the e-waste workers than the controls (76.82 µg/L vs 40.25 µg/L, p ≤ 0.001; and 6.89 µg/L vs 3.43 µg/L, p ≤ 0.001, respectively), whereas blood cadmium (BCd) concentration was lower in the e-waste workers compared to the controls (0.59 µg/L vs 0.81 µg/L, respectively, p = 0.003). There was no significant difference in LINE1 methylation between the e-waste and controls (85.16 ± 1.32% vs 85.17 ± 1.11%, p = 0.950). In our single metal linear regression models, BPb was significantly inversely associated with LINE1 methylation in the control group (βBPb = - 0.027, 95% CI - 0.045, - 0.010, p = 0.003). In addition, a weak association between BPb and LINE1 was observed in the multiple metals analysis in the e-waste worker group (βBPb = - 0.005, 95% CI - 0.011, 0.000, p = 0.058). CONCLUSION Continuous Pb exposure may interfere with LINE1 methylation, leading to epigenetic alterations, thus serving as an early epigenetic marker for future adverse health outcomes.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana.
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Duah Dwomoh
- Department of Biostatistics, School of Public Health, University of Ghana, P.O. Box LG13, Accra, Ghana
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
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Anghel SA, Ioniță-Mîndrican CB, Luca I, Pop AL. Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review. Cancers (Basel) 2021; 13:4965. [PMID: 34638449 PMCID: PMC8508438 DOI: 10.3390/cancers13194965] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
In CRC, screening compliance is decreased due to the experienced discomfort associated with colonoscopy, although this method is the gold standard in terms of sensitivity and specificity. Promoter DNA methylation (hypomethylation or hypermethylation) has been linked to all CRC stages. Study objectives: to systematically review the current knowledge on approved biomarkers, reveal new potential ones, and inspect tactics that can improve performance. This research was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines; the risk of bias was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies criteria (QUADAS-2). The Web of Science® Core Collection, MEDLINE® and Scopus® databases were searched for original articles published in peer-reviewed journals with the specific keywords "colorectal cancer", "early detection", "early-stage colorectal cancer", "epigenetics", "biomarkers", "DNA methylation biomarkers", "stool or blood or tissue or biopsy", "NDRG4", "BMP3", "SEPT9", and "SDC2". Based on eligibility criteria, 74 articles were accepted for analysis. mSDC2 and mSEPT9 were frequently assessed in studies, alone or together as part of the ColoDefense panel test-the latter with the greatest performance. mBMP3 may not be an appropriate marker for detecting CRC. A panel of five methylated binding sites of the CTCF gene holds the promise for early-stage specific detection of CRC. CRC screening compliance and accuracy can be enhanced by employing a stool mt-DNA methylation test.
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Affiliation(s)
- Sorina Andreea Anghel
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
- Department of Toxicology, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020945 Bucharest, Romania
| | - Ioana Luca
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
| | - Anca Lucia Pop
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
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Vasilyev SA, Markov AV, Vasilyeva OY, Tolmacheva EN, Zatula LA, Sharysh DV, Zhigalina DI, Demeneva VV, Lebedev IN. Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter. MethodsX 2021; 8:101445. [PMID: 34434857 PMCID: PMC8374674 DOI: 10.1016/j.mex.2021.101445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022] Open
Abstract
The methylation index of the LINE-1 promoter is one of the most commonly used markers for assessing the global level of genome methylation in various human cells and tissues. We developed an NGS-based protocol for DNA methylation analysis of the LINE-1 retrotransposon promoter. This approach allows assessment of the DNA methylation index of 19 CpG sites in the LINE-1 promoter that have the highest tissue- or tumor-specific variability. The method provides a DNA methylation profile for analyzing either the methylation index of each CpG site independently or the mean DNA methylation index across the LINE-1 promoter. The results obtained using the developed method corresponded well to the level of methylation assessed using a commercially available kit for DNA pyrosequencing. In addition, our method provides much more information: 1) the DNA methylation profile of a significant part of the LINE-1 promoter and 2) the level of DNA methylation at individual LINE-1 loci in the genome. The method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter can be used in large-scale studies of the global level of genome methylation in normal human cells or tumors. To accomplish this, we modified the targeted massive parallel sequencing method based on 16S Metagenomic Sequencing Library Preparation protocol (Illumina, USA) by:Introduction of the stage of bisulfite conversion of DNA. Development of specific primers for the LINE-1 sequence.
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Affiliation(s)
- Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Anton V Markov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | | | - Diana V Sharysh
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Victoria V Demeneva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
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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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Turner MC, Andersen ZJ, Baccarelli A, Diver WR, Gapstur SM, Pope CA, Prada D, Samet J, Thurston G, Cohen A. Outdoor air pollution and cancer: An overview of the current evidence and public health recommendations. CA Cancer J Clin 2020; 70:10.3322/caac.21632. [PMID: 32964460 PMCID: PMC7904962 DOI: 10.3322/caac.21632] [Citation(s) in RCA: 267] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/24/2022] Open
Abstract
Outdoor air pollution is a major contributor to the burden of disease worldwide. Most of the global population resides in places where air pollution levels, because of emissions from industry, power generation, transportation, and domestic burning, considerably exceed the World Health Organization's health-based air-quality guidelines. Outdoor air pollution poses an urgent worldwide public health challenge because it is ubiquitous and has numerous serious adverse human health effects, including cancer. Currently, there is substantial evidence from studies of humans and experimental animals as well as mechanistic evidence to support a causal link between outdoor (ambient) air pollution, and especially particulate matter (PM) in outdoor air, with lung cancer incidence and mortality. It is estimated that hundreds of thousands of lung cancer deaths annually worldwide are attributable to PM air pollution. Epidemiological evidence on outdoor air pollution and the risk of other types of cancer, such as bladder cancer or breast cancer, is more limited. Outdoor air pollution may also be associated with poorer cancer survival, although further research is needed. This report presents an overview of outdoor air pollutants, sources, and global levels, as well as a description of epidemiological evidence linking outdoor air pollution with cancer incidence and mortality. Biological mechanisms of air pollution-derived carcinogenesis are also described. This report concludes by summarizing public health/policy recommendations, including multilevel interventions aimed at individual, community, and regional scales. Specific roles for medical and health care communities with regard to prevention and advocacy and recommendations for further research are also described.
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Affiliation(s)
- Michelle C. Turner
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada
| | - Zorana J. Andersen
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, United States
| | - W. Ryan Diver
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, United States
| | - Susan M. Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, United States
| | - C. Arden Pope
- Department of Economics, Brigham Young University, Provo, Utah, United States
| | - Diddier Prada
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, United States
- Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Jonathan Samet
- Colorado School of Public Health, Aurora, Colorado, United States
| | - George Thurston
- New York University School of Medicine, New York, New York, United States
| | - Aaron Cohen
- Health Effects Institute, Boston, Massachusetts, United States
- Institute for Health Metrics and Evaluation, Seattle, Washington, United States
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