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2. Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies

Author

Dugué, Pierre-Antoine, Bodelon, Clara, Chung, Felicia F., Brewer, Hannah R., Ambatipudi, Srikant, Sampson, Joshua N., Cuenin, Cyrille, Chajès, Veronique, Romieu, Isabelle, Fiorito, Giovanni, Sacerdote, Carlotta, Krogh, Vittorio, Panico, Salvatore, Tumino, Rosario, Vineis, Paolo, Polidoro, Silvia, Baglietto, Laura, English, Dallas, Severi, Gianluca, Giles, Graham G., Milne, Roger L., Herceg, Zdenko, Garcia-Closas, Montserrat, Flanagan, James M., and Southey, Melissa C.

Published
2022
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4. Role of DNA methylation‐based mitotic ageing indices in oral cancer development and recurrence.

Author

Ambatipudi, Srikant, Inchanalkar, Mayuri, and Mahimkar, Manoj B.

Subjects
*CYTOGENETICS, *SQUAMOUS cell carcinoma, *RISK assessment, *MOUTH tumors, *CANCER relapse, *RESEARCH funding, *HOSPITALS, *ORAL leukoplakia, *DESCRIPTIVE statistics, *DNA methylation, *FROZEN tissue sections, *PROGRESSION-free survival, *CONFIDENCE intervals, *KARYOKINESIS, *DISEASE risk factors
Abstract

Objective: DNA methylation data can be used to derive mitotic indices from complex tissues. Here, we assessed if the DNA methylation‐derived mitotic ageing indices are associated with oral squamous cell carcinoma (OSCC) development and recurrence‐free survival (RFS). Methods: DNA methylation‐based mitotic indices (MitoticAge, TNSC and hypoSC) were derived using algorithms "MitoticAge" and "epiTOC2" for the discovery [non‐malignant (n = 22), premalignant (n = 22) and OSCC (n = 68) tissues] and validation datasets (GSE87053, GSE136704 and TCGA‐HNSCC). Differences in mitotic indices between non‐malignant, premalignant and OSCC tissues were assessed. Finally, the association between estimated mitotic indices and RFS was evaluated in OSCCs. Results: In the discovery and validation datasets, increased mitotic ageing was observed in OSCC compared to non‐malignant and premalignant oral tissues. HPV‐positive HNSCCs had higher mitotic index TNSC. Mitotic age index hypoSC was associated with RFS in OSCC (p = 0.011, HR 2.61, 95% CI 1.24–5.48). Conclusions: DNA methylation‐derived mitotic indices are associated with OSCC development and RFS. Thus, DNA methylation‐derived mitotic indices may be a valuable research tool to reliably estimate the cumulative number of stem cell divisions in malignant and non‐malignant oral tissues. Future research utilizing mitotic indices for predicting clinical outcomes in OSCC is warranted. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption

Author

Karabegović, Irma, Portilla-Fernandez, Eliana, Li, Yang, Ma, Jiantao, Maas, Silvana C. E., Sun, Daokun, Hu, Emily A., Kühnel, Brigitte, Zhang, Yan, Ambatipudi, Srikant, Fiorito, Giovanni, Huang, Jian, Castillo-Fernandez, Juan E., Wiggins, Kerri L., de Klein, Niek, Grioni, Sara, Swenson, Brenton R., Polidoro, Silvia, Treur, Jorien L., Cuenin, Cyrille, Tsai, Pei-Chien, Costeira, Ricardo, Chajes, Veronique, Braun, Kim, Verweij, Niek, Kretschmer, Anja, Franke, Lude, van Meurs, Joyce B. J., Uitterlinden, André G., de Knegt, Robert J., Ikram, M. Arfan, Dehghan, Abbas, Peters, Annette, Schöttker, Ben, Gharib, Sina A., Sotoodehnia, Nona, Bell, Jordana T., Elliott, Paul, Vineis, Paolo, Relton, Caroline, Herceg, Zdenko, Brenner, Hermann, Waldenberger, Melanie, Rebholz, Casey M., Voortman, Trudy, Pan, Qiuwei, Fornage, Myriam, Levy, Daniel, Kayser, Manfred, and Ghanbari, Mohsen

Published
2021
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7. DNA methylation derived systemic inflammation indices are associated with head and neck cancer development and survival

Author

Ambatipudi, Srikant, Langdon, Ryan, Richmond, Rebecca C., Suderman, Matthew, Koestler, Devin C., Kelsey, Karl T., Kazmi, Nabila, Penfold, Christopher, Ho, Karen M., McArdle, Wendy, Ring, Susan M., Pring, Miranda, Waterboer, Tim, Pawlita, Michael, Gaunt, Tom R., Davey Smith, George, Thomas, Steve, Ness, Andy R., and Relton, Caroline L.

Published
2018
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8. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H.M., Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, and Herceg, Zdenko

Published
2017
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9. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies

Author

Bodelon, Clara, Ambatipudi, Srikant, Dugué, Pierre-Antoine, Johansson, Annelie, Sampson, Joshua N., Hicks, Belynda, Karlins, Eric, Hutchinson, Amy, Cuenin, Cyrille, Chajès, Veronique, Southey, Melissa C., Romieu, Isabelle, Giles, Graham G., English, Dallas, Polidoro, Silvia, Assumma, Manuela, Baglietto, Laura, Vineis, Paolo, Severi, Gianluca, Herceg, Zdenko, Flanagan, James M., Milne, Roger L., and Garcia-Closas, Montserrat

Published
2019
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10. Epigenome-wide association study for lifetime estrogen exposure identifies an epigenetic signature associated with breast cancer risk

Author

Johansson, Annelie, Palli, Domenico, Masala, Giovanna, Grioni, Sara, Agnoli, Claudia, Tumino, Rosario, Giurdanella, Maria Concetta, Fasanelli, Francesca, Sacerdote, Carlotta, Panico, Salvatore, Mattiello, Amalia, Polidoro, Silvia, Jones, Michael E., Schoemaker, Minouk J., Orr, Nick, Tomczyk, Katarzyna, Johnson, Nichola, Fletcher, Olivia, Perduca, Vittorio, Baglietto, Laura, Dugué, Pierre-Antoine, Southey, Melissa C., Giles, Graham G., English, Dallas R., Milne, Roger L., Severi, Gianluca, Ambatipudi, Srikant, Cuenin, Cyrille, Chajès, Veronique, Romieu, Isabelle, Herceg, Zdenko, Swerdlow, Anthony J., Vineis, Paolo, and Flanagan, James M.

Published
2019
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13. Additional file 2 of Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers

Author

Inchanalkar, Mayuri, Srivatsa, Sumana, Ambatipudi, Srikant, Bhosale, Priyanka G., Patil, Asawari, Schäffer, Alejandro A., Beerenwinkel, Niko, and Mahimkar, Manoj B.

Abstract

Additional file 2. Figure S1: Principal component analysisof methylation sites in the promoter region. Figure S2: Distribution of differential methylation at CpG sites in leukoplakia and OSCC. Figure S3: Volcano plots of −log10against the average methylation differenceshowing differentially hypo and hyper methylated promoters in OPL vs normal, tumor vs normal and tumor vs OPL. Figure S4: Distribution of differentially methylated promoters. Figure S5: Venn diagram. Figure S6: Boxplots showing differential promoter methylation between early and advanced-stage OSCC.

Published
2023
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14. Roadmap for investigating epigenome deregulation and environmental origins of cancer

Author

Herceg, Zdenko, Ghantous, Akram, Wild, Christopher P., Sklias, Athena, Casati, Lavinia, Duthie, Susan J., Fry, Rebecca, Issa, Jean‐Pierre, Kellermayer, Richard, Koturbash, Igor, Kondo, Yukata, Lepeule, Johanna, Lima, Sheila C.S., Marsit, Carmen J, Rakyan, Vardhman, Saffery, Richard, Taylor, Jack A., Teschendorff, Andrew E., Ushijima, Toshikazu, Vineis, Paolo, Walker, Cheryl Lyn, Waterland, Robert A., Wiemels, Joe, Ambatipudi, Srikant, Degli Esposti, Davide, and Hernandez‐Vargas, Hector

Published
2018
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15. Identifying and correcting epigenetics measurements for systematic sources of variation

Author

Perrier, Flavie, Novoloaca, Alexei, Ambatipudi, Srikant, Baglietto, Laura, Ghantous, Akram, Perduca, Vittorio, Barrdahl, Myrto, Harlid, Sophia, Ong, Ken K., Cardona, Alexia, Polidoro, Silvia, Nøst, Therese Haugdahl, Overvad, Kim, Omichessan, Hanane, Dollé, Martijn, Bamia, Christina, Huerta, José Marìa, Vineis, Paolo, Herceg, Zdenko, Romieu, Isabelle, and Ferrari, Pietro

Published
2018
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17. Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: A pooled analysis of four prospective studies

Author

Dugué, Pierre-Antoine, primary, Bodelon, Clara, additional, Chung, Felicia, additional, Brewer, Hannah, additional, Ambatipudi, Srikant, additional, Sampson, Joshua, additional, Cuenin, Cyrille, additional, Chajès, Véronique, additional, Romieu, Isabelle, additional, Fiorito, Giovanni, additional, Sacerdote, Carlotta, additional, Krogh, Vittorio, additional, Panico, Salvatore, additional, Tumino, Rosario, additional, Vineis, Paolo, additional, Polidoro, Silvia, additional, Baglietto, Laura, additional, English, Dallas, additional, Severi, Gianluca, additional, Giles, Graham, additional, Milne, Roger, additional, Herceg, Zdenko, additional, Garcia-Closas, Montserrat, additional, Flanagan, James, additional, and Southey, Melissa, additional

Published
2022
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18. Additional file 1 of Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies

Author

Dugué, Pierre-Antoine, Bodelon, Clara, Chung, Felicia F., Brewer, Hannah R., Ambatipudi, Srikant, Sampson, Joshua N., Cuenin, Cyrille, Chajès, Veronique, Romieu, Isabelle, Fiorito, Giovanni, Sacerdote, Carlotta, Krogh, Vittorio, Panico, Salvatore, Tumino, Rosario, Vineis, Paolo, Polidoro, Silvia, Baglietto, Laura, English, Dallas, Severi, Gianluca, Giles, Graham G., Milne, Roger L., Herceg, Zdenko, Garcia-Closas, Montserrat, Flanagan, James M., and Southey, Melissa C.

Abstract

Additional file 1. Supplementary Methods and Tables.

Published
2022
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19. Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption

Author

Karabegović, Irma, primary, Portilla-Fernandez, Eliana, additional, Li, Yang, additional, Ma, Jiantao, additional, Maas, Silvana C.E., additional, Sun, Daokun, additional, Hu, Emily A., additional, Kühnel, Brigitte, additional, Zhang, Yan, additional, Ambatipudi, Srikant, additional, Fiorito, Giovanni, additional, Huang, Jian, additional, Castillo-Fernandez, Juan E., additional, Wiggins, Kerri L., additional, de Klein, Niek, additional, Grioni, Sara, additional, Swenson, Brenton R., additional, Polidoro, Silvia, additional, Treur, Jorien L., additional, Cuenin, Cyrille, additional, Tsai, Pei-Chien, additional, Costeira, Ricardo, additional, Chajes, Veronique, additional, Braun, Kim, additional, Verweij, Niek, additional, Kretschmer, Anja, additional, Franke, Lude, additional, van Meurs, Joyce B.J., additional, Uitterlinden, André G., additional, de Knegt, Robert J., additional, Ikram, M. Arfan, additional, Dehghan, Abbas, additional, Peters, Annette, additional, Schöttker, Ben, additional, Gharib, Sina A., additional, Sotoodehnia, Nona, additional, Bell, Jordana T., additional, Elliott, Paul, additional, Vineis, Paolo, additional, Relton, Caroline, additional, Herceg, Zdenko, additional, Brenner, Hermann, additional, Waldenberger, Melanie, additional, Rebholz, Casey M., additional, Voortman, Trudy, additional, Pan, Qiuwei, additional, Fornage, Myriam, additional, Levy, Daniel, additional, Kayser, Manfred, additional, and Ghanbari, Mohsen, additional

Published
2020
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20. Roadmap for investigating epigenome deregulation and environmental origins of cancer: Epigenetics and cancer

Author

Marsit, Carmen J, Waterland, Robert A., Ghantous, Akram, Kondo, Yukata, Lima, Sheila C.S., Fry, Rebecca, Sklias, Athena, Duthie, Susan J., Lepeule, Johanna, Wiemels, Joe, Degli Esposti, Davide, Hernandez-Vargas, Hector, Ambatipudi, Srikant, Wild, Christopher P., Herceg, Zdenko, Teschendorff, Andrew E., Rakyan, Vardhman, Taylor, Jack A., Vineis, Paolo, Koturbash, Igor, Ushijima, Toshikazu, Casati, Lavinia, Walker, Cheryl Lyn, Kellermayer, Richard, Saffery, Richard, and Issa, Jean-Pierre

Abstract

The interaction between the (epi)genetic makeup of an individual and his/her environmental exposure record (exposome) is accepted as a determinant factor for a significant proportion of human malignancies. Recent evidence has highlighted the key role of epigenetic mechanisms in mediating gene–environment interactions and translating exposures into tumorigenesis. There is also growing evidence that epigenetic changes may be risk factor‐specific (“fingerprints”) that should prove instrumental in the discovery of new biomarkers in cancer. Here, we review the state of the science of epigenetics associated with environmental stimuli and cancer risk, highlighting key developments in the field. Critical knowledge gaps and research needs are discussed and advances in epigenomics that may help in understanding the functional relevance of epigenetic alterations. Key elements required for causality inferences linking epigenetic changes to exposure and cancer are discussed and how these alterations can be incorporated in carcinogen evaluation and in understanding mechanisms underlying epigenome deregulation by the environment.

Published
2018
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22. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Ambatipudi, Srikant Horvath, Steve Perrier, Flavie Cuenin, Cyrille Hernandez-Vargas, Hector Le Calvez-Kelm, Florence and Durand, Geoffroy Byrnes, Graham Ferrari, Pietro Bouaoun, Liacine Sklias, Athena Chajes, Veronique Overvad, Kim and Seven, Gianluca Baglietto, Laura Clavel-Chapelon, Francoise and Kaaks, Rudolf Barrdahl, Myrto Boeing, Heiner Trichopoulou, Antonia Lagiou, Pagona Naska, Androniki Masala, Giovanna and Agnoli, Claudia Polidoro, Silvia Tumino, Rosario Panico, Salvatore Dolle, Martijn Peeters, Petra H. M. Onland-Moret, N. Charlotte Sandanger, Torkjel M. Nost, Therese H. and Weiderpass, Elisabete Quiros, J. Ramon Agudo, Antonio and Rodriguez-Barranco, Miguel Castano, Jose Maria Huerta and Barricarte, Aurelio Fernandez, Ander Matheu Travis, Ruth C. and Vineis, Paolo Muller, David C. Riboli, Elio Gunter, Marc and Romieu, Isabelle Herceg, Zdenko

Abstract

Aim of the study: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as ‘epigenetic clock’, has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. Methods: Here, we profiled DNA methylation changes in a nested case control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples. Intrinsic epigenetic age acceleration (IEAA) was estimated as the residuals by regressing epigenetic age on chronological age. Results: We observed an association between IEAA and breast cancer risk (OR, 1.04; 95% CI, 1.007-1.076, P = 0.016). One unit increase in IEAA was associated with a 4% increased odds of developing breast cancer (OR, 1.04; 95% CI, 1.007-1.076). Stratified analysis based on menopausal status revealed that IEAA was associated with development of postmenopausal breast cancers (OR, 1.07; 95% CI, 1.020-1.11, P = 0.003). In addition, methylome-wide analyses revealed that a higher mean DNA methylation at cytosine-phosphate-guanine (CpG) islands was associated with increased risk of breast cancer development (OR per 1 SD = 1.20; 95 %CI: 1.03-1.40, P = 0.02) whereas mean methylation levels at non-island CpGs were indistinguishable between cancer cases and controls. Conclusion: Epigenetic age acceleration and CpG island methylation have a weak, but statistically significant, association with breast cancer susceptibility. (C) 2017 Elsevier Ltd. All rights reserved.

Published
2017

24. Abstract 3230: Genome-wide blood DNA methylation and breast cancer risk: A meta-analysis of four prospective studies

Author

Bodelon, Clara, primary, Ambatipudi, Srikant, additional, Dugué, Pierre-Antoine, additional, Johansson, Annelie, additional, Sampson, Joshua N., additional, Southey, Melissa C., additional, Giles, Graham G., additional, Polidoro, Silvia, additional, Herceg, Zdenko, additional, Flanagan, James M., additional, Milne, Roger L., additional, and Garcia-Closas, Montserrat, additional

Published
2018
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25. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Epidemiology & Health Economics, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Cancer, Cardiovasculaire Epi Team 3, Brain, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H M, Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass Vainio, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, Herceg, Zdenko, Epidemiology & Health Economics, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Cancer, Cardiovasculaire Epi Team 3, Brain, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H M, Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass Vainio, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, and Herceg, Zdenko

Published
2017

26. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study

Author

Ambatipudi, Srikant Cuenin, Cyrille Hernandez-Vargas, Hector and Ghantous, Akram Le Calvez-Kelm, Florence Kaaks, Rudolf and Barrdahl, Myrto Boeing, Heiner Aleksandrova, Krasimira and Trichopoulou, Antonia Lagiou, Pagona Naska, Androniki Palli, Domenico Krogh, Vittorio Polidoro, Silvia Tumino, Rosario and Panico, Salvatore Bueno-de-Mesquita, Bas Peeters, Petra H. M. Quiros, Jose Ramon Navarro, Carmen Ardanaz, Eva and Dorronsoro, Miren Key, Tim Vineis, Paolo Murphy, Neil and Riboli, Elio Romieu, Isabelle Herceg, Zdenko

Abstract

Aim: Epigenetic changes may occur in response to environmental stressors, and an altered epigenome pattern may represent a stable signature of environmental exposure. Materials & methods: Here, we examined the potential of DNA methylation changes in 910 prediagnostic peripheral blood samples as a marker of exposure to tobacco smoke in a large multinational cohort. Results: We identified 748 CpG sites that were differentially methylated between smokers and nonsmokers, among which we identified novel regionally clustered CpGs associated with active smoking. Importantly, we found a marked reversibility of methylation changes after smoking cessation, although specific genes remained differentially methylated up to 22 years after cessation. Conclusion: Our study has comprehensively cataloged the smoking-associated DNA methylation alterations and showed that these alterations are reversible after smoking cessation.

Published
2016

27. Roadmap for investigating epigenome deregulation and environmental origins of cancer

Author

Herceg, Zdenko, primary, Ghantous, Akram, additional, Wild, Christopher P., additional, Sklias, Athena, additional, Casati, Lavinia, additional, Duthie, Susan J., additional, Fry, Rebecca, additional, Issa, Jean‐Pierre, additional, Kellermayer, Richard, additional, Koturbash, Igor, additional, Kondo, Yukata, additional, Lepeule, Johanna, additional, Lima, Sheila C.S., additional, Marsit, Carmen J, additional, Rakyan, Vardhman, additional, Saffery, Richard, additional, Taylor, Jack A., additional, Teschendorff, Andrew E., additional, Ushijima, Toshikazu, additional, Vineis, Paolo, additional, Walker, Cheryl Lyn, additional, Waterland, Robert A., additional, Wiemels, Joe, additional, Ambatipudi, Srikant, additional, Degli Esposti, Davide, additional, and Hernandez‐Vargas, Hector, additional

Published
2017
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28. Prognostic Classifier Based on Genome-Wide DNA Methylation Profiling in Well-Differentiated Thyroid Tumors

Author

Bisarro dos Reis, Mariana, primary, Barros-Filho, Mateus Camargo, additional, Marchi, Fábio Albuquerque, additional, Beltrami, Caroline Moraes, additional, Kuasne, Hellen, additional, Pinto, Clóvis Antônio Lopes, additional, Ambatipudi, Srikant, additional, Herceg, Zdenko, additional, Kowalski, Luiz Paulo, additional, and Rogatto, Silvia Regina, additional

Published
2017
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29. Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer

Author

Bhosale, Priyanka G., primary, Cristea, Simona, additional, Ambatipudi, Srikant, additional, Desai, Rajiv S., additional, Kumar, Rajiv, additional, Patil, Asawari, additional, Kane, Shubhada, additional, Borges, Anita M., additional, Schäffer, Alejandro A., additional, Beerenwinkel, Niko, additional, and Mahimkar, Manoj B., additional

Published
2017
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30. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

Author

Beltrami, Caroline Moraes, primary, dos Reis, Mariana Bisarro, additional, Barros-Filho, Mateus Camargo, additional, Marchi, Fabio Albuquerque, additional, Kuasne, Hellen, additional, Pinto, Clóvis Antônio Lopes, additional, Ambatipudi, Srikant, additional, Herceg, Zdenko, additional, Kowalski, Luiz Paulo, additional, and Rogatto, Silvia Regina, additional

Published
2017
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31. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study

Author

Ambatipudi, Srikant, Cuenin, Cyrille, Hernandez-Vargas, Hector, Ghantous, Akram, Le Calvez-Kelm, Florence, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Aleksandrova, Krasimira, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Palli, Domenico, Krogh, Vittorio, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Bueno-De-Mesquita, Bas, Peeters, Petra HM, Quirós, José Ramón, Navarro, Carmen, Ardanaz, Eva, Dorronsoro, Miren, Key, Tim, Vineis, Paolo, Murphy, Neil, Riboli, Elio, Romieu, Isabelle, Herceg, Zdenko, Ambatipudi, Srikant, Cuenin, Cyrille, Hernandez-Vargas, Hector, Ghantous, Akram, Le Calvez-Kelm, Florence, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Aleksandrova, Krasimira, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Palli, Domenico, Krogh, Vittorio, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Bueno-De-Mesquita, Bas, Peeters, Petra HM, Quirós, José Ramón, Navarro, Carmen, Ardanaz, Eva, Dorronsoro, Miren, Key, Tim, Vineis, Paolo, Murphy, Neil, Riboli, Elio, Romieu, Isabelle, and Herceg, Zdenko

Published
2016

32. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study

Author

Infection & Immunity, Cancer, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Ambatipudi, Srikant, Cuenin, Cyrille, Hernandez-Vargas, Hector, Ghantous, Akram, Le Calvez-Kelm, Florence, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Aleksandrova, Krasimira, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Palli, Domenico, Krogh, Vittorio, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Bueno-De-Mesquita, Bas, Peeters, Petra HM, Quirós, José Ramón, Navarro, Carmen, Ardanaz, Eva, Dorronsoro, Miren, Key, Tim, Vineis, Paolo, Murphy, Neil, Riboli, Elio, Romieu, Isabelle, Herceg, Zdenko, Infection & Immunity, Cancer, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Ambatipudi, Srikant, Cuenin, Cyrille, Hernandez-Vargas, Hector, Ghantous, Akram, Le Calvez-Kelm, Florence, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Aleksandrova, Krasimira, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Palli, Domenico, Krogh, Vittorio, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Bueno-De-Mesquita, Bas, Peeters, Petra HM, Quirós, José Ramón, Navarro, Carmen, Ardanaz, Eva, Dorronsoro, Miren, Key, Tim, Vineis, Paolo, Murphy, Neil, Riboli, Elio, Romieu, Isabelle, and Herceg, Zdenko

Published
2016

33. Epigenetic Signatures of Cigarette Smoking

Author

Joehanes, Roby, primary, Just, Allan C., additional, Marioni, Riccardo E., additional, Pilling, Luke C., additional, Reynolds, Lindsay M., additional, Mandaviya, Pooja R., additional, Guan, Weihua, additional, Xu, Tao, additional, Elks, Cathy E., additional, Aslibekyan, Stella, additional, Moreno-Macias, Hortensia, additional, Smith, Jennifer A., additional, Brody, Jennifer A., additional, Dhingra, Radhika, additional, Yousefi, Paul, additional, Pankow, James S., additional, Kunze, Sonja, additional, Shah, Sonia H., additional, McRae, Allan F., additional, Lohman, Kurt, additional, Sha, Jin, additional, Absher, Devin M., additional, Ferrucci, Luigi, additional, Zhao, Wei, additional, Demerath, Ellen W., additional, Bressler, Jan, additional, Grove, Megan L., additional, Huan, Tianxiao, additional, Liu, Chunyu, additional, Mendelson, Michael M., additional, Yao, Chen, additional, Kiel, Douglas P., additional, Peters, Annette, additional, Wang-Sattler, Rui, additional, Visscher, Peter M., additional, Wray, Naomi R., additional, Starr, John M., additional, Ding, Jingzhong, additional, Rodriguez, Carlos J., additional, Wareham, Nicholas J., additional, Irvin, Marguerite R., additional, Zhi, Degui, additional, Barrdahl, Myrto, additional, Vineis, Paolo, additional, Ambatipudi, Srikant, additional, Uitterlinden, André G., additional, Hofman, Albert, additional, Schwartz, Joel, additional, Colicino, Elena, additional, Hou, Lifang, additional, Vokonas, Pantel S., additional, Hernandez, Dena G., additional, Singleton, Andrew B., additional, Bandinelli, Stefania, additional, Turner, Stephen T., additional, Ware, Erin B., additional, Smith, Alicia K., additional, Klengel, Torsten, additional, Binder, Elisabeth B., additional, Psaty, Bruce M., additional, Taylor, Kent D., additional, Gharib, Sina A., additional, Swenson, Brenton R., additional, Liang, Liming, additional, DeMeo, Dawn L., additional, O’Connor, George T., additional, Herceg, Zdenko, additional, Ressler, Kerry J., additional, Conneely, Karen N., additional, Sotoodehnia, Nona, additional, Kardia, Sharon L. R., additional, Melzer, David, additional, Baccarelli, Andrea A., additional, van Meurs, Joyce B. J., additional, Romieu, Isabelle, additional, Arnett, Donna K., additional, Ong, Ken K., additional, Liu, Yongmei, additional, Waldenberger, Melanie, additional, Deary, Ian J., additional, Fornage, Myriam, additional, Levy, Daniel, additional, and London, Stephanie J., additional

Published
2016
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34. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study

Author

Ambatipudi, Srikant, primary, Cuenin, Cyrille, additional, Hernandez-Vargas, Hector, additional, Ghantous, Akram, additional, Le Calvez-Kelm, Florence, additional, Kaaks, Rudolf, additional, Barrdahl, Myrto, additional, Boeing, Heiner, additional, Aleksandrova, Krasimira, additional, Trichopoulou, Antonia, additional, Lagiou, Pagona, additional, Naska, Androniki, additional, Palli, Domenico, additional, Krogh, Vittorio, additional, Polidoro, Silvia, additional, Tumino, Rosario, additional, Panico, Salvatore, additional, Bueno-de-Mesquita, Bas, additional, Peeters, Petra HM, additional, Quirós, José Ramón, additional, Navarro, Carmen, additional, Ardanaz, Eva, additional, Dorronsoro, Miren, additional, Key, Tim, additional, Vineis, Paolo, additional, Murphy, Neil, additional, Riboli, Elio, additional, Romieu, Isabelle, additional, and Herceg, Zdenko, additional

Published
2016
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38. 14-3-3γ meditated transport of plakoglobin to the cell border is required for the initiation of desmosome assembly in vitro and in vivo

Author

Sehgal, Lalit, primary, Mukhopadhyay, Amitabha, additional, Rajan, Anandi, additional, Khapare, Nileema, additional, Sawant, Mugdha, additional, Vishal, Sonali S., additional, Bhatt, Khyati, additional, Ambatipudi, Srikant, additional, Antao, Noelle, additional, Alam, Hunain, additional, Gurjar, Mansa, additional, Basu, Srikanta, additional, Mathur, Rohit, additional, Borde, Lalit, additional, Hosing, Amol S., additional, Vaidya, Milind M., additional, Thorat, Rahul, additional, Samaniego, Felipe, additional, Kolthur-Seetharam, Ullas, additional, and Dalal, Sorab N., additional

Published
2014
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43. DNA methylome analysis identifies accelerated epigenetic aging associated with postmenopausal breast cancer susceptibility

Author

Salvatore Panico, Ander Matheu Fernández, Françoise Clavel-Chapelon, Liacine Bouaoun, J. Ramón Quirós, Athena Sklias, Gianluca Severi, Elisabete Weiderpass, Myrto Barrdahl, Ruth C. Travis, Graham Byrnes, Paolo Vineis, Pagona Lagiou, Kim Overvad, Steve Horvath, Flavie Perrier, Antonia Trichopoulou, Rosario Tumino, Heiner Boeing, Therese Haugdahl Nøst, Laura Baglietto, Geoffroy Durand, Giovanna Masala, Pietro Ferrari, Elio Riboli, N. Charlotte Onland-Moret, Srikant Ambatipudi, Veronique Chajes, José María Huerta Castaño, Florence Le Calvez-Kelm, Cyrille Cuenin, Miguel Rodríguez-Barranco, Petra H.M. Peeters, Martijn E.T. Dollé, Androniki Naska, Claudia Agnoli, Torkjel M. Sandanger, Aurelio Barricarte, Silvia Polidoro, Antonio Agudo, Isabelle Romieu, Zdenko Herceg, Rudolf Kaaks, Hector Hernandez-Vargas, Marc J. Gunter, David C. Muller, University Medical Center Utrecht, Imperial College Trust, Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez Vargas, Hector, Le Calvez Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H. M, Onland Moret, N. Charlotte, Sandanger, Torkjel M, Nøst, Therese H, Weiderpass, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C, Vineis, Paolo, Muller, David C, Riboli, Elio, Gunter, Marc, Romieu, Isabelle, and Herceg, Zdenko

Subjects
0301 basic medicine, Oncology, Adult, Epigenomics, medicine.medical_specialty, Cancer Research, Epigenomic, Population, Breast Neoplasms, Biology, Article, Epigenesis, Genetic, 03 medical and health sciences, Breast cancer, Internal medicine, Journal Article, medicine, Humans, Genetic Predisposition to Disease, Epigenetics, Oncology & Carcinogenesis, Prospective cohort study, education, Aged, education.field_of_study, DNA methylation, VDP::Medical disciplines: 700::Clinical medical disciplines: 750::Oncology: 762, Age Factors, Cancer, Biomarker, Middle Aged, medicine.disease, European Prospective Investigation into Cancer and Nutrition, VDP::Medisinske Fag: 700::Klinisk medisinske fag: 750::Onkologi: 762, Postmenopause, 030104 developmental biology, Age acceleration, Case-Control Studies, Female, Biomarkers, Prospective studies, 1112 Oncology And Carcinogenesis
Abstract

Accepted manuscript version, licensed CC BY-NC-ND 4.0. Published version available in European Journal of Cancer, 75, 299-307. Aim of the study: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as ‘epigenetic clock’, has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. Methods: Here, we profiled DNA methylation changes in a nested caseecontrol study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n Z 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples. Intrinsic epigenetic age acceleration (IEAA) was estimated as the residuals by regressing epigenetic age on chronological age. Results: We observed an association between IEAA and breast cancer risk (OR, 1.04; 95% CI, 1.007e1.076, P Z 0.016). One unit increase in IEAA was associated with a 4% increased odds of developing breast cancer (OR, 1.04; 95% CI, 1.007e1.076). Stratified analysis based on menopausal status revealed that IEAA was associated with development of postmenopausal breast cancers (OR, 1.07; 95% CI, 1.020e1.11, P Z 0.003). In addition, methylome-wide analyses revealed that a higher mean DNA methylation at cytosine-phosphate-guanine (CpG) islands was associated with increased risk of breast cancer development (OR per 1 SD Z 1.20; 95 %CI: 1.03e1.40, P Z 0.02) whereas mean methylation levels at non-island CpGs were indistinguishable between cancer cases and controls. Conclusion: Epigenetic age acceleration and CpG island methylation have a weak, but statistically significant, association with breast cancer susceptibility.

Published
2017

44. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study

Author

Androniki Naska, Rosario Tumino, Salvatore Panico, Eva Ardanaz, Bas Bueno-de-Mesquita, Krasimira Aleksandrova, Akram Ghantous, Paolo Vineis, Timothy J. Key, Neil Murphy, Florence Le Calvez-Kelm, Petra H.M. Peeters, Heiner Boeing, Antonia Trichopoulou, José Ramón Quirós, Cyrille Cuenin, Isabelle Romieu, Elio Riboli, Miren Dorronsoro, Carmen Navarro, Silvia Polidoro, Myrto Barrdahl, Srikant Ambatipudi, Domenico Palli, Pagona Lagiou, Hector Hernandez-Vargas, Vittorio Krogh, Zdenko Herceg, Rudolf Kaaks, Ambatipudi, Srikant, Cuenin, Cyrille, Hernandez Vargas, Hector, Ghantous, Akram, Le Calvez Kelm, Florence, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Aleksandrova, Krasimira, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Palli, Domenico, Krogh, Vittorio, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Bueno de Mesquita, Ba, Peeters, Petra Hm, Quirós, José Ramón, Navarro, Carmen, Ardanaz, Eva, Dorronsoro, Miren, Key, Tim, Vineis, Paolo, Murphy, Neil, Riboli, Elio, Romieu, Isabelle, Herceg, Zdenko, Commission of the European Communities, University Medical Center Utrecht, and Imperial College Trust

Subjects
0301 basic medicine, Adult, Male, tobacco smoking, prospective cohort, epigenetic signature, DNA methylome, Cancer Research, medicine.medical_treatment, Physiology, Biology, Tobacco smoke, Epigenesis, Genetic, 03 medical and health sciences, medicine, Genetics, Journal Article, Tobacco Smoking, Humans, Epigenetics, Prospective Studies, Aged, Environmental exposure, Epigenome, Methylation, Sequence Analysis, DNA, DNA Methylation, Middle Aged, 030104 developmental biology, CpG site, DNA methylation, Smoking cessation, CpG Islands, Female, Smoking Cessation
Abstract

Aim: Epigenetic changes may occur in response to environmental stressors, and an altered epigenome pattern may represent a stable signature of environmental exposure. Materials & methods: Here, we examined the potential of DNA methylation changes in 910 prediagnostic peripheral blood samples as a marker of exposure to tobacco smoke in a large multinational cohort. Results: We identified 748 CpG sites that were differentially methylated between smokers and nonsmokers, among which we identified novel regionally clustered CpGs associated with active smoking. Importantly, we found a marked reversibility of methylation changes after smoking cessation, although specific genes remained differentially methylated up to 22 years after cessation. Conclusion: Our study has comprehensively cataloged the smoking-associated DNA methylation alterations and showed that these alterations are reversible after smoking cessation.

Published
2016

45. Burnout, stress, and their correlates among bank employees of South India: a cross-sectional study.

Author

Vinod G and Ambatipudi S

Abstract

Background: The banking sector is one of the job sectors that experience high stress, workload, complex interpersonal relationships, and job burnout as it involves interaction with the public and financial responsibilities, which leads to high burnout and stress. The present study was conducted to assess the prevalence of burnout and stress among bank employees and to find the associated factors., Methods: This cross-sectional survey was conducted among 282 bank employees of Kollam district, Kerala, India. Data was collected using a self-administered questionnaire related to the socio-demographic and professional details. We used the Oldenburg Burnout Inventory (OLBI) to screen for burnout levels. Depression Anxiety Stress Scale (DASS 21) to screen for the levels of depression, anxiety, and stress among study participants. Descriptive statistics were used to summarize the data, and logistic regression was used to identify the factors associated with the levels of burnout and stress., Results: Of 282 study participants, moderate to high levels of burnout were observed in 232 participants (82.2%), and 74 participants (26.2%) had mild to extremely severe levels of stress. Daily average working duration showed an association with higher levels of burnout (adjusted odds ratio [ORAdj]: 2.391; 95% confidence interval [CI]: 1.12-5.10) and stress (ORAdj: 3.37; 95% CI: 1.58-7.16)., Conclusions: A high prevalence of burnout and stress was observed in the present study. The duration of working hours was associated with both burnout and stress. Therefore, regulating the working hours may help adequately manage stress and burnout, thereby improving the mental health of bank employees.

Published
2024
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