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1. DNA demethylation triggers cell free DNA release in colorectal cancer cells

Author

Valeria Pessei, Marco Macagno, Elisa Mariella, Noemi Congiusta, Vittorio Battaglieri, Paolo Battuello, Marco Viviani, Giulia Gionfriddo, Simona Lamba, Annalisa Lorenzato, Daniele Oddo, Fariha Idrees, Alessandro Cavaliere, Alice Bartolini, Simonetta Guarrera, Michael Linnebacher, Laura Monteonofrio, Luca Cardone, Michele Milella, Andrea Bertotti, Silvia Soddu, Elena Grassi, Giovanni Crisafulli, Alberto Bardelli, Ludovic Barault, and Federica Di Nicolantonio

Subjects
Colorectal cancer, cfDNA, Cell cycle, Cell death, MSI, DNA methylation, Medicine, Genetics, QH426-470
Abstract

Abstract Background Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release. Methods We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (N = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release. Results Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding. Conclusions Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.

Published
2024
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2. Cancer-associated foam cells hamper protective T cell immunity and favor tumor progression in human colon carcinogenesis

Author

Barbara Vergani, Massimo Milione, Marco Vitellaro, Giulio Ferrero, Veronica Huber, Luca Lalli, Agata Cova, Paola Frati, Flavio Arienti, Licia Rivoltini, Simonetta Guarrera, Laura Cattaneo, Luca Sorrentino, Elena Daveri, Elena Casiraghi, Marta Zorza, Manuela Gariboldi, Patrizia Pasanisi, Daniele Morelli, Paola A Corsetto, Angela M Rizzo, Martina Stroscia, Vincenzo Lagano, Giovanna Sabella, and Biagio E Leone

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background Colorectal cancer (CRC) remains a significant healthcare burden worldwide, characterized by a complex interplay between obesity and chronic inflammation. While the relationship between CRC, obesity and altered lipid metabolism is not fully understood, there are evidences suggesting a link between them. In this study, we hypothesized that dysregulated lipid metabolism contributes to local accumulation of foam cells (FC) in CRC, which in turn disrupts antitumor immunosurveillance.Methods Tumor infiltrating FC and CD8+ were quantified by digital pathology in patients affected by T2–T4 CRC with any N stage undergoing radical upfront surgery (n=65) and correlated with patients’ clinical outcomes. Multiparametric high-resolution flow cytometry analysis and bulk RNAseq of CRC tissue were conducted to evaluate the phenotype and transcriptomic program of immune cell infiltrate in relation to FC accumulation. The immunosuppressive effects of FC and mechanistic studies on FC-associated transforming growth factor-beta (TGF-β) and anti-PD-L1 inhibition were explored using an in-vitro human model of lipid-engulfed macrophages.Results FC (large CD68+ Bodipy+ macrophages) accumulated at the tumor margin in CRC samples. FChigh tumors exhibited reduced CD8+ T cells and increased regulatory T cells (Tregs). Functional transcriptional profiling depicted an immunosuppressed milieu characterized by reduced interferon gamma, memory CD8+ T cells, and activated macrophages mirrored by increased T-cell exhaustion and Treg enrichment. Furthermore, FChigh tumor phenotype was independent of standard clinical factors but correlated with high body mass index (BMI) and plasma saturated fatty acid levels. In CD8low tumors, the FChigh phenotype was associated with a 3-year disease-free survival rate of 8.6% compared with 28.7% of FClow (p=0.001). In-vitro studies demonstrated that FC significantly impact on CD8 proliferation in TFG-β dependent manner, while inhibition of TGF-β FC-related factors restored antitumor immunity.Conclusions FC exert immunosuppressive activity through a TGF-β-related pathway, resulting in a CD8-excluded microenvironment and identifying immunosuppressed tumors with worse prognosis in patients with primary CRC. FC association with patient BMI and dyslipidemia might explain the link of CRC with obesity, and offers novel therapeutic and preventive perspectives in this specific clinical setting.

Published
2024
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3. Impaired neutrophil-mediated cell death drives Ewing’s Sarcoma in the background of Down syndrome

Author

Serena Peirone, Elisa Tirtei, Anna Campello, Caterina Parlato, Simonetta Guarrera, Katia Mareschi, Elena Marini, Sebastian Dorin Asaftei, Luca Bertero, Mauro Papotti, Francesca Priante, Sarah Perrone, Matteo Cereda, and Franca Fagioli

Subjects
Ewing Sarcoma, Down syndrome, paediatric bone sarcoma, genomics, transcriptomics, neutrophils, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

IntroductionEwing Sarcoma (EWS) has been reported in seven children with Down syndrome (DS). To date, a detailed assessment of this solid tumour in DS patients is yet to be made.MethodsHere, we characterise a chemo-resistant mediastinal EWS in a 2-year-old DS child, the youngest ever reported case, by exploiting sequencing approaches.ResultsThe tumour showed a neuroectodermal development driven by the EWSR1-FLI1 fusion. The inherited myeloperoxidase deficiency of the patient caused failure of neutrophil-mediated cell death and promoted genomic instability.DiscussionIn this context, the tumour underwent genome-wide near haploidisation resulting in a massive overexpression of pro-inflammatory cytokines. Recruitment of defective neutrophils fostered rapid evolution of this EWS.

Published
2024
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4. Integrative genomic and transcriptomic analyses illuminate the ontology of HER2-low breast carcinomas

Author

Enrico Berrino, Laura Annaratone, Sara Erika Bellomo, Giulio Ferrero, Amedeo Gagliardi, Alberto Bragoni, Dora Grassini, Simonetta Guarrera, Caterina Parlato, Laura Casorzo, Mara Panero, Ivana Sarotto, Silvia Giordano, Matteo Cereda, Filippo Montemurro, Riccardo Ponzone, Nicola Crosetto, Alessio Naccarati, Anna Sapino, and Caterina Marchiò

Subjects
Breast cancer, HER2, HER2-low, Heterogeneity, Classification, Mutation, Medicine, Genetics, QH426-470
Abstract

Abstract Background The “HER2-low” nomenclature identifies breast carcinomas (BCs) displaying a HER2 score of 1+/2+ in immunohistochemistry and lacking ERBB2 amplification. Whether HER2-low BCs (HLBCs) constitute a distinct entity is debated. Methods We performed DNA and RNA high-throughput analysis on 99 HLBC samples (n = 34 cases with HER2 score 1+/HLBC-1, n = 15 cases with HER2 score 2+ and ERBB2 not amplified/HLBC-2N, and n = 50 cases with score 2+ and ERBB2 copy number in the equivocal range/HLBC-2E). We compared the mutation rates with data from 1317 samples in the Memorial Sloan-Kettering Cancer Center (MSKCC) BC cohort and gene expression data with those from an internal cohort of HER2-negative and HER2-positive BCs. Results The most represented mutations affected PIK3CA (31/99, 31%), GATA3 (18/99, 18%), TP53 (17/99, 17%), and ERBB2 (8/99, 8%, private to HLBC-2E). Tumor mutational burden was significantly higher in HLBC-1 compared to HLBC-2E/N (P = 0.04). Comparison of mutation spectra revealed that HLBCs were different from both HER2-negative and HER2-positive BCs, with HLBC-1 resembling more HER2-negative tumors and HLBC-2 mutationally related to HER2-addicted tumors. Potentially actionable alterations (annotated by using OncoKB/ESCAT classes) affected 52 patients. Intra-group gene expression revealed overlapping features between HLBC-1 and control HER2-negative BCs, whereas the HLBC-2E tumors showed the highest diversity overall. The RNA-based class discovery analysis unveiled four subsets of tumors with (i) lymphocyte activation, (ii) unique enrichment in HER2-related features, (iii) stromal remodeling alterations, and (iv) actionability of PIK3CA mutations (LAURA classification). Conclusions HLBCs harbor distinct genomic features when compared with HER2-positive and HER2-negative BCs; however, differences across IHC classes were also unveiled thus dissecting the full picture of heterogeneity across HER2-low disease. The HLBC-2E category harbors most distinctive features, whereas HLBC-1 seems superimposable to HER2-negative disease. Further studies are needed to ascertain whether the four genomic-driver classes of the LAURA classification hold prognostic and/or predictive implications.

Published
2022
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5. MicroRNA 146a is associated with diabetic complications in type 1 diabetic patients from the EURODIAB PCS

Author

Federica Barutta, Beatrice Corbetta, Stefania Bellini, Simonetta Guarrera, Giuseppe Matullo, Michela Scandella, Casper Schalkwijk, Coen D. Stehouwer, Nish Chaturvedi, Sabita S. Soedamah-Muthu, Marilena Durazzo, and Gabriella Gruden

Subjects
MicroRNAs, Type 1 diabetes, Retinopathy, Cardiovascular diseases, Medicine
Abstract

Abstract Background MicroRNA-146a-5p (miR-146a-5p) is a key regulator of inflammatory processes. Expression of miR-146a-5p is altered in target organs of diabetic complications and deficiency of miR-146a-5p has been implicated in their pathogenesis. We investigated if serum miR-146a-5p levels were independently associated with micro/macrovascular complications of type 1 diabetes (DM1). Methods A nested case–control study from the EURODIAB PCS of 447 DM1 patients was performed. Cases (n = 294) had one or more complications of diabetes, whereas controls (n = 153) did not have any complication. Total RNA was isolated from all subjects and miR-146a-5p levels measured by qPCR. Both the endogenous controls U6 snRNA and the spike (Cel-miR-39) were used to normalize the results. Logistic regression analysis was carried out to investigate the association of miR-146a-5p with diabetes complications. Results MiR-146a-5p levels were significantly lower in cases [1.15 (0.32–3.34)] compared to controls [1.74 (0.44–6.74) P = 0.039]. Logistic regression analysis showed that levels of miR-146a-5p in the upper quartile were inversely associated with reduced odds ratio (OR) of all complications (OR 0.34 [95% CI 0.14–0.76]) and particularly with cardiovascular diseases (CVD) (OR 0.31 [95% CI 0.11–0.84]) and diabetic retinopathy (OR 0.40 [95% CI 0.16–0.99]), independently of age, sex, diabetes duration, A1c, hypertension, AER, eGFR, NT-proBNP, and TNF-α. Conclusions In this large cohort of DM1 patients, we reported an inverse and independent association of miR-146a-5p with diabetes chronic complications and in particular with CVD and retinopathy, suggesting that miR-146a-5p may be a novel candidate biomarker of DM1 complications.

Published
2021
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6. Associations of autozygosity with a broad range of human phenotypes

Author

David W Clark, Yukinori Okada, Kristjan H S Moore, Dan Mason, Nicola Pirastu, Ilaria Gandin, Hannele Mattsson, Catriona L K Barnes, Kuang Lin, Jing Hua Zhao, Patrick Deelen, Rebecca Rohde, Claudia Schurmann, Xiuqing Guo, Franco Giulianini, Weihua Zhang, Carolina Medina-Gomez, Robert Karlsson, Yanchun Bao, Traci M Bartz, Clemens Baumbach, Ginevra Biino, Matthew J Bixley, Marco Brumat, Jin-Fang Chai, Tanguy Corre, Diana L Cousminer, Annelot M Dekker, David A Eccles, Kristel R van Eijk, Christian Fuchsberger, He Gao, Marine Germain, Scott D Gordon, Hugoline G de Haan, Sarah E Harris, Edith Hofer, Alicia Huerta-Chagoya, Catherine Igartua, Iris E Jansen, Yucheng Jia, Tim Kacprowski, Torgny Karlsson, Marcus E Kleber, Shengchao Alfred Li, Ruifang Li-Gao, Anubha Mahajan, Koichi Matsuda, Karina Meidtner, Weihua Meng, May E Montasser, Peter J van der Most, Matthias Munz, Teresa Nutile, Teemu Palviainen, Gauri Prasad, Rashmi B Prasad, Tallapragada Divya Sri Priyanka, Federica Rizzi, Erika Salvi, Bishwa R Sapkota, Daniel Shriner, Line Skotte, Melissa C Smart, Albert Vernon Smith, Ashley van der Spek, Cassandra N Spracklen, Rona J Strawbridge, Salman M Tajuddin, Stella Trompet, Constance Turman, Niek Verweij, Clara Viberti, Lihua Wang, Helen R Warren, Robyn E Wootton, Lisa R Yanek, Jie Yao, Noha A Yousri, Wei Zhao, Adebowale A Adeyemo, Saima Afaq, Carlos Alberto Aguilar-Salinas, Masato Akiyama, Matthew L Albert, Matthew A Allison, Maris Alver, Tin Aung, Fereidoun Azizi, Amy R Bentley, Heiner Boeing, Eric Boerwinkle, Judith B Borja, Gert J de Borst, Erwin P Bottinger, Linda Broer, Harry Campbell, Stephen Chanock, Miao-Li Chee, Guanjie Chen, Yii-Der I Chen, Zhengming Chen, Yen-Feng Chiu, Massimiliano Cocca, Francis S Collins, Maria Pina Concas, Janie Corley, Giovanni Cugliari, Rob M van Dam, Anna Damulina, Maryam S Daneshpour, Felix R Day, Graciela E Delgado, Klodian Dhana, Alexander S F Doney, Marcus Dörr, Ayo P Doumatey, Nduna Dzimiri, S Sunna Ebenesersdóttir, Joshua Elliott, Paul Elliott, Ralf Ewert, Janine F Felix, Krista Fischer, Barry I Freedman, Giorgia Girotto, Anuj Goel, Martin Gögele, Mark O Goodarzi, Mariaelisa Graff, Einat Granot-Hershkovitz, Francine Grodstein, Simonetta Guarrera, Daniel F Gudbjartsson, Kamran Guity, Bjarni Gunnarsson, Yu Guo, Saskia P Hagenaars, Christopher A Haiman, Avner Halevy, Tamara B Harris, Mehdi Hedayati, David A van Heel, Makoto Hirata, Imo Höfer, Chao Agnes Hsiung, Jinyan Huang, Yi-Jen Hung, M Arfan Ikram, Anuradha Jagadeesan, Pekka Jousilahti, Yoichiro Kamatani, Masahiro Kanai, Nicola D Kerrison, Thorsten Kessler, Kay-Tee Khaw, Chiea Chuen Khor, Dominique P V de Kleijn, Woon-Puay Koh, Ivana Kolcic, Peter Kraft, Bernhard K Krämer, Zoltán Kutalik, Johanna Kuusisto, Claudia Langenberg, Lenore J Launer, Deborah A Lawlor, I-Te Lee, Wen-Jane Lee, Markus M Lerch, Liming Li, Jianjun Liu, Marie Loh, Stephanie J London, Stephanie Loomis, Yingchang Lu, Jian’an Luan, Reedik Mägi, Ani W Manichaikul, Paolo Manunta, Gísli Másson, Nana Matoba, Xue W Mei, Christa Meisinger, Thomas Meitinger, Massimo Mezzavilla, Lili Milani, Iona Y Millwood, Yukihide Momozawa, Amy Moore, Pierre-Emmanuel Morange, Hortensia Moreno-Macías, Trevor A Mori, Alanna C Morrison, Taulant Muka, Yoshinori Murakami, Alison D Murray, Renée de Mutsert, Josyf C Mychaleckyj, Mike A Nalls, Matthias Nauck, Matt J Neville, Ilja M Nolte, Ken K Ong, Lorena Orozco, Sandosh Padmanabhan, Gunnar Pálsson, James S Pankow, Cristian Pattaro, Alison Pattie, Ozren Polasek, Neil Poulter, Peter P Pramstaller, Lluis Quintana-Murci, Katri Räikkönen, Sarju Ralhan, Dabeeru C Rao, Wouter van Rheenen, Stephen S Rich, Paul M Ridker, Cornelius A Rietveld, Antonietta Robino, Frank J A van Rooij, Daniela Ruggiero, Yasaman Saba, Charumathi Sabanayagam, Maria Sabater-Lleal, Cinzia Felicita Sala, Veikko Salomaa, Kevin Sandow, Helena Schmidt, Laura J Scott, William R Scott, Bahareh Sedaghati-Khayat, Bengt Sennblad, Jessica van Setten, Peter J Sever, Wayne H-H Sheu, Yuan Shi, Smeeta Shrestha, Sharvari Rahul Shukla, Jon K Sigurdsson, Timo Tonis Sikka, Jai Rup Singh, Blair H Smith, Alena Stančáková, Alice Stanton, John M Starr, Lilja Stefansdottir, Leon Straker, Patrick Sulem, Gardar Sveinbjornsson, Morris A Swertz, Adele M Taylor, Kent D Taylor, Natalie Terzikhan, Yih-Chung Tham, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Annika Tillander, Russell P Tracy, Teresa Tusié-Luna, Ioanna Tzoulaki, Simona Vaccargiu, Jagadish Vangipurapu, Jan H Veldink, Veronique Vitart, Uwe Völker, Eero Vuoksimaa, Salma M Wakil, Melanie Waldenberger, Gurpreet S Wander, Ya Xing Wang, Nicholas J Wareham, Sarah Wild, Chittaranjan S Yajnik, Jian-Min Yuan, Lingyao Zeng, Liang Zhang, Jie Zhou, Najaf Amin, Folkert W Asselbergs, Stephan J L Bakker, Diane M Becker, Benjamin Lehne, David A Bennett, Leonard H van den Berg, Sonja I Berndt, Dwaipayan Bharadwaj, Lawrence F Bielak, Murielle Bochud, Mike Boehnke, Claude Bouchard, Jonathan P Bradfield, Jennifer A Brody, Archie Campbell, Shai Carmi, Mark J Caulfield, David Cesarini, John C Chambers, Giriraj Ratan Chandak, Ching-Yu Cheng, Marina Ciullo, Marilyn Cornelis, Daniele Cusi, George Davey Smith, Ian J Deary, Rajkumar Dorajoo, Cornelia M van Duijn, David Ellinghaus, Jeanette Erdmann, Johan G Eriksson, Evangelos Evangelou, Michele K Evans, Jessica D Faul, Bjarke Feenstra, Mary Feitosa, Sylvain Foisy, Andre Franke, Yechiel Friedlander, Paolo Gasparini, Christian Gieger, Clicerio Gonzalez, Philippe Goyette, Struan F A Grant, Lyn R Griffiths, Leif Groop, Vilmundur Gudnason, Ulf Gyllensten, Hakon Hakonarson, Anders Hamsten, Pim van der Harst, Chew-Kiat Heng, Andrew A Hicks, Hagit Hochner, Heikki Huikuri, Steven C Hunt, Vincent W V Jaddoe, Philip L De Jager, Magnus Johannesson, Åsa Johansson, Jost B Jonas, J Wouter Jukema, Juhani Junttila, Jaakko Kaprio, Sharon L. R. Kardia, Fredrik Karpe, Meena Kumari, Markku Laakso, Sander W van der Laan, Jari Lahti, Matthias Laudes, Rodney A Lea, Wolfgang Lieb, Thomas Lumley, Nicholas G Martin, Winfried März, Giuseppe Matullo, Mark I McCarthy, Sarah E Medland, Tony R Merriman, Andres Metspalu, Brian F Meyer, Karen L Mohlke, Grant W Montgomery, Dennis Mook-Kanamori, Patricia B Munroe, Kari E North, Dale R Nyholt, Jeffery R O’connell, Carole Ober, Albertine J Oldehinkel, Walter Palmas, Colin Palmer, Gerard G Pasterkamp, Etienne Patin, Craig E Pennell, Louis Perusse, Patricia A Peyser, Mario Pirastu, Tinca J. C. Polderman, David J Porteous, Danielle Posthuma, Bruce M Psaty, John D Rioux, Fernando Rivadeneira, Charles Rotimi, Jerome I Rotter, Igor Rudan, Hester M Den Ruijter, Dharambir K Sanghera, Naveed Sattar, Reinhold Schmidt, Matthias B Schulze, Heribert Schunkert, Robert A Scott, Alan R Shuldiner, Xueling Sim, Neil Small, Jennifer A Smith, Nona Sotoodehnia, E-Shyong Tai, Alexander Teumer, Nicholas J Timpson, Daniela Toniolo, David-Alexandre Tregouet, Tiinamaija Tuomi, Peter Vollenweider, Carol A Wang, David R Weir, John B Whitfield, Cisca Wijmenga, Tien-Yin Wong, John Wright, Jingyun Yang, Lei Yu, Babette S Zemel, Alan B Zonderman, Markus Perola, Patrik K. E. Magnusson, André G Uitterlinden, Jaspal S Kooner, Daniel I Chasman, Ruth J. F. Loos, Nora Franceschini, Lude Franke, Chris S Haley, Caroline Hayward, Robin G Walters, John R. B. Perry, Tōnu Esko, Agnar Helgason, Kari Stefansson, Peter K Joshi, Michiaki Kubo, and James F Wilson

Subjects
Science
Abstract

Inbreeding depression has been observed in many different species, but in humans a systematic analysis has been difficult so far. Here, analysing more than 1.3 million individuals, the authors show that a genomic inbreeding coefficient (FROH) is associated with disadvantageous outcomes in 32 out of 100 traits tested.

Published
2019
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7. Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9

Author

Amand F. Schmidt, Michael V. Holmes, David Preiss, Daniel I. Swerdlow, Spiros Denaxas, Ghazaleh Fatemifar, Rupert Faraway, Chris Finan, Dennis Valentine, Zammy Fairhurst-Hunter, Fernando Pires Hartwig, Bernardo Lessa Horta, Elina Hypponen, Christine Power, Max Moldovan, Erik van Iperen, Kees Hovingh, Ilja Demuth, Kristina Norman, Elisabeth Steinhagen-Thiessen, Juri Demuth, Lars Bertram, Christina M. Lill, Stefan Coassin, Johann Willeit, Stefan Kiechl, Karin Willeit, Dan Mason, John Wright, Richard Morris, Goya Wanamethee, Peter Whincup, Yoav Ben-Shlomo, Stela McLachlan, Jackie F. Price, Mika Kivimaki, Catherine Welch, Adelaida Sanchez-Galvez, Pedro Marques-Vidal, Andrew Nicolaides, Andrie G. Panayiotou, N. Charlotte Onland-Moret, Yvonne T. van der Schouw, Giuseppe Matullo, Giovanni Fiorito, Simonetta Guarrera, Carlotta Sacerdote, Nicholas J. Wareham, Claudia Langenberg, Robert A. Scott, Jian’an Luan, Martin Bobak, Sofia Malyutina, Andrzej Pająk, Ruzena Kubinova, Abdonas Tamosiunas, Hynek Pikhart, Niels Grarup, Oluf Pedersen, Torben Hansen, Allan Linneberg, Tine Jess, Jackie Cooper, Steve E. Humphries, Murray Brilliant, Terrie Kitchner, Hakon Hakonarson, David S. Carrell, Catherine A. McCarty, Kirchner H. Lester, Eric B. Larson, David R. Crosslin, Mariza de Andrade, Dan M. Roden, Joshua C. Denny, Cara Carty, Stephen Hancock, John Attia, Elizabeth Holliday, Rodney Scott, Peter Schofield, Martin O’Donnell, Salim Yusuf, Michael Chong, Guillaume Pare, Pim van der Harst, M. Abdullah Said, Ruben N. Eppinga, Niek Verweij, Harold Snieder, Lifelines Cohort authors, Tim Christen, D. O. Mook-Kanamori, the ICBP Consortium, Stefan Gustafsson, Lars Lind, Erik Ingelsson, Raha Pazoki, Oscar Franco, Albert Hofman, Andre Uitterlinden, Abbas Dehghan, Alexander Teumer, Sebastian Baumeister, Marcus Dörr, Markus M. Lerch, Uwe Völker, Henry Völzke, Joey Ward, Jill P. Pell, Tom Meade, Ingrid E. Christophersen, Anke H. Maitland-van der Zee, Ekaterina V. Baranova, Robin Young, Ian Ford, Archie Campbell, Sandosh Padmanabhan, Michiel L. Bots, Diederick E. Grobbee, Philippe Froguel, Dorothée Thuillier, Ronan Roussel, Amélie Bonnefond, Bertrand Cariou, Melissa Smart, Yanchun Bao, Meena Kumari, Anubha Mahajan, Jemma C. Hopewell, Sudha Seshadri, the METASTROKE Consortium of the ISGC, Caroline Dale, Rui Providencia E. Costa, Paul M. Ridker, Daniel I. Chasman, Alex P. Reiner, Marylyn D. Ritchie, Leslie A. Lange, Alex J. Cornish, Sara E. Dobbins, Kari Hemminki, Ben Kinnersley, Marc Sanson, Karim Labreche, Matthias Simon, Melissa Bondy, Philip Law, Helen Speedy, James Allan, Ni Li, Molly Went, Niels Weinhold, Gareth Morgan, Pieter Sonneveld, Björn Nilsson, Hartmut Goldschmidt, Amit Sud, Andreas Engert, Markus Hansson, Harry Hemingway, Folkert W. Asselbergs, Riyaz S. Patel, Brendan J. Keating, Naveed Sattar, Richard Houlston, Juan P. Casas, and Aroon D. Hingorani

Subjects
Genetic association studies, Mendelian randomisation, LDL-cholesterol, Phenome-wide association scan, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Abstract Background We characterised the phenotypic consequence of genetic variation at the PCSK9 locus and compared findings with recent trials of pharmacological inhibitors of PCSK9. Methods Published and individual participant level data (300,000+ participants) were combined to construct a weighted PCSK9 gene-centric score (GS). Seventeen randomized placebo controlled PCSK9 inhibitor trials were included, providing data on 79,578 participants. Results were scaled to a one mmol/L lower LDL-C concentration. Results The PCSK9 GS (comprising 4 SNPs) associations with plasma lipid and apolipoprotein levels were consistent in direction with treatment effects. The GS odds ratio (OR) for myocardial infarction (MI) was 0.53 (95% CI 0.42; 0.68), compared to a PCSK9 inhibitor effect of 0.90 (95% CI 0.86; 0.93). For ischemic stroke ORs were 0.84 (95% CI 0.57; 1.22) for the GS, compared to 0.85 (95% CI 0.78; 0.93) in the drug trials. ORs with type 2 diabetes mellitus (T2DM) were 1.29 (95% CI 1.11; 1.50) for the GS, as compared to 1.00 (95% CI 0.96; 1.04) for incident T2DM in PCSK9 inhibitor trials. No genetic associations were observed for cancer, heart failure, atrial fibrillation, chronic obstructive pulmonary disease, or Alzheimer’s disease – outcomes for which large-scale trial data were unavailable. Conclusions Genetic variation at the PCSK9 locus recapitulates the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and MI. While indicating an increased risk of T2DM, no other possible safety concerns were shown; although precision was moderate.

Published
2019
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8. Association of maternal prenatal smoking GFI1-locus and cardio-metabolic phenotypes in 18,212 adultsResearch in context

Author

Priyanka Parmar, Estelle Lowry, Giovanni Cugliari, Matthew Suderman, Rory Wilson, Ville Karhunen, Toby Andrew, Petri Wiklund, Matthias Wielscher, Simonetta Guarrera, Alexander Teumer, Benjamin Lehne, Lili Milani, Niek de Klein, Pashupati P. Mishra, Phillip E. Melton, Pooja R. Mandaviya, Silva Kasela, Jana Nano, Weihua Zhang, Yan Zhang, Andre G. Uitterlinden, Annette Peters, Ben Schöttker, Christian Gieger, Denise Anderson, Dorret I. Boomsma, Hans J. Grabe, Salvatore Panico, Jan H. Veldink, Joyce B.J. van Meurs, Leonard van den Berg, Lawrence J. Beilin, Lude Franke, Marie Loh, Marleen M.J. van Greevenbroek, Matthias Nauck, Mika Kähönen, Mikko A. Hurme, Olli T. Raitakari, Oscar H. Franco, P.Eline Slagboom, Pim van der Harst, Sonja Kunze, Stephan B. Felix, Tao Zhang, Wei Chen, Trevor A. Mori, Amelie Bonnefond, Bastiaan T. Heijmans, Taulant Muka, Jaspal S. Kooner, Krista Fischer, Melanie Waldenberger, Philippe Froguel, Rae-Chi Huang, Terho Lehtimäki, Wolfgang Rathmann, Caroline L. Relton, Giuseppe Matullo, Hermann Brenner, Niek Verweij, Shengxu Li, John C. Chambers, Marjo-Riitta Järvelin, and Sylvain Sebert

Subjects
Medicine, Medicine (General), R5-920
Abstract

Background: DNA methylation at the GFI1-locus has been repeatedly associated with exposure to smoking from the foetal period onwards. We explored whether DNA methylation may be a mechanism that links exposure to maternal prenatal smoking with offspring's adult cardio-metabolic health. Methods: We meta-analysed the association between DNA methylation at GFI1-locus with maternal prenatal smoking, adult own smoking, and cardio-metabolic phenotypes in 22 population-based studies from Europe, Australia, and USA (n = 18,212). DNA methylation at the GFI1-locus was measured in whole-blood. Multivariable regression models were fitted to examine its association with exposure to prenatal and own adult smoking. DNA methylation levels were analysed in relation to body mass index (BMI), waist circumference (WC), fasting glucose (FG), high-density lipoprotein cholesterol (HDL—C), triglycerides (TG), diastolic, and systolic blood pressure (BP). Findings: Lower DNA methylation at three out of eight GFI1-CpGs was associated with exposure to maternal prenatal smoking, whereas, all eight CpGs were associated with adult own smoking. Lower DNA methylation at cg14179389, the strongest maternal prenatal smoking locus, was associated with increased WC and BP when adjusted for sex, age, and adult smoking with Bonferroni-corrected P

Published
2018
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9. Genetic and Epigenetic Characterization of a Discordant KMT2A/AFF1-Rearranged Infant Monozygotic Twin Pair

Author

Alessia Russo, Clara Viberti, Katia Mareschi, Elisabetta Casalone, Simonetta Guarrera, Giovanni Birolo, Giovanni Cazzaniga, Lilia Corral, Luca Trentin, Giuseppe Basso, Franca Fagioli, and Giuseppe Matullo

Subjects
acute lymphoblastic leukemia, exome, DNA methylation, RNA sequencing, NRAS, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

The KMT2A/AFF1 rearrangement is associated with an unfavorable prognosis in infant acute lymphocytic leukemia (ALL). Discordant ALL in monozygotic twins is uncommon and represents an attractive resource to evaluate intrauterine environment–genetic interplay in ALL. Mutational and epigenetic profiles were characterized for a discordant KMT2A/AFF1-rearranged infant monozygotic twin pair and their parents, and they were compared to three independent KMT2A/AFF1-positive ALL infants, in which the DNA methylation and gene expression profiles were investigated. A de novo Q61H NRAS mutation was detected in the affected twin at diagnosis and backtracked in both twins at birth. The KMT2A/AFF1 rearrangement was absent at birth in both twins. Genetic analyses conducted at birth gave more insights into the timing of the mutation hit. We identified correlations between DNA methylation and gene expression changes for 32 genes in the three independent affected versus remitted patients. The strongest correlations were observed for the RAB32, PDK4, CXCL3, RANBP17, and MACROD2 genes. This epigenetic signature could be a putative target for the development of novel epigenetic-based therapies and could help in explaining the molecular mechanisms characterizing ALL infants with KMT2A/AFF1 fusions.

Published
2021
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10. Epigenetic Signatures at AQP3 and SOCS3 Engage in Low-Grade Inflammation across Different Tissues.

Author

Carola Marzi, Lesca M Holdt, Giovanni Fiorito, Pei-Chien Tsai, Anja Kretschmer, Simone Wahl, Simonetta Guarrera, Daniel Teupser, Tim D Spector, Licia Iacoviello, Carlotta Sacerdote, Konstantin Strauch, Serene Lee, Wolfgang E Thasler, Annette Peters, Barbara Thorand, Petra Wolf, Holger Prokisch, Rosario Tumino, Christian Gieger, Vittorio Krogh, Salvatore Panico, Jordana T Bell, Giuseppe Matullo, Melanie Waldenberger, Harald Grallert, and Wolfgang Koenig

Subjects
Medicine, Science
Abstract

Elevated levels of C-reactive protein (CRP, determined by a high-sensitivity assay) indicate low-grade inflammation which is implicated in many age-related disorders. Epigenetic studies on CRP might discover molecular mechanisms underlying CRP regulation. We aimed to identify DNA methylation sites related to CRP concentrations in cells and tissues regulating low-grade inflammation.Genome-wide DNA methylation was measured in peripheral blood in 1,741 participants of the KORA F4 study using Illumina HumanMethylation450 BeadChip arrays. Four CpG sites (located at BCL3, AQP3, SOCS3, and cg19821297 intergenic at chromosome 19p13.2, P ≤ 1.01E-07) were significantly hypomethylated at high CRP concentrations independent of various confounders including age, sex, BMI, smoking, and white blood cell composition. Findings were not sex-specific. CRP-related top genes were enriched in JAK/STAT pathways (Benjamini-Hochberg corrected P < 0.05). Results were followed-up in three studies using DNA from peripheral blood (EPICOR, n = 503) and adipose tissue (TwinsUK, n = 368) measured as described above and from liver tissue (LMU liver cohort, n = 286) measured by MALDI-TOF mass spectrometry using EpiTYPER. CpG sites at the AQP3 locus (significant p-values in peripheral blood = 1.72E-03 and liver tissue = 1.51E-03) and the SOCS3 locus (p-values in liver < 2.82E-05) were associated with CRP in the validation panels.Epigenetic modifications seem to engage in low-grade inflammation, possibly via JAK/STAT mediated pathways. Results suggest a shared relevance across different tissues at the AQP3 locus and highlight a role of DNA methylation for CRP regulation at the SOCS3 locus.

Published
2016
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11. Correction: genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study.

Author

Giuseppe Matullo, Simonetta Guarrera, Marta Betti, Giovanni Fiorito, Daniela Ferrante, Floriana Voglino, Gemma Cadby, Cornelia Di Gaetano, Fabio Rosa, Alessia Russo, Ari Hirvonen, Elisabetta Casalone, Sara Tunesi, Marina Padoan, Mara Giordano, Anna Aspesi, Caterina Casadio, Francesco Ardissone, Enrico Ruffini, Pier Giacomo Betta, Roberta Libener, Roberto Guaschino, Ezio Piccolini, Monica Neri, Arthur W B Musk, Nicholas H de Klerk, Jennie Hui, John Beilby, Alan L James, Jenette Creaney, Bruce W Robinson, Sutapa Mukherjee, Lyle J Palmer, Dario Mirabelli, Donatella Ugolini, Stefano Bonassi, Corrado Magnani, and Irma Dianzani

Subjects
Medicine, Science
Published
2015
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12. Novel epigenetic changes unveiled by monozygotic twins discordant for smoking habits.

Author

Alessandra Allione, Francesca Marcon, Giovanni Fiorito, Simonetta Guarrera, Ester Siniscalchi, Andrea Zijno, Riccardo Crebelli, and Giuseppe Matullo

Subjects
Medicine, Science
Abstract

Exposure to cigarette smoking affects the epigenome and could increase the risk of developing diseases such as cancer and cardiovascular disorders. Changes in DNA methylation associated with smoking may help to identify molecular pathways that contribute to disease etiology. Previous studies are not completely concordant in the identification of differentially methylated regions in the DNA of smokers. We performed an epigenome-wide DNA methylation study in a group of monozygotic (MZ) twins discordant for smoking habits to determine the effect of smoking on DNA methylation. As MZ twins are considered genetically identical, this model allowed us to identify smoking-related DNA methylation changes independent from genetic components. We investigated the whole blood genome-wide DNA methylation profiles in 20 MZ twin pairs discordant for smoking habits by using the Illumina HumanMethylation450 BeadChip. We identified 22 CpG sites that were differentially methylated between smoker and non-smoker MZ twins by intra-pair analysis. We confirmed eight loci already described by other groups, located in AHRR, F2RL3, MYOG1 genes, at 2q37.1 and 6p21.33 regions, and also identified several new loci. Moreover, pathway analysis showed an enrichment of genes involved in GTPase regulatory activity. Our study confirmed the evidence of smoking-related DNA methylation changes, emphasizing that well-designed MZ twin models can aid the discovery of novel DNA methylation signals, even in a limited sample population.

Published
2015
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13. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Author

Clive J Hoggart, Giulia Venturini, Massimo Mangino, Felicia Gomez, Giulia Ascari, Jing Hua Zhao, Alexander Teumer, Thomas W Winkler, Natalia Tšernikova, Jian'an Luan, Evelin Mihailov, Georg B Ehret, Weihua Zhang, David Lamparter, Tõnu Esko, Aurelien Macé, Sina Rüeger, Pierre-Yves Bochud, Matteo Barcella, Yves Dauvilliers, Beben Benyamin, David M Evans, Caroline Hayward, Mary F Lopez, Lude Franke, Alessia Russo, Iris M Heid, Erika Salvi, Sailaja Vendantam, Dan E Arking, Eric Boerwinkle, John C Chambers, Giovanni Fiorito, Harald Grallert, Simonetta Guarrera, Georg Homuth, Jennifer E Huffman, David Porteous, Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Darius Moradpour, Alex Iranzo, Johannes Hebebrand, John P Kemp, Gert J Lammers, Vincent Aubert, Markus H Heim, Nicholas G Martin, Grant W Montgomery, Rosa Peraita-Adrados, Joan Santamaria, Francesco Negro, Carsten O Schmidt, Robert A Scott, Tim D Spector, Konstantin Strauch, Henry Völzke, Nicholas J Wareham, Wei Yuan, Jordana T Bell, Aravinda Chakravarti, Jaspal S Kooner, Annette Peters, Giuseppe Matullo, Henri Wallaschofski, John B Whitfield, Fred Paccaud, Peter Vollenweider, Sven Bergmann, Jacques S Beckmann, Mehdi Tafti, Nicholas D Hastie, Daniele Cusi, Murielle Bochud, Timothy M Frayling, Andres Metspalu, Marjo-Riitta Jarvelin, André Scherag, George Davey Smith, Ingrid B Borecki, Valentin Rousson, Joel N Hirschhorn, Carlo Rivolta, Ruth J F Loos, and Zoltán Kutalik

Subjects
Genetics, QH426-470
Abstract

The phenotypic effect of some single nucleotide polymorphisms (SNPs) depends on their parental origin. We present a novel approach to detect parent-of-origin effects (POEs) in genome-wide genotype data of unrelated individuals. The method exploits increased phenotypic variance in the heterozygous genotype group relative to the homozygous groups. We applied the method to >56,000 unrelated individuals to search for POEs influencing body mass index (BMI). Six lead SNPs were carried forward for replication in five family-based studies (of ∼4,000 trios). Two SNPs replicated: the paternal rs2471083-C allele (located near the imprinted KCNK9 gene) and the paternal rs3091869-T allele (located near the SLC2A10 gene) increased BMI equally (beta = 0.11 (SD), P

Published
2014
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14. Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection.

Author

Cornelia Di Gaetano, Giovanni Fiorito, Maria Francesca Ortu, Fabio Rosa, Simonetta Guarrera, Barbara Pardini, Daniele Cusi, Francesca Frau, Cristina Barlassina, Chiara Troffa, Giuseppe Argiolas, Roberta Zaninello, Giovanni Fresu, Nicola Glorioso, Alberto Piazza, and Giuseppe Matullo

Subjects
Medicine, Science
Abstract

The peculiar position of Sardinia in the Mediterranean sea has rendered its population an interesting biogeographical isolate. The aim of this study was to investigate the genetic population structure, as well as to estimate Runs of Homozygosity and regions under positive selection, using about 1.2 million single nucleotide polymorphisms genotyped in 1077 Sardinian individuals. Using four different methods--fixation index, inflation factor, principal component analysis and ancestry estimation--we were able to highlight, as expected for a genetic isolate, the high internal homogeneity of the island. Sardinians showed a higher percentage of genome covered by RoHs>0.5 Mb (F(RoH%0.5)) when compared to peninsular Italians, with the only exception of the area surrounding Alghero. We furthermore identified 9 genomic regions showing signs of positive selection and, we re-captured many previously inferred signals. Other regions harbor novel candidate genes for positive selection, like TMEM252, or regions containing long non coding RNA. With the present study we confirmed the high genetic homogeneity of Sardinia that may be explained by the shared ancestry combined with the action of evolutionary forces.

Published
2014
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15. Genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study.

Author

Giuseppe Matullo, Simonetta Guarrera, Marta Betti, Giovanni Fiorito, Daniela Ferrante, Floriana Voglino, Gemma Cadby, Cornelia Di Gaetano, Fabio Rosa, Alessia Russo, Ari Hirvonen, Elisabetta Casalone, Sara Tunesi, Marina Padoan, Mara Giordano, Anna Aspesi, Caterina Casadio, Francesco Ardissone, Enrico Ruffini, Pier Giacomo Betta, Roberta Libener, Roberto Guaschino, Ezio Piccolini, Monica Neri, Arthur W B Musk, Nicholas H de Klerk, Jennie Hui, John Beilby, Alan L James, Jenette Creaney, Bruce W Robinson, Sutapa Mukherjee, Lyle J Palmer, Dario Mirabelli, Donatella Ugolini, Stefano Bonassi, Corrado Magnani, and Irma Dianzani

Subjects
Medicine, Science
Abstract

Asbestos exposure is the main risk factor for malignant pleural mesothelioma (MPM), a rare aggressive tumor. Nevertheless, only 5-17% of those exposed to asbestos develop MPM, suggesting the involvement of other environmental and genetic risk factors. To identify the genetic risk factors that may contribute to the development of MPM, we conducted a genome-wide association study (GWAS; 370,000 genotyped SNPs, 5 million imputed SNPs) in Italy, among 407 MPM cases and 389 controls with a complete history of asbestos exposure. A replication study was also undertaken and included 428 MPM cases and 1269 controls from Australia. Although no single marker reached the genome-wide significance threshold, several associations were supported by haplotype-, chromosomal region-, gene- and gene-ontology process-based analyses. Most of these SNPs were located in regions reported to harbor aberrant alterations in mesothelioma (SLC7A14, THRB, CEBP350, ADAMTS2, ETV1, PVT1 and MMP14 genes), causing at most a 2-3-fold increase in MPM risk. The Australian replication study showed significant associations in five of these chromosomal regions (3q26.2, 4q32.1, 7p22.2, 14q11.2, 15q14). Multivariate analysis suggested an independent contribution of 10 genetic variants, with an Area Under the ROC Curve (AUC) of 0.76 when only exposure and covariates were included in the model, and of 0.86 when the genetic component was also included, with a substantial increase of asbestos exposure risk estimation (odds ratio, OR: 45.28, 95% confidence interval, CI: 21.52-95.28). These results showed that genetic risk factors may play an additional role in the development of MPM, and that these should be taken into account to better estimate individual MPM risk in individuals who have been exposed to asbestos.

Published
2013
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16. An overview of the genetic structure within the Italian population from genome-wide data.

Author

Cornelia Di Gaetano, Floriana Voglino, Simonetta Guarrera, Giovanni Fiorito, Fabio Rosa, Anna Maria Di Blasio, Paola Manzini, Irma Dianzani, Marta Betti, Daniele Cusi, Francesca Frau, Cristina Barlassina, Dario Mirabelli, Corrado Magnani, Nicola Glorioso, Stefano Bonassi, Alberto Piazza, and Giuseppe Matullo

Subjects
Medicine, Science
Abstract

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F(ST) statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.

Published
2012
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17. Telomere length variation in juvenile acute myocardial infarction.

Author

Alessia Russo, Luigi Palumbo, Cristina Fornengo, Cornelia Di Gaetano, Fulvio Ricceri, Simonetta Guarrera, Rossana Critelli, Matteo Anselmino, Alberto Piazza, Fiorenzo Gaita, Serena Bergerone, and Giuseppe Matullo

Subjects
Medicine, Science
Abstract

Leukocyte telomere length (LTL) provides a potential marker of biological age, closely related to the endothelial dysfunction and consequently to the atherosclerotic process. To investigate the relationship between the LTL and the risk of premature acute myocardial infarction and to evaluate the predictive value of LTL on the onset of major cardiovascular events, 199 patients from 18 to 48 years old with first diagnosis of acute myocardial infarction were enrolled and were matched with 190 controls for sex and age (± 1 year). Clinical data and coronary artery disease were evaluated at enrollment and at follow up. LTL was measured at enrollment using a quantitative PCR-based method. No significant differences were observed in LTL between cases and controls (p = 0.20) and with the presence of coronary artery disease in patients (p = 0.47). Hypercholesterolemic cases presented LTL significantly longer than cases without hypercholesterolemia (t/s: 0.82 ± 0.16 p = 0.79 and t/s norm: 0.79 ± 0.19 p = 0.01), as confirmed in multivariate regression analysis (p = 0.005, β = 0.09). Furthermore, multivariate regression analysis showed LTL significantly shorter in hypertensive cases than in normotensive cases (p = 0.04, β = -0.07). One hundred seventy-one cases (86%) ended the average follow up of 9 ± 5 years, 92 (54%) presented a major cardiovascular event. At multivariate regression analysis the LTL detected at enrollment did not represent a predictive factor of major cardiovascular events nor it significantly impacted with cumulative events. Based on present cohort of young Italian patients, the LTL did not represent a marker of acute myocardial infarction nor had a predictive role at medium term follow up.

Published
2012
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19. Impaired neutrophil-mediated cell death drives Ewing's Sarcoma in a two years old child with Down Syndrome

Author

Serena Peirone, Elisa Tirtei, Anna Campello, Caterina Parlato, Simonetta Guarrera, Katia Mareschi, Elena Marini, Sebastian Dorin Asaftei, Luca Bertero, Mauro Papotti, Matteo Cereda, and Franca Fagioli

Abstract

Ewing's Sarcoma (EWS) has been reported in seven children with Down Syndrome (DS). To date, a detailed assessment of this solid tumor in DS patients is still missing. Here, we characterized a chemo-resistant mediastinal EWS in a 2-year-old DS child, the youngest ever reported case, by exploiting sequencing approaches. The tumor showed a neuroectodermal development driven by the EWSR1-FLI1 fusion. The inherited myeloperoxidase deficiency of the patient caused failure of neutrophil-mediated cell death and promoted genomic instability. In this context, the tumor underwent nearly genome-wide haploidization resulting in a massive overexpression of pro-inflammatory cytokines. Recruitment of defective neutrophils fostered the fast evolution of this EWS.

Published
2023

20. Supplementary Table S2 from Shorter Leukocyte Telomere Length Is Independently Associated with Poor Survival in Patients with Bladder Cancer

Author

Giuseppe Matullo, Carlotta Sacerdote, Paolo Vineis, Bruno Frea, Dario Fontana, Andrea Zitella, Luigi Rolle, Paolo Gontero, Paolo Destefanis, Giuseppina Cucchiarale, Giovanni Casetta, Andrea Bosio, Rossana Critelli, Alessandra Allione, Clara Viberti, Barbara Pardini, Giovanni Fiorito, Simonetta Guarrera, Federica Modica, and Alessia Russo

Abstract

Supplementary Table S2. TL quartiles and OS association analysis (Crude Cox regression).

Published
2023

21. Supplementary Figure S1 from Shorter Leukocyte Telomere Length Is Independently Associated with Poor Survival in Patients with Bladder Cancer

Author

Giuseppe Matullo, Carlotta Sacerdote, Paolo Vineis, Bruno Frea, Dario Fontana, Andrea Zitella, Luigi Rolle, Paolo Gontero, Paolo Destefanis, Giuseppina Cucchiarale, Giovanni Casetta, Andrea Bosio, Rossana Critelli, Alessandra Allione, Clara Viberti, Barbara Pardini, Giovanni Fiorito, Simonetta Guarrera, Federica Modica, and Alessia Russo

Abstract

Supplementary Figure S1. Kaplan-Meier OS curves of bladder cancer patients stratified for TL quartiles. OS, overall survival; TL, telomere length.

Published
2023

22. Data from Shorter Leukocyte Telomere Length Is Independently Associated with Poor Survival in Patients with Bladder Cancer

Author

Giuseppe Matullo, Carlotta Sacerdote, Paolo Vineis, Bruno Frea, Dario Fontana, Andrea Zitella, Luigi Rolle, Paolo Gontero, Paolo Destefanis, Giuseppina Cucchiarale, Giovanni Casetta, Andrea Bosio, Rossana Critelli, Alessandra Allione, Clara Viberti, Barbara Pardini, Giovanni Fiorito, Simonetta Guarrera, Federica Modica, and Alessia Russo

Abstract

Background: Shorter telomere length (TL) has been reported to be associated with increased risk of early death in elder individuals. Telomere shortening has been also related to chromosomal instability, which may possibly contribute to the development of several types of digestive or urogenital system cancers and smoking-related tumors. Therefore, we investigated the impact of TL on bladder cancer survival.Methods: TL was measured in leukocyte DNA from whole peripheral blood using quantitative real-time PCR in 463 patients with bladder cancer from a total 726 cases who were followed for up to 18 years.Results: Patients with muscle-invasive tumor/any grade had shorter telomere than patients with non–muscle-invasive tumor/high-grade and with non–muscle-invasive tumor/non–high-grade (TL reference 0.7 ± 0.2; vs. respectively, 0.8 ± 0.2, P = 3.4 × 10−2 and 0.8 ± 0.2, P = 3.6 × 10−2). Moreover, patients in the lowest quartiles of TL were associated with decreased survival after diagnosis (log-rank test, P = 3.9 × 10−4). A Cox regression adjusted by age, cancer aggressiveness, Bacillus Calmette-Guérin, radical cystectomy, radiotherapy, and chemotherapy showed an independent effect of TL on bladder cancer survival (HR, 3.9; 95% confidence interval, 1.7–9.1; P = 1.2 × 10−3).Conclusions: Our results suggest that leukocyte TL is only partly related to tumor aggressiveness and that shorter telomeres act as independent prognostic predictor of survival in patients with bladder cancer. TL information may allow to better select therapeutic approaches in patients with the same stage and grade.Impact: Blood leukocyte TL levels could provide an additional noninvasive prognostic marker to better predict survival and personalize therapies in patients with bladder cancer. Cancer Epidemiol Biomarkers Prev; 23(11); 2439–46. ©2014 AACR.

Published
2023

23. Data from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Author

Montserrat Garcia-Closas, Sung Shim Lani Park, Cecilia Arici, Marcello Campagna, Angela Carta, Stefano Porru, Peter Rudnai, Rajiv Kumar, Kvetoslava Koppova, Eugen Gurzau, Alessandra Allione, Silvia Polidoro, Simonetta Guarrera, Carlotta Sacerdote, Paolo Vineis, Yu-Tang Gao, Yong-Bing Xiang, Victoria K. Cortessis, Manuela Gago-Dominguez, Amit D. Joshi, Román Corral, Faye Elliot, Jennifer H. Barrett, Ananya Choudhury, Sei Chung Sak, D. Timothy Bishop, Heather H. Nelson, Angeline S. Andrew, Margaret R. Karagas, Xifeng Wu, Stephen Chanock, Nuria Malats, Debra Silverman, Manolis Kogevinas, Nathaniel Rothman, Gunnar Steineck, Zuo-Feng Zhang, Donatella Placidi, Jack A. Taylor, Simone Benhamou, Tony Fletcher, Giuseppe Matullo, Jian-Min Yuan, Anne E. Kiltie, Karl T. Kelsey, Jonine D. Figueroa, Jie Lin, and Mariana C. Stern

Abstract

Tobacco smoking is the most important and well-established bladder cancer risk factor and a rich source of chemical carcinogens and reactive oxygen species that can induce damage to DNA in urothelial cells. Therefore, common variation in DNA repair genes might modify bladder cancer risk. In this study, we present results from meta-analyses and pooled analyses conducted as part of the International Consortium of Bladder Cancer. We included data on 10 single nucleotide polymorphisms corresponding to seven DNA repair genes from 13 studies. Pooled analyses and meta-analyses included 5,282 cases and 5,954 controls of non-Latino white origin. We found evidence for weak but consistent associations with ERCC2 D312N [rs1799793; per-allele odds ratio (OR), 1.10; 95% confidence interval (95% CI), 1.01–1.19; P = 0.021], NBN E185Q (rs1805794; per-allele OR, 1.09; 95% CI, 1.01–1.18; P = 0.028), and XPC A499V (rs2228000; per-allele OR, 1.10; 95% CI, 1.00–1.21; P = 0.044). The association with NBN E185Q was limited to ever smokers (interaction P = 0.002) and was strongest for the highest levels of smoking dose and smoking duration. Overall, our study provides the strongest evidence to date for a role of common variants in DNA repair genes in bladder carcinogenesis. [Cancer Res 2009;69(17):6857–64]

Published
2023

24. Supplementary Tables 1-8 from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Author

Montserrat Garcia-Closas, Sung Shim Lani Park, Cecilia Arici, Marcello Campagna, Angela Carta, Stefano Porru, Peter Rudnai, Rajiv Kumar, Kvetoslava Koppova, Eugen Gurzau, Alessandra Allione, Silvia Polidoro, Simonetta Guarrera, Carlotta Sacerdote, Paolo Vineis, Yu-Tang Gao, Yong-Bing Xiang, Victoria K. Cortessis, Manuela Gago-Dominguez, Amit D. Joshi, Román Corral, Faye Elliot, Jennifer H. Barrett, Ananya Choudhury, Sei Chung Sak, D. Timothy Bishop, Heather H. Nelson, Angeline S. Andrew, Margaret R. Karagas, Xifeng Wu, Stephen Chanock, Nuria Malats, Debra Silverman, Manolis Kogevinas, Nathaniel Rothman, Gunnar Steineck, Zuo-Feng Zhang, Donatella Placidi, Jack A. Taylor, Simone Benhamou, Tony Fletcher, Giuseppe Matullo, Jian-Min Yuan, Anne E. Kiltie, Karl T. Kelsey, Jonine D. Figueroa, Jie Lin, and Mariana C. Stern

Abstract

Supplementary Tables 1-8 from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Published
2023

25. Data from TP53 and KRAS2 Mutations in Plasma DNA of Healthy Subjects and Subsequent Cancer Occurrence: A Prospective Study

Author

Pierre Hainaut, Elio Riboli, Rudolf Kaaks, Rodolfo Saracci, Timothy J. Key, Nicholas E. Day, Göran Hallmans, José Ramón Quirós, Carmen Navarro, Aurelio Barricarte, Miren Dorronsoro, Carmen Martinez, Guillem Pera, Petra H. Peeters, H. Bas Bueno-de-Mesquita, Salvatore Panico, Rosario Tumino, Vittorio Krogh, Domenico Palli, Antonia Trichopoulou, Heiner Boeing, Françoise Clavel-Chapelon, Eiliv Lund, Anne Tjønneland, Kim Overvad, Alison Dunning, Christian Malaveille, Herman Autrup, Luisa Airoldi, Armelle Munnia, Simonetta Guarrera, Seymour Garte, Marco Peluso, Emilie Le Roux, Elodie Caboux, Fabrizio Veglia, Giuseppe Matullo, Paolo Vineis, and Emmanuelle Gormally

Abstract

In cancer patients, plasma often contains mutant DNA released by cancer cells. We have assessed the significance of plasma DNA mutations for subsequent cancer development in healthy subjects in a large longitudinal prospective study. The European Prospective Investigation into Cancer and Nutrition study was analyzed with a nested case-control design. Cases were nonsmokers or ex-smokers for >10 years and newly diagnosed with lung, bladder, or upper aerodigestive tract cancers or leukemia accrued after a median follow-up of 6.3 years. Controls were matched 2:1 for follow-up, age, sex, area of recruitment, and smoking status. KRAS2 mutations were detected by mutant-enriched PCR and sequencing (n = 1,098). TP53 mutations were detected by denaturing high-performance liquid chromatography, temporal temperature gradient electrophoresis, and sequencing (n = 550). KRAS2 or TP53 mutations were detected in 13 of 1,098 (1.2%) and 20 of 550 (3.6%) subjects, respectively, 16 of whom developed cancer on average after 18.3 months of follow-up. Among 137 subjects who developed bladder cancer, 5 had KRAS2 mutations [odds ratio (OR), 4.25; 95% confidence interval (95% CI), 1.27-14.15] and 7 had TP53 mutations (OR, 1.81; 95% CI, 0.66-4.97). There was a nonsignificant trend for association between TP53 mutations and bulky adducts in lymphocyte DNA (OR, 2.78; 95% CI, 0.64-12.17). This is the first report of TP53 or KRAS2 mutations in the plasma of healthy subjects in a prospective study, suggesting that KRAS2 mutation is detectable ahead of bladder cancer diagnosis. TP53 mutation may be associated with environmental exposures. These observations have implications for monitoring early steps of carcinogenesis. (Cancer Res 2006; 66(13): 6871-6)

Published
2023

26. Supplementary Figure Legend from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Author

Montserrat Garcia-Closas, Sung Shim Lani Park, Cecilia Arici, Marcello Campagna, Angela Carta, Stefano Porru, Peter Rudnai, Rajiv Kumar, Kvetoslava Koppova, Eugen Gurzau, Alessandra Allione, Silvia Polidoro, Simonetta Guarrera, Carlotta Sacerdote, Paolo Vineis, Yu-Tang Gao, Yong-Bing Xiang, Victoria K. Cortessis, Manuela Gago-Dominguez, Amit D. Joshi, Román Corral, Faye Elliot, Jennifer H. Barrett, Ananya Choudhury, Sei Chung Sak, D. Timothy Bishop, Heather H. Nelson, Angeline S. Andrew, Margaret R. Karagas, Xifeng Wu, Stephen Chanock, Nuria Malats, Debra Silverman, Manolis Kogevinas, Nathaniel Rothman, Gunnar Steineck, Zuo-Feng Zhang, Donatella Placidi, Jack A. Taylor, Simone Benhamou, Tony Fletcher, Giuseppe Matullo, Jian-Min Yuan, Anne E. Kiltie, Karl T. Kelsey, Jonine D. Figueroa, Jie Lin, and Mariana C. Stern

Abstract

Supplementary Figure Legend from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Published
2023

27. Supplementary Table 1 from TP53 and KRAS2 Mutations in Plasma DNA of Healthy Subjects and Subsequent Cancer Occurrence: A Prospective Study

Author

Pierre Hainaut, Elio Riboli, Rudolf Kaaks, Rodolfo Saracci, Timothy J. Key, Nicholas E. Day, Göran Hallmans, José Ramón Quirós, Carmen Navarro, Aurelio Barricarte, Miren Dorronsoro, Carmen Martinez, Guillem Pera, Petra H. Peeters, H. Bas Bueno-de-Mesquita, Salvatore Panico, Rosario Tumino, Vittorio Krogh, Domenico Palli, Antonia Trichopoulou, Heiner Boeing, Françoise Clavel-Chapelon, Eiliv Lund, Anne Tjønneland, Kim Overvad, Alison Dunning, Christian Malaveille, Herman Autrup, Luisa Airoldi, Armelle Munnia, Simonetta Guarrera, Seymour Garte, Marco Peluso, Emilie Le Roux, Elodie Caboux, Fabrizio Veglia, Giuseppe Matullo, Paolo Vineis, and Emmanuelle Gormally

Abstract

Supplementary Table 1 from TP53 and KRAS2 Mutations in Plasma DNA of Healthy Subjects and Subsequent Cancer Occurrence: A Prospective Study

Published
2023

28. Supplementary Figure 1 from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Author

Montserrat Garcia-Closas, Sung Shim Lani Park, Cecilia Arici, Marcello Campagna, Angela Carta, Stefano Porru, Peter Rudnai, Rajiv Kumar, Kvetoslava Koppova, Eugen Gurzau, Alessandra Allione, Silvia Polidoro, Simonetta Guarrera, Carlotta Sacerdote, Paolo Vineis, Yu-Tang Gao, Yong-Bing Xiang, Victoria K. Cortessis, Manuela Gago-Dominguez, Amit D. Joshi, Román Corral, Faye Elliot, Jennifer H. Barrett, Ananya Choudhury, Sei Chung Sak, D. Timothy Bishop, Heather H. Nelson, Angeline S. Andrew, Margaret R. Karagas, Xifeng Wu, Stephen Chanock, Nuria Malats, Debra Silverman, Manolis Kogevinas, Nathaniel Rothman, Gunnar Steineck, Zuo-Feng Zhang, Donatella Placidi, Jack A. Taylor, Simone Benhamou, Tony Fletcher, Giuseppe Matullo, Jian-Min Yuan, Anne E. Kiltie, Karl T. Kelsey, Jonine D. Figueroa, Jie Lin, and Mariana C. Stern

Abstract

Supplementary Figure 1 from Polymorphisms in DNA Repair Genes, Smoking, and Bladder Cancer Risk: Findings from the International Consortium of Bladder Cancer

Published
2023

29. Blood cell DNA methylation biomarkers in preclinical malignant pleural mesothelioma: The EPIC prospective cohort

Author

Alessandra Allione, Clara Viberti, Ilaria Cotellessa, Chiara Catalano, Elisabetta Casalone, Giovanni Cugliari, Alessia Russo, Simonetta Guarrera, Dario Mirabelli, Carlotta Sacerdote, Marco Gentile, Fabian Eichelmann, Matthias B. Schulze, Sophia Harlid, Anne Kirstine Eriksen, Anne Tjønneland, Martin Andersson, Martijn E.T. Dollé, Heleen Van Puyvelde, Elisabete Weiderpass, Miguel Rodriguez‐Barranco, Antonio Agudo, Alicia K. Heath, María‐Dolores Chirlaque, Thérèse Truong, Dzevka Dragic, Gianluca Severi, Sabina Sieri, Torkjel M. Sandanger, Eva Ardanaz, Paolo Vineis, and Giuseppe Matullo

Subjects
Cancer Research, DNA methylation, Oncology, cancer biomarkers, mesothelioma, prospective nested case-control study
Abstract

Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer mainly caused by asbestos exposure. Specific and sensitive non-invasive biomarkers may facilitate and enhance screening programs for the early detection of cancer. We investigated DNA methylation (DNAm) profiles in MPM pre-diagnostic blood samples in a case-control study nested in the European Prospective Investigation into Cancer and nutrition (EPIC) cohort, aiming to characterise DNAm biomarkers associated with MPM. From the EPIC cohort, we included samples from 135 participants who developed MPM during 20 years of follow up and from 135 matched, cancer-free, controls. For the discovery phase we selected EPIC participants who developed MPM within five years from enrolment (n=36) with matched controls. We identified nine differentially methylated CpGs, selected by 10-fold cross-validation and correlation analyses: cg25755428 (MRI1), cg20389709 (KLF11), cg23870316, cg13862711 (LHX6), cg06417478 (HOOK2), cg00667948, cg01879420 (AMD1), cg25317025 (RPL17) and cg06205333 (RAP1A). Receiver operating characteristic (ROC) analysis showed that the model including baseline characteristics (age, sex, PC1wbc) along with the nine MPM-related CpGs has a better predictive value for MPM occurrence than the baseline model alone, maintaining some performance also at more than five years before diagnosis [AUC (area under the curve) 10 years=0.75; baseline AUC range=0.63-0.67)]. DNAm changes as non-invasive biomarkers in pre-diagnostic blood samples of MPM cases were investigated for the first time. Their application can improve the identification of asbestos-exposed individuals at higher MPM risk in order to possibly adopt more intensive monitoring for early disease identification.

Published
2022

30. Personalized therapeutic strategies in HER2-driven gastric cancer

Author

Daniel Moya-Rull, Annunziata Gloghini, Andrea Sartore-Bianchi, Salvatore Siena, Ivana Sarotto, Simonetta Guarrera, Sara Erika Bellomo, Stefania Manenti, Emanuele Rausa, Laura D'Errico, Ida Rapa, Sabrina Rizzolio, Uberto Fumagalli, Rossella Reddavid, Claudia Castelli, Caterina Marchiò, Carla Baronchelli, Tania Capeloa, Federica Morano, Simona Corso, Michele Sacco, Dario Ribero, Stefano De Pascale, Gian Luca Baiocchi, Federica Tosi, Maria Apicella, Salvatore Ribisi, Paola Cassoni, Maurizio Degiuli, Sarah Molfino, Giovanni Sgroi, Silvia Marsoni, Michele Prisciandaro, Stefania Durando, Cristina Migliore, Annalisa Petrelli, Antonino Sottile, Filippo Pietrantonio, Silvia Giordano, Alessandra Raimondi, Anna Sapino, Maria Bencivenga, and Stefano Ughetto

Subjects
Drug resistance, Gastric cancer, HER2, Targeted therapy, Trastuzumab, Oncology, Cancer Research, Immunoconjugates, Receptor, ErbB-2, medicine.medical_treatment, chemistry.chemical_compound, ErbB-2, Antineoplastic Agents, Immunological, 0302 clinical medicine, Surgical oncology, Antineoplastic Combined Chemotherapy Protocols, Prospective Studies, Enzyme Inhibitors, Precision Medicine, skin and connective tissue diseases, Gastroenterology, General Medicine, Protein-Tyrosine Kinases, Immunological, 030220 oncology & carcinogenesis, 030211 gastroenterology & hepatology, Pertuzumab, Receptor, medicine.drug, medicine.medical_specialty, Antineoplastic Agents, Lapatinib, 03 medical and health sciences, Stomach Neoplasms, Internal medicine, medicine, Humans, neoplasms, business.industry, Cancer, medicine.disease, Xenograft Model Antitumor Assays, Blockade, chemistry, Trastuzumab emtansine, business
Abstract

Trastuzumab is the only approved targeted therapy in patients with HER2-amplified metastatic gastric cancer (GC). Regrettably, in clinical practice, only a fraction of them achieves long-term benefit from trastuzumab-based upfront strategy. To advance precision oncology, we investigated the therapeutic efficacy of different HER2-targeted strategies, in HER2 “hyper”-amplified (≥ 8 copies) tumors. We undertook a prospective evaluation of HER2 targeting with monoclonal antibodies, tyrosine kinase inhibitors and antibody–drug conjugates, in a selected subgroup of HER2 “hyper”-amplified gastric patient-derived xenografts (PDXs), through the design of ad hoc preclinical trials. Despite the high level of HER2 amplification, trastuzumab elicited a partial response only in 2 out of 8 PDX models. The dual-HER2 blockade with trastuzumab plus either pertuzumab or lapatinib led to complete and durable responses in 5 (62.5%) out of 8 models, including one tumor bearing a concomitant HER2 mutation. In a resistant PDX harboring KRAS amplification, the novel antibody–drug conjugate trastuzumab deruxtecan (but not trastuzumab emtansine) overcame KRAS-mediated resistance. We also identified a HGF-mediated non-cell-autonomous mechanism of secondary resistance to anti-HER2 drugs, responsive to MET co-targeting. These preclinical randomized trials clearly indicate that in HER2-driven gastric tumors, a boosted HER2 therapeutic blockade is required for optimal efficacy, leading to complete and durable responses in most of the cases. Our results suggest that a selected subpopulation of HER2-“hyper”-amplified GC patients could strongly benefit from this strategy. Despite the negative results of clinical trials, the dual blockade should be reconsidered for patients with clearly HER2-addicted cancers.

Published
2021

31. Association of serum MicroRNA-145-5p levels with microvascular complications of type 1 Diabetes

Author

Federica Barutta, Stefania Bellini, Simonetta Guarrera, Giuseppe Matullo, Casper Schalkwijk, Coen D. Stehouwer, Nish Chaturvedi, Sabita S. Soedamah-Muthu, Marilena Durazzo, Gabriella Gruden, Interne Geneeskunde, RS: Carim - V01 Vascular complications of diabetes and metabolic syndrome, MUMC+: MA Interne Geneeskunde (3), and Medical and Clinical Psychology

Subjects
EXPRESSION, Endocrinology, Diabetes and Metabolism, SMOOTH-MUSCLE-CELLS, BIOMARKERS, Diabetic nephropathy, RETINOPATHY, Diabetic complications, MECHANISMS, Endocrinology, CIRCULATING MICRORNAS, MARKERS, Risk Factors, TARGETS, TGF-β1, Internal Medicine, Humans, Albuminuria, Prospective Studies, Diabetic kidney disease, General Medicine, microRNAs, Cross-Sectional Studies, Diabetes Mellitus, Type 1, Cardiovascular diseases, Type 1 diabetes, CARDIOVASCULAR-DISEASE, MIRNAS, Case-Control Studies, Hypertension, TGF-beta 1
Abstract

AimsTo investigate whether serum miR-145-5p levels were associated with micro-macrovascular chronic complications in patients with type 1 diabetes (DM1).MethodsA nested case-control study from the EURODIAB Prospective Complications Study was performed. Cases (n = 289) had one or more complications of diabetes, whereas controls (n = 153) did not have any complication. We measured miR-145-5p levels by qPCR and investigated the association with diabetes complications.ResultsMean miR-145-5p levels were significantly lower in cases with microangiopathy [2.12 (0.86–4.94)] compared to controls [3.15 (1.21–7.36), P < 0.05] even after adjustment for age, gender, and diabetes duration. In logistic regression analysis, miR-145-5p levels in the lowest tertile were associated with an over three-fold increased odds ratio (OR) of albuminuria [3.22 (1.17–8.81)], independently of both demographic and diabetes-related factors. In addition, mir145-5p levels in the lowest tertile were independently and inversely associated with arterial hypertension [1.96 (1.08–3.56)] and hypertension was the mediator of the relationship between miR-145-5p and albuminuria.ConclusionsIn this large cohort of DM1 patients, we found an inverse association between miR-145-5p and albuminuria that was mediated by systemic hypertension.

Published
2022

32. FOXA1 regulates alternative splicing in prostate cancer

Author

Marco Del Giudice, John G. Foster, Serena Peirone, Alberto Rissone, Livia Caizzi, Federica Gaudino, Caterina Parlato, Francesca Anselmi, Rebecca Arkell, Simonetta Guarrera, Salvatore Oliviero, Giuseppe Basso, Prabhakar Rajan, and Matteo Cereda

Subjects
nonsense-mediated decay, Hepatocyte Nuclear Factor 3-alpha, Male, HNRNPK, Serine-Arginine Splicing Factors, biomarkers, Prostatic Neoplasms, prostate cancer, General Biochemistry, Genetics and Molecular Biology, Chromatin, CP: Cancer, CP: Molecular biology, FLNA, FOXA1, SRSF1, alternative splicing, poison exons, splicing factors, Alternative Splicing, Trans-Activators, Humans, RNA Splicing Factors, Neoplasm Recurrence, Local
Abstract

Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an "exon definition" mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.

Published
2021

33. New DNA methylation signals for malignant pleural mesothelioma risk assessment

Author

Federica Grosso, Marika Sculco, Roberta Libener, Corrado Magnani, Giuseppe Matullo, Alessia Russo, Dario Mirabelli, Alessandra Allione, Daniela Ferrante, Chiara Pirazzini, Marta La Vecchia, Elisabetta Casalone, Chiara Catalano, Simonetta Guarrera, Giovanni Cugliari, and Irma Dianzani

Subjects
0301 basic medicine, Oncology, False discovery rate, Cancer Research, medicine.medical_specialty, Malignant pleural mesothelioma, medicine.disease_cause, Asbestos, Article, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, RC254-282, Epigenome-wide analysis, DNA methylation, business.industry, Confounding, Area under the curve, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, dNaM, Asbestos exposure, Interaction analysis, Odds ratio, 030104 developmental biology, 030220 oncology & carcinogenesis, business, Risk assessment
Abstract

Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasm. Patients are usually diagnosed when current treatments have limited benefits, highlighting the need for noninvasive tests aimed at an MPM risk assessment tool that might improve life expectancy. Three hundred asbestos-exposed subjects (163 MPM cases and 137 cancer-free controls), from the same geographical region in Italy, were recruited. The evaluation of asbestos exposure was conducted considering the frequency, the duration and the intensity of occupational, environmental and domestic exposure. A genome-wide methylation array was performed to identify novel blood DNA methylation (DNAm) markers of MPM. Multiple regression analyses adjusting for potential confounding factors and interaction between asbestos exposure and DNAm on the MPM odds ratio were applied. Epigenome-wide analysis (EWAS) revealed 12 single-CpGs associated with the disease. Two of these showed high statistical power (99%) and effect size (&gt, 0.05) after false discovery rate (FDR) multiple comparison corrections: (i) cg03546163 in FKBP5, significantly hypomethylated in cases (Mean Difference in beta values (MD) = −0.09, 95% CI = −0.12|−0.06, p = 1.2 × 10−7), and (ii) cg06633438 in MLLT1, statistically hypermethylated in cases (MD = 0.07, 95% CI = 0.04|0.10, p = 1.0 × 10−6). Based on the interaction analysis, asbestos exposure and epigenetic profile together may improve MPM risk assessment. Above-median asbestos exposure and hypomethylation of cg03546163 in FKBP5 (OR = 20.84, 95% CI = 8.71|53.96, p = 5.5 × 10−11) and hypermethylation of cg06633438 in MLLT1 (OR = 11.71, 95% CI = 4.97|29.64, p = 5.9 × 10−8) genes compared to below-median asbestos exposure and hyper/hypomethylation of single-CpG DNAm, respectively. Receiver Operation Characteristics (ROC) for Case-Control Discrimination showed a significant increase in MPM discrimination when DNAm information was added in the model (baseline model, BM: asbestos exposure, age, gender and white blood cells), area under the curve, AUC = 0.75, BM + cg03546163 at FKBP5. AUC = 0.89, 2.1 × 10−7, BM + cg06633438 at MLLT1. AUC = 0.89, 6.3 × 10−8. Validation and replication procedures, considering independent sample size and a different DNAm analysis technique, confirmed the observed associations. Our results suggest the potential application of DNAm profiles in blood to develop noninvasive tests for MPM risk assessment in asbestos-exposed subjects.

Published
2021

34. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

Author

Giuseppe Matullo, John R. B. Perry, Meena Kumari, Gemma C Sharp, Tomáš Paus, E. Giralt-Steinhauer, Marta E. Alarcón-Riquelme, Koen F. Dekkers, F. Gagnon, Simonetta Guarrera, Cilla Söderhäll, Rosie M. Walker, Therese Tillin, M. Smarts, Juan E. Castillo-Fernandez, John M. Starr, Jean Shin, Dan Mason, T Esko, Christopher Shaw, Hannah R Elliott, Manon Bernard, David L. Corcoran, Yvonne Awaloff, Ahmad Al Khleifat, Bert Brunekreef, Clara Viberti, John Wright, Gibran Hemani, Kathryn L. Evans, Camilla Schmidt Morgen, Jouke J. Hottenga, Susan M. Ring, Terrie E. Moffitt, Silva Kasela, C. Hale, Idil Yet, Katri Räikkönen, René Luijk, Vanessa Schmoll, Kimberley Burrows, Annelot M. Dekker, D. VanHeemst, Jordana T. Bell, Jordi Jimenez-Conde, Carlotta Sacerdote, Salvatore Panico, Lili Milani, Nabila Kazmi, Torben Hansen, Aleksey Shatunov, J L Min, Richa Gupta, Henning Tiemeier, Grant W. Montgomery, Vincent W. V. Jaddoe, E.J.C. de Geus, Fernando Rivadeneira, Debbie A Lawlor, Carol A. Wang, Toni-Kim Clarke, Susanne Lucae, Nicholas J. Wareham, Jordi Sunyer, Felix R. Day, C. Soriano-Tarraga, Christoph Bock, Juan R. González, D. Aissi, J.B. van Meurs, Ian J. Deary, Ken K. Ong, Louise Arseneault, Eilis Hannon, Bastiaan T. Heijmans, Philip E. Melton, Ashok Kumar, Pierre-Emmanuel Morange, Zdenka Pausova, T.D. Spector, Nicholas G. Martin, J. Mill, Francesc Català-Moll, Alun D. Hughes, Leonard C. Schalkwyk, Giovanni Cugliari, Carlos Ruiz-Arenas, Elena Carnero-Montoro, Marine Germain, Yanni Zeng, Andrew M. McIntosh, Riccardo E. Marioni, Wilfried Karmaus, Ikram, Gonneke Willemsen, Miina Ollikainen, Karen M Ho, Craig E. Pennell, F.I. Rezwan, Darina Czamara, Ramona A. J. Zwamborn, Dorret I. Boomsma, Wendy L. McArdle, J. M. van Dongen, Guillermo Barturen, Matthew Suderman, Richie Poulton, Daniel Lawson, A. Metspalu, David-Alexandre Trégouët, Marian Beekman, Andrew D. Bretherick, Johanna Klughammer, Hongmei Zhang, M.H. van IJzendoorn, Nish Chaturvedi, Jari Lahti, Karen Sugden, Jan H. Veldink, Mariona Bustamante, Avshalom Caspi, Pooja R. Mandaviya, Judith M. Vonk, Tom R. Gaunt, Cheng-Jian Xu, John W. Holloway, Tian Lin, Tom G. Richardson, Caroline L Relton, Naomi R. Wray, Allan F. McRae, George Davey Smith, Erik Melén, Valentina Iotchkova, Ellen A. Nohr, Jaakko Kaprio, Göran Pershagen, Elisabeth B. Binder, A. al Chalabi, T.J. Gorrie-Stone, K. van Eijk, Gerard H. Koppelman, M. Lerro, Alexia Cardona, Sailalitha Bollepalli, P.E. Slagboom, Thorkild I. A. Sørensen, André G. Uitterlinden, Jaume Roquer, Peter M. Visscher, Janine F. Felix, Martin Kerick, Gail Davies, Rae-Chi Huang, Alfredo Iacoangeli, Alison D. Murray, Helsinki Institute of Life Science HiLIFE, Institute for Molecular Medicine Finland, Epigenetics of Complex Diseases and Traits, Department of Public Health, Department of Psychology and Logopedics, Biological Psychology, APH - Mental Health, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, APH - Methodology, Groningen Research Institute for Asthma and COPD (GRIAC), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Epidemiology, Internal Medicine, Pediatrics, Child and Adolescent Psychiatry / Psychology, and Clinical Child and Family Studies

Subjects
Multifactorial Inheritance, ADN, Quantitative Trait Loci, Genome-wide association study, VARIANTS, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, LINKS, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Quantitative Trait, Heritable, Genetic variation, Genetics, WIDE ASSOCIATION, GWAS, Humans, Genetic Predisposition to Disease, Genotip, METAANALYSIS, EQTL, 030304 developmental biology, Epigenesis, SNP ANALYSIS, 0303 health sciences, COMPLEX, dNaM, Chromosome Mapping, DNA, DNA Methylation, Phenotype, Genetic architecture, MODEL, Fenotip, Gene Expression Regulation, DNA methylation, MENDELIAN RANDOMIZATION, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 3111 Biomedicine, Metilació, Transcriptome, Genètica, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

DNA methylation quantitative trait locus (mQTL) analyses on 32,851 participants identify genetic variants associated with DNA methylation at 420,509 sites in blood, resulting in a database of >270,000 independent mQTLs. Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.

Published
2020

35. DNA Methylation of

Author

Giovanni, Cugliari, Chiara, Catalano, Simonetta, Guarrera, Alessandra, Allione, Elisabetta, Casalone, Alessia, Russo, Federica, Grosso, Daniela, Ferrante, Clara, Viberti, Anna, Aspesi, Marika, Sculco, Chiara, Pirazzini, Roberta, Libener, Dario, Mirabelli, Corrado, Magnani, Irma, Dianzani, and Giuseppe, Matullo

Subjects
asbestos exposure, DNA methylation, epigenome-wide analysis, lymphocyte-to-monocyte ratio, malignant pleural mesothelioma, Article, survival analysis
Abstract

Simple Summary Our study is the first one to investigate DNA methylation changes in white blood cells (WBCs) from easily accessible peripheral blood as malignant pleural mesothelioma (MPM) survival biomarker. The Cox proportional hazards regression model highlighted that the methylation status of the CpG dinucleotide cg03546163 is an independent marker of prognosis in MPM patients with a better performance than traditional inflammation-based scores such as lymphocyte-to-monocyte ratio (LMR). Biological validation and replication showed that epigenetic changes at the FKBP5 gene were robustly associated with overall survival (OS) in MPM cases. The identification of simple and valuable prognostic markers for MPM will enable clinicians to select patients who are most likely to benefit from aggressive therapies and avoid subjecting non-responder patients to ineffective treatment. Abstract Malignant pleural mesothelioma (MPM) is an aggressive tumor with median survival of 12 months and limited effective treatments. The scope of this study was to study the relationship between blood DNA methylation (DNAm) and overall survival (OS) aiming at a noninvasive prognostic test. We investigated a cohort of 159 incident asbestos exposed MPM cases enrolled in an Italian area with high incidence of mesothelioma. Considering 12 months as a cut-off for OS, epigenome-wide association study (EWAS) revealed statistically significant (p value = 7.7 × 10−9) OS-related differential methylation of a single-CpG (cg03546163), located in the 5′UTR region of the FKBP5 gene. This is an independent marker of prognosis in MPM patients with a better performance than traditional inflammation-based scores such as lymphocyte-to-monocyte ratio (LMR). Cases with DNAm < 0.45 at the cg03546163 had significantly poor survival compared with those showing DNAm ≥ 0.45 (mean: 243 versus 534 days; p value< 0.001). Epigenetic changes at the FKBP5 gene were robustly associated with OS in MPM cases. Our results showed that blood DNA methylation levels could be promising and dynamic prognostic biomarkers in MPM.

Published
2020

36. Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

Author

Carol A. Wang, Simonetta Guarrera, Avshalom Caspi, Eilis Hannon, Marta E. Alarcón-Riquelme, P. Eline Slagboom, Pooja R. Mandaviya, Koen F. Dekkers, Cheng-Jian Xu, Jari Lahti, Juan E. Castillo-Fernandez, Dan Mason, Dylan Aïssi, Jan H. Veldink, Mariona Bustamante, Melissa C. Smart, Guillermo Barturen, Zdenka Pausova, Jenny van Dongen, Jordi Jimenez-Conde, Craig E. Pennell, Gibran Hemani, Tom R. Gaunt, Camilla Schmidt Morgen, Ken K. Ong, Toni-Kim Clarke, Alexia Cardona, Susanne Lucae, René Luijk, T.J. Gorrie-Stone, Phillip E. Melton, Thorkild I. A. Sørensen, André G. Uitterlinden, Jordana T. Bell, Jouke-Jan Hottenga, Meena Kumari, Francesc Català-Moll, Jonathan Mill, Tõnu Esko, Sailalitha Bollepalli, Dorret I. Boomsma, Torben Hansen, Hongmei Zhang, Yanni Zeng, John Wright, Wilfried Karmaus, Martin Kerick, Carolina Soriano-Tárraga, Jaakko Kaprio, Miina Ollikainen, Eco J. C. de Geus, Jordi Sunyer, Therese Tillin, Juan R. González, Yvonne Awaloff, Faisal I. Rezwan, Karen Sugden, Nicholas G. Martin, Karen M Ho, Andres Metspalu, Marine Germain, Kristel R. van Eijk, Ramona A. J. Zwamborn, George Davey Smith, Judith M. Vonk, Tian Lin, Henning Tiemeier, Grant W. Montgomery, Naomi R. Wray, Rae-Chi Huang, Alfredo Iacoangeli, Wendy L. McArdle, Jean Shin, Michael Lerro, Darina Czamara, Valentina Iotchkova, David-Alexandre Trégouët, Johanna Klughammer, Elena Carnero-Montoro, Pierre-Emmanuel Morange, Andrew M. McIntosh, Gemma C Sharp, Alun D. Hughes, Carlos Ruiz-Arenas, John M. Starr, Riccardo E. Marioni, Peter M. Visscher, Nabila Kazmi, Ian J. Deary, Kathryn L. Evans, Terrie E. Moffitt, Janine F. Felix, Tomáš Paus, Ashok Kumar, Jaume Roquer, Christopher Shaw, Hannah R Elliott, Susan M. Ring, Nish Chaturvedi, Giovanni Cugliari, Ahmad Al Khleifat, Joyce B. J. van Meurs, Kimberley Burrows, Bert Brunekreef, Debbie A Lawlor, Clara Viberti, Louise Arseneault, Silva Kasela, Cilla Söderhäll, Idil Yet, Manon Bernard, Christoph Bock, Vincent W. V. Jaddoe, Felix R. Day, Diana van Heemst, Alison D. Murray, Nicholas J. Wareham, Giuseppe Matullo, John R. B. Perry, Gerard H. Koppelman, M. Arfan Ikram, Ammar Al Chalabi, Gonneke Willemsen, Richie Poulton, Daniel Lawson, Andrew D. Bretherick, Vanessa Schmoll, Carlotta Sacerdote, Annelot M. Dekker, Lili Milani, Fernando Rivadeneira, Erik Melén, John W. Holloway, Gareth E. Davies, Tom G. Richardson, Caroline L Relton, Josine L. Min, Göran Pershagen, Elisabeth B. Binder, Marian Beekman, Chris Haley, Richa Gupta, Bastiaan T. Heijmans, Ellen A. Nohr, Allan F. McRae, Matthew Suderman, Rosie M. Walker, David L. Corcoran, Katri Räikkönen, Marinus H. van IJzendoorn, Eva Giralt-Steinhauer, Leonard C. Schalkwyk, Aleksey Shatunov, and Tim D. Spector

Subjects
Genetics, Regulation of gene expression, 0303 health sciences, Natural selection, dNaM, Biology, Genetic architecture, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Genetic variation, DNA methylation, Trait, 030217 neurology & neurosurgery, DNA, 030304 developmental biology
Abstract

Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. Here we describe results of DNA methylation-quantitative trait loci (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTL of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We reveal that the genetic architecture of DNAm levels is highly polygenic and DNAm exhibits signatures of negative and positive natural selection. Using shared genetic control between distal DNAm sites we construct networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic factors are associated with both blood DNAm levels and complex diseases but in most cases these associations do not reflect causal relationships from DNAm to trait or vice versa indicating a more complex genotype-phenotype map than has previously been hypothesised.

Published
2020

37. Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer

Author

Karin B. Michels, Alexandra M. Binder, Benedetta Mussolin, Andrea Cassingena, Alice Vanzati, Mauro Truini, Salvatore Siena, Manel Esteller, Alessio Amatu, William M. Grady, Andrea Sartore-Bianchi, Simonetta Guarrera, Giulia Siravegna, Sebastian Moran, Sara Bustreo, Federica Di Nicolantonio, Alberto Bardelli, Patrizia Racca, Carlotta Cancelliere, Patrizia Zavattari, Daniele Oddo, Agostino Ponzetti, Giuseppe Matullo, Katia Bencardino, Carmen Cristiano, Sean K. Maden, Chiara Falcomatà, and Ludovic Barault

Subjects
Male, 0301 basic medicine, Oncology, Colorectal cancer, medicine.medical_treatment, chemotherapy, Bioinformatics, Polymerase Chain Reaction, Targeted therapy, 0302 clinical medicine, tumour markers, Digital polymerase chain reaction, Longitudinal Studies, Oligonucleotide Array Sequence Analysis, education.field_of_study, Gastroenterology, Methylation, Middle Aged, 3. Good health, Treatment Outcome, 030220 oncology & carcinogenesis, Female, Drug Monitoring, DNA microarray, Colorectal Neoplasms, Cell-Free Nucleic Acids, Adult, medicine.medical_specialty, Population, colorectal cancer, Antineoplastic Agents, Biology, Article, 03 medical and health sciences, Cell Line, Tumor, Internal medicine, Biomarkers, Tumor, medicine, Humans, Liquid biopsy, methylation, screening, education, Aged, Chemotherapy, DNA Methylation, medicine.disease, 030104 developmental biology, Mutation
Abstract

ObjectiveMutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC).DesignGenome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy.ResultsMethylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival.ConclusionThis five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.

Published
2017

38. Telomerase activity, telomere length andhTERTDNA methylation in peripheral blood mononuclear cells from monozygotic twins with discordant smoking habits

Author

Giuseppe Matullo, Emanuela Medda, Riccardo Crebelli, Simonetta Guarrera, Cristina Andreoli, Alessandra Allione, Francesca Marcon, Ester Siniscalchi, and Giovanni Fiorito

Subjects
0301 basic medicine, medicine.medical_specialty, Telomerase, Epidemiology, Health, Toxicology and Mutagenesis, Methylation, Biology, medicine.disease, Tobacco smoke, Telomere, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Endocrinology, CpG site, 030220 oncology & carcinogenesis, Internal medicine, DNA methylation, Immunology, medicine, Telomerase reverse transcriptase, Lung cancer, Genetics (clinical)
Abstract

Increased telomerase expression has been implicated in the pathogenesis of lung cancer and, since the primary cause of lung cancer is smoking, an association between telomerase reactivation and tobacco smoke has been proposed. In this work an investigation has been performed to assess the relationship between tobacco smoke exposure and telomerase activity (TA) in peripheral blood mononuclear cells of healthy smokers. The methylation status of the catalytic subunit of telomerase hTERT was concurrently investigated to assess the possible association between epigenetic modifications of hTERT and TA. Besides, the association between smoke and telomere length (TL) has been evaluated. Healthy monozygotic twins with discordant smoking habits were selected as study population to minimize inter-individual differences because of demographic characteristics and genetic heterogeneity. Statistically significant higher values of TA and TL were observed in smokers compared to nonsmoker co-twins. The multivariate analysis of data showed, besides smoking habits (P = 0.02), an influence of gender (P = 0.006) and BMI (P = 0.001) on TA and a borderline effect of gender (P = 0.05) on TL. DNA methylation analysis, focused on 100 CpG sites mapping in hTERT, highlighted nine CpG sites differentially methylated in smokers. When co-twins were contrasted, selecting as variables the intra-twin difference in TA and hTERT DNA methylation, a statistically significant inverse correlation (P = 0.003) was observed between TA and DNA methylation at the cg05521538 site. In conclusion, these results indicate an association of tobacco smoke with TA and TL and suggest a possible association between smoke-induced epigenetic effects and TA in healthy smokers. Environ. Mol. Mutagen. 58:551–559, 2017. © 2017 Wiley Periodicals, Inc.

Published
2017

39. Associations of autozygosity with a broad range of human phenotypes

Author

Dennis O. Mook-Kanamori, Salma M. Wakil, Lisa R. Yanek, Dominique P.V. de Kleijn, Gert J. de Borst, Alison D. Murray, Kamran Guity, Vincent W. V. Jaddoe, Mario Pirastu, Carole Ober, Giuseppe Matullo, Charles N. Rotimi, Daniela Ruggiero, Teresa Tusié-Luna, Wolfgang Lieb, Chew-Kiat Heng, John R. B. Perry, Hortensia Moreno-Macías, Jie Zhou, John M. Starr, Juhani Junttila, Lei Yu, Danielle Posthuma, Marcus Dörr, Yingchang Lu, Jonathan P. Bradfield, Einat Granot-Hershkovitz, Karina Meidtner, Wouter van Rheenen, T Esko, Maris Alver, Wen-Jane Lee, Zhengming Chen, Jennifer A. Brody, Paolo Gasparini, Yii-Der Ida Chen, Cinzia Sala, Peter P. Pramstaller, Gauri Prasad, Nana Matoba, Natalie Terzikhan, Simonetta Guarrera, Bjarke Feenstra, Peter Vollenweider, Smeeta Shrestha, Yi-Jen Hung, Lilja Stefansdottir, David R. Weir, Felix R. Day, Antonietta Robino, Liang Zhang, Lluis Quintana-Murci, Nicholas J. Timpson, Robyn E Wootton, Xue W. Mei, Dharambir K. Sanghera, Gisli Masson, Debbie A Lawlor, Thomas Meitinger, Sharon L.R. Kardia, Peter K. Joshi, Frank J. A. van Rooij, Claude Bouchard, Cassandra N. Spracklen, Ken K. Ong, Taulant Muka, Guanjie Chen, Laura J. Scott, Walter Palmas, Daniel I. Chasman, Sarah E. Medland, Krista Fischer, Blair H. Smith, Jon K. Sigurdsson, Leon Straker, Clara Viberti, Yuan Shi, Louis Pérusse, Peter J. van der Most, Timo Tõnis Sikka, Chris Haley, Kuang Lin, Leif Groop, Hester M. den Ruijter, Hakon Hakonarson, Masato Akiyama, Stephan J. L. Bakker, Sonja I. Berndt, Jeffery R. O'Connell, Cisca Wijmenga, Daniele Cusi, Lorena Orozco, Kristjan H. S. Moore, Kevin Sandow, Stephen S. Rich, Stephanie J. Loomis, George Davey Smith, Cornelia M. van Duijn, Sharvari Rahul Shukla, Agnar Helgason, Thorsten Kessler, Anuj Goel, Dan Mason, David W. Clark, James S. Pankow, Simona Vaccargiu, Uwe Völker, Tamara B. Harris, Matthew A. Allison, Clicerio Gonzalez, Sarju Ralhan, I-Te Lee, Matthias Laudes, Yen-Feng Chiu, Neil Poulter, Benjamin Lehne, John Wright, Lawrence F. Bielak, Philip L. De Jager, Reinhold Schmidt, Ya Xing Wang, Matthias Nauck, Diana L. Cousminer, Patrick Deelen, Ani Manichaikul, Stephen J. Chanock, Anders Hamsten, Barry I. Freedman, Gudmar Thorleifsson, Peter Kraft, Ozren Polasek, Jie Yao, Yoshinori Murakami, Paul M. Ridker, Anubha Mahajan, Struan F.A. Grant, Claudia Schurmann, Bjarni Gunnarsson, Catriona L. K. Barnes, Jessica van Setten, Sandosh Padmanabhan, Alena Stančáková, Markus M. Lerch, Anuradha Jagadeesan, Franco Giulianini, Daniel F. Gudbjartsson, Dwaipayan Bharadwaj, Shengchao Alfred Li, Peter S. Sever, Trevor A. Mori, Albertine J. Oldehinkel, Koichi Matsuda, Xueling Sim, Evangelos Evangelou, André G. Uitterlinden, Pekka Jousilahti, Yukihide Momozawa, Ioanna Tzoulaki, Chao A. Hsiung, Ginevra Biino, Murielle Bochud, Hannele Mattsson, Ilja M. Nolte, Sarah H. Wild, Patricia B. Munroe, Jianjun Liu, Bruce M. Psaty, Giriraj R. Chandak, Masahiro Kanai, Tony R. Merriman, Teemu Palviainen, Rodney A. Lea, Janie Corley, Nicholas J. Wareham, Alan B. Zonderman, Makoto Hirata, Matthew J. Bixley, Caroline Hayward, Nora Franceschini, Kristel R van Eijk, Etienne Patin, Daniel Shriner, Niek Verweij, Xiuqing Guo, Fredrik Karpe, Ruth J. F. Loos, Tiinamaija Tuomi, Ashley van der Spek, Patricia A. Peyser, Jessica D. Faul, Christian Fuchsberger, David Cesarini, Alex S. F. Doney, Janine F. Felix, Cornelius A. Rietveld, Jagadish Vangipurapu, Tanguy Corre, Line Skotte, Rajkumar Dorajoo, Catherine Igartua, Meena Kumari, Nona Sotoodehnia, Leonard H. van den Berg, Najaf Amin, Dale R. Nyholt, Harry Campbell, Massimiliano Cocca, Scott D. Gordon, Patrik K. E. Magnusson, John C. Chambers, Traci M. Bartz, Mike A. Nalls, Tin Aung, Nduna Dzimiri, Colin N. A. Palmer, Rob M. van Dam, Johanna Kuusisto, Russell P. Tracy, Anna Damulina, Pierre-Emmanuel Morange, Sylvain Foisy, Jing Hua Zhao, Nicholas G. Martin, Ching-Yu Cheng, Mariaelisa Graff, Rashmi B. Prasad, Alice Stanton, David-Alexandre Trégouët, Yu Guo, Helen R. Warren, Lyn R. Griffiths, Weihua Meng, Annika Tillander, Christa Meisinger, Albert V. Smith, Mark I. McCarthy, Jingyun Yang, Marine Germain, Neil Small, Linda Broer, Vilmundur Gudnason, Gunnar K. Pálsson, Michele K. Evans, Alexander Teumer, Mark J. Caulfield, Giorgia Girotto, Thomas Lumley, Tinca J. C. Polderman, Wei Zhao, Carlos A. Aguilar-Salinas, Jari Lahti, Matthew L. Albert, Yechiel Friedlander, Veikko Salomaa, Iona Y Millwood, Jan H. Veldink, Archie Campbell, Andres Metspalu, Ulf Gyllensten, Grant W. Montgomery, Veronique Vitart, Jai Rup Singh, Saima Afaq, Alan R. Shuldiner, Miao-Li Chee, Adebowale Adeyemo, Jennifer A. Smith, David A. van Heel, Jaspal S. Kooner, Daniela Toniolo, Cristian Pattaro, Jerome I. Rotter, John Whitfield, Melissa C. Smart, Kari E. North, Salman M. Tajuddin, Tallapragada Divya Sri Priyanka, Christopher A. Haiman, Diane M. Becker, Bernhard K. Krämer, Paul Elliott, Lihua Wang, He Gao, Patrick Sulem, Jinyan Huang, Chiea Chuen Khor, Ruifang Li-Gao, Åsa Johansson, Winfried März, Shai Carmi, Ilaria Gandin, Eric Boerwinkle, Gardar Sveinbjornsson, Saskia P. Hagenaars, Sander W. van der Laan, Gerard Pasterkamp, E-Shyong Tai, Hagit Hochner, Yih Chung Tham, Kent D. Taylor, Kari Stefansson, Matt J. Neville, Craig E. Pennell, Yanchun Bao, Annelot M. Dekker, Helena Schmidt, Mehdi Hedayati, Joshua Elliott, Ian J. Deary, Iris E. Jansen, Judith B. Borja, Edith Hofer, Martin Gögele, Igor Rudan, Lude Franke, Matthias Munz, Folkert W. Asselbergs, Bengt Sennblad, Imo Hofer, John D. Rioux, Pim van der Harst, Bahareh Sedaghati-khayat, Giovanni Cugliari, Morris A. Swertz, Francine Grodstein, Erwin P. Bottinger, Carol A. Wang, Andre Franke, Brian F. Meyer, Adele M. Taylor, Klodian Dhana, Jian'an Luan, Constance Turman, Robert A. Scott, May E. Montasser, Alison Pattie, Marco Brumat, Liming Li, Heiner Boeing, Karen L. Mohlke, Clemens Baumbach, Bishwa Raj Sapkota, Unnur Thorsteinsdottir, Naveed Sattar, Amy R. Bentley, Matthias B. Schulze, Ivana Kolcic, Stella Trompet, Sarah E. Harris, Ayo P. Doumatey, Charumathi Sabanayagam, David Eccles, Mary F. Feitosa, Jost B. Jonas, Massimo Mezzavilla, Mark O. Goodarzi, David Ellinghaus, Heribert Schunkert, Christian Gieger, Heikki V. Huikuri, Lingyao Zeng, Johan G. Eriksson, Woon-Puay Koh, Yucheng Jia, Gurpreet Singh Wander, James F. Wilson, Torgny Karlsson, Steven C. Hunt, Weihua Zhang, Maria Pina Concas, Zoltán Kutalik, Rebecca Rohde, Chittaranjan S. Yajnik, Yasaman Saba, Dabeeru C. Rao, Robin G. Walters, Reedik Mägi, Marie Loh, Eero Vuoksimaa, Josyf C. Mychaleckyj, Katri Räikkönen, Philippe Goyette, M. Arfan Ikram, Alicia Huerta-Chagoya, David J. Porteous, Teresa Nutile, J. Wouter Jukema, Noha A. Yousri, Yoichiro Kamatani, Maryam S. Daneshpour, Babette S. Zemel, Rona J. Strawbridge, Tien Yin Wong, Claudia Langenberg, Amy Moore, Marcus E. Kleber, Fereidoun Azizi, Avner Halevy, Erika Salvi, Francis S. Collins, Markku Laakso, Tim Kacprowski, S. Sunna Ebenesersdóttir, William R. Scott, Michael Boehnke, Jin-Fang Chai, Markus Perola, Nicola Pirastu, Wayne Huey-Herng Sheu, Robert Karlsson, Lenore J. Launer, Lili Milani, Renée de Mutsert, Fernando Rivadeneira, David A. Bennett, Nicola D. Kerrison, Paolo Manunta, Graciela E. Delgado, Magnus Johannesson, Carolina Medina-Gomez, Alanna C. Morrison, Kay-Tee Khaw, Jian-Min Yuan, Jaakko Kaprio, Melanie Waldenberger, Ralf Ewert, Hugoline G. de Haan, Andrew A. Hicks, Yukinori Okada, Maria Sabater-Lleal, Marilyn C. Cornelis, Stephanie J. London, Federica Rizzi, Jeanette Erdmann, Marina Ciullo, Michiaki Kubo, University of Edinburgh, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Osaka University Graduate School of Medicine, Laboratory for Cardiovascular Genomics and Informatics [Yokohama] (RIKEN IMS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), deCODE genetics [Reykjavik], Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK (BIHR), Area Science Park, Università degli studi di Trieste = University of Trieste, MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, Harbor UCLA Medical Center [Torrance, Ca.], Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, Department of Electrical and Computer Engineering [Waterloo] (ECE), University of Waterloo [Waterloo], Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], Institute of Pop. Genetics, CNR, Sassari, Shardna life science Pula Cagliari, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Medstar Research Institute, Florida State University [Tallahassee] (FSU), University Medical Center [Utrecht], Centre for Population Health Sciences, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), California State University [Sacramento], Department of Thrombosis and Haemostasis, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Medical University Graz, Department of Neurology, Alzheimer Centre, VU Medical Centre, Amsterdam, Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Frederick National Laboratory for Cancer Research (FNLCR), Wellcome Trust Centre of Human Genetics, University of Oxford, Department of Epidemiology, German Institute of Human Nutrition, University Medical Center Groningen [Groningen] (UMCG), Institute of Genetics and Biophysics, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Medicine, Surgery, and Dentistry, University of Milano, Icelandic Heart Association, Kopavogur, Iceland., Department of Epidemiology [Rotterdam], Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Glasgow, Department of Cardiology, Leiden University Medical Center, Leiden, Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, Queen Mary University of London (QMUL), General Internal Medicine, Johns Hopkins School of Medicine, Johns Hopkins University School of Medicine [Baltimore], Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Genentech, Inc., Genentech, Inc. [San Francisco], University of Tartu, Duke-NUS Medical School [Singapore], Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke (DifE), Leibniz Association, Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of San Carlos, Office of Population Studies Foundation, Icahn School of Medicine at Mount Sinai [New York] (MSSM), King‘s College London, Division of Cancer Epidemiology and Genetics, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), University of Oxford, Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Department of Internal Medicine B, University Medicine Greifswald, Greifswald, University of Chicago, University of Huddersfield, Infectious diseases division, Department of internal medicine, Washington University in Saint Louis (WUSTL), Section on Nephrology [Winston-Salem, NC, USA] (Department of Internal Medicine), Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center-Wake Forest Baptist Medical Center, Radcliffe Department of Medicine [Oxford], Harvard School of Public Health, Kunming University of Science and Technology (KMUST), Sans affiliation, University of Southern California (USC), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), MRC Centrer for Nutritional Epidemiology and Cancer Prevention and Survival, University of Cambridge [UK] (CAM), National University of Singapore (NUS), Experimental Cardiology Laboratory (ECL), Unirversity Medical Center, Department of Medical Statistics, Epidemiology and Medical Informatics, University of Zagreb, Department of Medical Genetics, Department of Medicine, University of Eastern Finland-Kuopio University Hospital, MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, Capital Normal University [Beijing], Saw Swee Hock School of Public Health, National Institute for Environmental Health Sciences Research Triangle Park, Brown University, MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, Toyota Research Institute, Helmholtz Zentrum München = German Research Center for Environmental Health, Department of Chemistry and Biochemistry [Boulder], University of Colorado [Boulder], Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital de la Timone [CHU - APHM] (TIMONE), Metacohorts Consortium, Universiteit Leiden, Institute of Clinical Chemistry and Laboratory Medicine, University of Groningen [Groningen], Medical Research Concil Epidemiology Unit, Institute of Medical Science, Faculty of Medicine, Genetics and Pathology, Imperial College London, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Brigham and Women's Hospital [Boston], Erasmus University Rotterdam, Department of Chronic Disease Prevention, National Institute for Health and Welfare [Helsinki], Department of Biostatistics and Center for Statistical Genetics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System-School of public health, The University of Hong Kong (HKU)-The University of Hong Kong (HKU), Stockholm Bioinformatics Center (SBC), Stockholm University, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, INRH, Department of Genetics, Los Angeles Biomedical Research Institute (LA BioMed), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Western General Hospital, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Medical Research Council, Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute-University of Pittsburgh Graduate School of Public Health, Zhengzhou University of Light Industry, Department of Electrical and Electronic Engineering [Niigata Univ.], Niigata University, Genetic Epidemiology Unit, University College of London [London] (UCL), Aston Business School, Aston University [Birmingham], Division of Cancer Epidemiology and Genetics [Bethesda, MD, États-Unis], Centre Hospitalier Universitaire Vaudois (CHUV), Pennington Biomedical Research Center, University of Washington [Seattle], Guy's and St Thomas' Hospitals, Northwestern Polytechnical University [Xi'an] (NPU), Department of Social Medicine, University of Bristol [Bristol], Department of Genomics of Common Disease [London, UK], Imperial College London-Hammersmith Hospital NHS Imperial College Healthcare, Department of Internal Medicine, Institute of Clinical Molecular Biology, Kiel University, Medizinische Klinik II, Universität zu Lübeck = University of Lübeck [Lübeck], Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, Institute for Social Research, University of Michigan System-University of Michigan System, Division of Statistical Genomics, Washington University School of Medicine, Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel (CAU), Department of Physics, RISSC-Lab-University of Naples Federico II = Università degli studi di Napoli Federico II, Lund University [Lund], Icelandic Heart Association, Heart Preventive Clinic and Research Institute, The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Génétique moléculaire de la neurotransmission et des processus neurodégénératifs (LGMNPN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Medical Research Center Oulu, University of Oulu, University of Utah School of Medicine [Salt Lake City], The Generation R Study, Pediatrics, Epidemiology, Center for Translational and Computational Neuroimmunology [New York, NY, États-Unis] (CTCN), Department of Neurology [New York, NY, États-Unis], Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York]-Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York], Universität Heidelberg [Heidelberg] = Heidelberg University, Interuniversity Cardiology Institute Netherlands, School of Public Health, University of Michigan [Dearborn], Department of Epidemiology and Public Health, University of Kuopio, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Institute of Epidemiology and Biobank PopGen, Department of Biostatistics, University of Washington, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Clinical Institute of Medical and Chemical Laboratory Diagnostics, Karl-Franzens-Universität Graz, Department of Genetics, Biology and Biochemistry, Università degli studi di Torino = University of Turin (UNITO), Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), QIMR Berghofer Medical Research Institute, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC)-UNC Gillings School of Global Public Health-Carolina Center for Genome Sciences, University of Illinois [Chicago] (UIC), University of Illinois System, Experimental Cardiology Laboratory, Genetic Epidemiology and Clinical Research Group, Umea University Hospital, Functional Genomics, Erasmus Medical Centre, National Human Genome Research Institute (NHGRI), School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Department of Pathological Biochemistry, Royal Infirmary, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Institute of Metabolic Science, MRC, University of Maryland School of Medicine [Baltimore, MD, USA], Centre for Molecular Epidemiology, Centre for Causal Analyses in Translational Epidemiology, University of Bristol [Bristol]-Medical Research Council, IRCCS San Raffaele Scientific Institute [Milan, Italie], U937, Génomique cardiovasculaire, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), University of Michigan System, HMNC Brain Health, Singapore Eye Research Institute, Partenaires INRAE, Institut d'Électronique et des Technologies du numéRique (IETR), Université de Nantes (UN)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Psychiatry and Psychotherapy, Rheinische Friedrich-Wilhelms-Universität Bonn, University of Groningen, Department of Genomics of Common Disease, Department of Microbiology, The Freeman Hospital, Department Biostatistics University of North Carolina, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, Clark, D. W., Okada, Y., Moore, K. H. S., Mason, D., Pirastu, N., Gandin, I., Mattsson, H., Barnes, C. L. K., Lin, K., Zhao, J. H., Deelen, P., Rohde, R., Schurmann, C., Guo, X., Giulianini, F., Zhang, W., Medina-Gomez, C., Karlsson, R., Bao, Y., Bartz, T. M., Baumbach, C., Biino, G., Bixley, M. J., Brumat, M., Chai, J. -F., Corre, T., Cousminer, D. L., Dekker, A. M., Eccles, D. A., van Eijk, K. R., Fuchsberger, C., Gao, H., Germain, M., Gordon, S. D., de Haan, H. G., Harris, S. E., Hofer, E., Huerta-Chagoya, A., Igartua, C., Jansen, I. E., Jia, Y., Kacprowski, T., Karlsson, T., Kleber, M. E., Li, S. A., Li-Gao, R., Mahajan, A., Matsuda, K., Meidtner, K., Meng, W., Montasser, M. E., van der Most, P. J., Munz, M., Nutile, T., Palviainen, T., Prasad, G., Prasad, R. B., Priyanka, T. D. S., Rizzi, F., Salvi, E., Sapkota, B. R., Shriner, D., Skotte, L., Smart, M. C., Smith, A. V., van der Spek, A., Spracklen, C. N., Strawbridge, R. J., Tajuddin, S. M., Trompet, S., Turman, C., Verweij, N., Viberti, C., Wang, L., Warren, H. R., Wootton, R. E., Yanek, L. R., Yao, J., Yousri, N. A., Zhao, W., Adeyemo, A. A., Afaq, S., Aguilar-Salinas, C. A., Akiyama, M., Albert, M. L., Allison, M. A., Alver, M., Aung, T., Azizi, F., Bentley, A. R., Boeing, H., Boerwinkle, E., Borja, J. B., de Borst, G. J., Bottinger, E. P., Broer, L., Campbell, H., Chanock, S., Chee, M. -L., Chen, G., Chen, Y. -D. I., Chen, Z., Chiu, Y. -F., Cocca, M., Collins, F. S., Concas, M. P., Corley, J., Cugliari, G., van Dam, R. M., Damulina, A., Daneshpour, M. S., Day, F. R., Delgado, G. E., Dhana, K., Doney, A. S. F., Dorr, M., Doumatey, A. P., Dzimiri, N., Ebenesersdottir, S. S., Elliott, J., Elliott, P., Ewert, R., Felix, J. F., Fischer, K., Freedman, B. I., Girotto, G., Goel, A., Gogele, M., Goodarzi, M. O., Graff, M., Granot-Hershkovitz, E., Grodstein, F., Guarrera, S., Gudbjartsson, D. F., Guity, K., Gunnarsson, B., Guo, Y., Hagenaars, S. P., Haiman, C. A., Halevy, A., Harris, T. B., Hedayati, M., van Heel, D. A., Hirata, M., Hofer, I., Hsiung, C. A., Huang, J., Hung, Y. -J., Ikram, M. A., Jagadeesan, A., Jousilahti, P., Kamatani, Y., Kanai, M., Kerrison, N. D., Kessler, T., Khaw, K. -T., Khor, C. C., de Kleijn, D. P. V., Koh, W. -P., Kolcic, I., Kraft, P., Kramer, B. K., Kutalik, Z., Kuusisto, J., Langenberg, C., Launer, L. J., Lawlor, D. A., Lee, I. -T., Lee, W. -J., Lerch, M. M., Li, L., Liu, J., Loh, M., London, S. J., Loomis, S., Lu, Y., Luan, J., Magi, R., Manichaikul, A. W., Manunta, P., Masson, G., Matoba, N., Mei, X. W., Meisinger, C., Meitinger, T., Mezzavilla, M., Milani, L., Millwood, I. Y., Momozawa, Y., Moore, A., Morange, P. -E., Moreno-Macias, H., Mori, T. A., Morrison, A. C., Muka, T., Murakami, Y., Murray, A. D., de Mutsert, R., Mychaleckyj, J. C., Nalls, M. A., Nauck, M., Neville, M. J., Nolte, I. M., Ong, K. K., Orozco, L., Padmanabhan, S., Palsson, G., Pankow, J. S., Pattaro, C., Pattie, A., Polasek, O., Poulter, N., Pramstaller, P. P., Quintana-Murci, L., Raikkonen, K., Ralhan, S., Rao, D. C., van Rheenen, W., Rich, S. S., Ridker, P. M., Rietveld, C. A., Robino, A., van Rooij, F. J. A., Ruggiero, D., Saba, Y., Sabanayagam, C., Sabater-Lleal, M., Sala, C. F., Salomaa, V., Sandow, K., Schmidt, H., Scott, L. J., Scott, W. R., Sedaghati-Khayat, B., Sennblad, B., van Setten, J., Sever, P. J., Sheu, W. H. -H., Shi, Y., Shrestha, S., Shukla, S. R., Sigurdsson, J. K., Sikka, T. T., Singh, J. R., Smith, B. H., Stancakova, A., Stanton, A., Starr, J. M., Stefansdottir, L., Straker, L., Sulem, P., Sveinbjornsson, G., Swertz, M. A., Taylor, A. M., Taylor, K. D., Terzikhan, N., Tham, Y. -C., Thorleifsson, G., Thorsteinsdottir, U., Tillander, A., Tracy, R. P., Tusie-Luna, T., Tzoulaki, I., Vaccargiu, S., Vangipurapu, J., Veldink, J. H., Vitart, V., Volker, U., Vuoksimaa, E., Wakil, S. M., Waldenberger, M., Wander, G. S., Wang, Y. X., Wareham, N. J., Wild, S., Yajnik, C. S., Yuan, J. -M., Zeng, L., Zhang, L., Zhou, J., Amin, N., Asselbergs, F. W., Bakker, S. J. L., Becker, D. M., Lehne, B., Bennett, D. A., van den Berg, L. H., Berndt, S. I., Bharadwaj, D., Bielak, L. F., Bochud, M., Boehnke, M., Bouchard, C., Bradfield, J. P., Brody, J. A., Campbell, A., Carmi, S., Caulfield, M. J., Cesarini, D., Chambers, J. C., Chandak, G. R., Cheng, C. -Y., Ciullo, M., Cornelis, M., Cusi, D., Smith, G. D., Deary, I. J., Dorajoo, R., van Duijn, C. M., Ellinghaus, D., Erdmann, J., Eriksson, J. G., Evangelou, E., Evans, M. K., Faul, J. D., Feenstra, B., Feitosa, M., Foisy, S., Franke, A., Friedlander, Y., Gasparini, P., Gieger, C., Gonzalez, C., Goyette, P., Grant, S. F. A., Griffiths, L. R., Groop, L., Gudnason, V., Gyllensten, U., Hakonarson, H., Hamsten, A., van der Harst, P., Heng, C. -K., Hicks, A. A., Hochner, H., Huikuri, H., Hunt, S. C., Jaddoe, V. W. V., De Jager, P. L., Johannesson, M., Johansson, A., Jonas, J. B., Jukema, J. W., Junttila, J., Kaprio, J., Kardia, S. L. R., Karpe, F., Kumari, M., Laakso, M., van der Laan, S. W., Lahti, J., Laudes, M., Lea, R. A., Lieb, W., Lumley, T., Martin, N. G., Marz, W., Matullo, G., Mccarthy, M. I., Medland, S. E., Merriman, T. R., Metspalu, A., Meyer, B. F., Mohlke, K. L., Montgomery, G. W., Mook-Kanamori, D., Munroe, P. B., North, K. E., Nyholt, D. R., O'Connell, J. R., Ober, C., Oldehinkel, A. J., Palmas, W., Palmer, C., Pasterkamp, G. G., Patin, E., Pennell, C. E., Perusse, L., Peyser, P. A., Pirastu, M., Polderman, T. J. C., Porteous, D. J., Posthuma, D., Psaty, B. M., Rioux, J. D., Rivadeneira, F., Rotimi, C., Rotter, J. I., Rudan, I., Den Ruijter, H. M., Sanghera, D. K., Sattar, N., Schmidt, R., Schulze, M. B., Schunkert, H., Scott, R. A., Shuldiner, A. R., Sim, X., Small, N., Smith, J. A., Sotoodehnia, N., Tai, E. -S., Teumer, A., Timpson, N. J., Toniolo, D., Tregouet, D. -A., Tuomi, T., Vollenweider, P., Wang, C. A., Weir, D. R., Whitfield, J. B., Wijmenga, C., Wong, T. -Y., Wright, J., Yang, J., Yu, L., Zemel, B. S., Zonderman, A. B., Perola, M., Magnusson, P. K. E., Uitterlinden, A. G., Kooner, J. S., Chasman, D. I., Loos, R. J. F., Franceschini, N., Franke, L., Haley, C. S., Hayward, C., Walters, R. G., Perry, J. R. B., Esko, T., Helgason, A., Stefansson, K., Joshi, P. K., Kubo, M., Wilson, J. F., Læknadeild (HÍ), Faculty of Medicine (UI), Félagsfræði-, mannfræði- og þjóðfræðideild (HÍ), Faculty of Sociology, Anthropology and Folkloristics (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), School of Engineering and Natural Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), Félagsvísindasvið (HÍ), School of Social Sciences (UI), Háskóli Íslands, University of Iceland, Clark, David W [0000-0002-1025-9185], Okada, Yukinori [0000-0002-0311-8472], Moore, Kristjan H S [0000-0002-9579-4362], Mason, Dan [0000-0002-0026-9216], Pirastu, Nicola [0000-0002-5363-3886], Gandin, Ilaria [0000-0003-3196-2491], Deelen, Patrick [0000-0002-5654-3966], Schurmann, Claudia [0000-0003-4158-9192], Medina-Gomez, Carolina [0000-0001-7999-5538], Karlsson, Robert [0000-0002-8949-2587], Bao, Yanchun [0000-0002-6102-5098], Biino, Ginevra [0000-0002-9936-946X], Brumat, Marco [0000-0003-3268-039X], Chai, Jin-Fang [0000-0003-3770-1137], Eccles, David A [0000-0003-4634-4995], Gordon, Scott D [0000-0001-7623-328X], Harris, Sarah E [0000-0002-4941-5106], Kacprowski, Tim [0000-0002-5393-2413], Karlsson, Torgny [0000-0001-8095-6149], Kleber, Marcus E [0000-0003-0663-7275], Mahajan, Anubha [0000-0001-5585-3420], Matsuda, Koichi [0000-0001-7292-2686], Meng, Weihua [0000-0001-5388-8494], van der Most, Peter J [0000-0001-8450-3518], Munz, Matthias [0000-0002-4728-3357], Palviainen, Teemu [0000-0002-7847-8384], Prasad, Rashmi B [0000-0002-4400-6741], Salvi, Erika [0000-0002-2724-2291], Skotte, Line [0000-0002-7398-1271], van der Spek, Ashley [0000-0001-7136-0159], Spracklen, Cassandra N [0000-0003-3590-7182], Strawbridge, Rona J [0000-0001-8506-3585], Tajuddin, Salman M [0000-0002-7919-8528], Verweij, Niek [0000-0002-4303-7685], Yanek, Lisa R [0000-0001-7117-1075], Zhao, Wei [0000-0001-7388-0692], Albert, Matthew L [0000-0001-7285-6973], Bentley, Amy R [0000-0002-0827-9101], Chanock, Stephen [0000-0002-2324-3393], Chen, Zhengming [0000-0001-6423-105X], Chiu, Yen-Feng [0000-0002-3352-4500], Cocca, Massimiliano [0000-0002-1127-7596], Collins, Francis S [0000-0002-1023-7410], Cugliari, Giovanni [0000-0002-6080-0718], Damulina, Anna [0000-0001-8241-2727], Day, Felix R [0000-0003-3789-7651], Dhana, Klodian [0000-0002-6397-7009], Dzimiri, Nduna [0000-0003-3395-5754], Elliott, Paul [0000-0002-7511-5684], Felix, Janine F [0000-0002-9801-5774], Freedman, Barry I [0000-0003-0275-5530], Girotto, Giorgia [0000-0003-4507-6589], Goel, Anuj [0000-0003-2307-4021], Goodarzi, Mark O [0000-0001-6364-5103], Gudbjartsson, Daniel F [0000-0002-5222-9857], Guity, Kamran [0000-0002-8379-9668], van Heel, David A [0000-0002-0637-2265], Hirata, Makoto [0000-0002-9994-9958], Ikram, M Arfan [0000-0003-0372-8585], Kamatani, Yoichiro [0000-0001-8748-5597], Kanai, Masahiro [0000-0001-5165-4408], Khor, Chiea Chuen [0000-0002-1128-4729], Kolcic, Ivana [0000-0001-7918-6052], Langenberg, Claudia [0000-0002-5017-7344], Lawlor, Deborah A [0000-0002-6793-2262], Liu, Jianjun [0000-0002-3255-3019], London, Stephanie J [0000-0003-4911-5290], Luan, Jian’an [0000-0003-3137-6337], Matoba, Nana [0000-0001-5329-0134], Mei, Xue W [0000-0002-6279-4884], Mezzavilla, Massimo [0000-0002-9000-4595], Milani, Lili [0000-0002-5323-3102], Mori, Trevor A [0000-0002-5264-9229], Murakami, Yoshinori [0000-0002-2826-4396], Murray, Alison D [0000-0003-4915-4847], Mychaleckyj, Josyf C [0000-0003-2595-0005], Neville, Matt J [0000-0002-6004-5433], Nolte, Ilja M [0000-0001-5047-4077], Ong, Ken K [0000-0003-4689-7530], Pálsson, Gunnar [0000-0002-8231-3961], Pankow, James S [0000-0001-7076-483X], Pattaro, Cristian [0000-0002-4119-0109], Quintana-Murci, Lluis [0000-0003-2429-6320], van Rheenen, Wouter [0000-0002-5860-1533], Rich, Stephen S [0000-0003-3872-7793], Rietveld, Cornelius A [0000-0003-4053-1861], Ruggiero, Daniela [0000-0003-3898-7827], Sabanayagam, Charumathi [0000-0002-4042-4719], Sabater-Lleal, Maria [0000-0002-0128-379X], Sala, Cinzia Felicita [0000-0003-2514-2075], 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Mark J [0000-0001-9295-3594], Smith, George Davey [0000-0002-1407-8314], Dorajoo, Rajkumar [0000-0001-6608-2051], Ellinghaus, David [0000-0002-4332-6110], Erdmann, Jeanette [0000-0002-4486-6231], Evangelou, Evangelos [0000-0002-5488-2999], Feenstra, Bjarke [0000-0003-1478-649X], Feitosa, Mary [0000-0002-0933-2410], Franke, Andre [0000-0003-1530-5811], Grant, Struan F A [0000-0003-2025-5302], Griffiths, Lyn R [0000-0002-6774-5475], Groop, Leif [0000-0002-0187-3263], Gudnason, Vilmundur [0000-0001-5696-0084], van der Harst, Pim [0000-0002-2713-686X], Heng, Chew-Kiat [0000-0002-7309-9473], Hicks, Andrew A [0000-0001-6320-0411], Jaddoe, Vincent W V [0000-0003-2939-0041], De Jager, Philip L [0000-0002-8057-2505], Johannesson, Magnus [0000-0001-8759-6393], Johansson, Åsa [0000-0002-2915-4498], Jonas, Jost B [0000-0003-2972-5227], Jukema, J Wouter [0000-0002-3246-8359], Kaprio, Jaakko [0000-0002-3716-2455], Laakso, Markku [0000-0002-3394-7749], van der Laan, Sander W [0000-0001-6888-1404], Lahti, Jari [0000-0002-4310-5297], Martin, Nicholas G [0000-0003-4069-8020], Medland, Sarah E [0000-0003-1382-380X], Merriman, Tony R [0000-0003-0844-8726], Metspalu, Andres [0000-0002-3718-796X], Mohlke, Karen L [0000-0001-6721-153X], Montgomery, Grant W [0000-0002-4140-8139], Munroe, Patricia B [0000-0002-4176-2947], Nyholt, Dale R [0000-0001-7159-3040], Ober, Carole [0000-0003-4626-9809], Oldehinkel, Albertine J [0000-0003-3925-3913], Palmer, Colin [0000-0002-6415-6560], Perusse, Louis [0000-0001-6440-9698], Polderman, Tinca J. C. [0000-0001-5564-301X], Porteous, David J [0000-0003-1249-6106], Rioux, John D [0000-0001-7560-8326], Rivadeneira, Fernando [0000-0001-9435-9441], Rotimi, Charles [0000-0001-5759-053X], Rotter, Jerome I [0000-0001-7191-1723], Rudan, Igor [0000-0001-6993-6884], Sattar, Naveed [0000-0002-1604-2593], Sim, Xueling [0000-0002-1233-7642], Smith, Jennifer A [0000-0002-3575-5468], Teumer, Alexander [0000-0002-8309-094X], Timpson, Nicholas J [0000-0002-7141-9189], Tuomi, Tiinamaija [0000-0002-8306-6202], Wang, Carol A [0000-0002-4301-3974], Weir, David R [0000-0002-1661-2402], Whitfield, John B [0000-0002-1103-0876], Magnusson, Patrik K. E. [0000-0002-7315-7899], Uitterlinden, André G [0000-0002-7276-3387], Loos, Ruth J. F. [0000-0002-8532-5087], Franke, Lude [0000-0002-5159-8802], Haley, Chris S [0000-0002-9811-0210], Hayward, Caroline [0000-0002-9405-9550], Walters, Robin G [0000-0002-9179-0321], Joshi, Peter K [0000-0002-6361-5059], Wilson, James F [0000-0001-5751-9178], Apollo - University of Cambridge Repository, Moore, Kristjan HS [0000-0002-9579-4362], Luan, Jian'an [0000-0003-3137-6337], Grant, Struan FA [0000-0003-2025-5302], Jaddoe, Vincent WV [0000-0003-2939-0041], Polderman, Tinca JC [0000-0001-5564-301X], Magnusson, Patrik KE [0000-0002-7315-7899], Loos, Ruth JF [0000-0002-8532-5087], Neurology, Human genetics, Amsterdam Reproduction & Development (AR&D), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Stem Cell Aging Leukemia and Lymphoma (SALL), Institute for Molecular Medicine Finland, Department of Psychology and Logopedics, University Management, Developmental Psychology Research Group, Staff Services, Cognitive and Brain Aging, Research Programs Unit, Diabetes and Obesity Research Program, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, Clinicum, University of Helsinki, Centre of Excellence in Complex Disease Genetics, Department of Public Health, Genetic Epidemiology, Helsinki Collegium for Advanced Studies, HUS Abdominal Center, Endokrinologian yksikkö, Bradford Teaching Hospitals NHS Foundation Trust [Bradford, UK] (BTHFT), University of Trieste, Université de Lausanne (UNIL), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Institut Pasteur [Paris], University of Oxford [Oxford], Medical Genetics, Dept. RSD and Public Health, IRCCS-Burlo Garofolo/University of Trieste, sans affiliation, Helmholtz-Zentrum München (HZM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute of Cardiovascular Science, University College London, Hammersmith Hospital NHS Imperial College Healthcare-Imperial College London, Universität zu Lübeck [Lübeck], University of Ioannina Medical School, Università degli studi di Napoli Federico II-RISSC-Lab, Universität Heidelberg [Heidelberg], University of Turin, University of California-University of California, Nantes Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), University of Helsinki-University of Helsinki, Université de Nantes (UN)-Université de Rennes 1 (UR1), Erasmus MC other, Internal Medicine, and Applied Economics

Subjects
0301 basic medicine, 631/208/1397, Chemistry(all), Health Status, [SDV]Life Sciences [q-bio], LOCI, General Physics and Astronomy, MESH: Haplotype, MESH: Cognition, 030105 genetics & heredity, Runs of Homozygosity, Biochemistry, Consanguinity, Cognition, Inbreeding depression, 2.1 Biological and endogenous factors, Body Size, Inbreeding, Skyldleikarækt, Aetiology, Human phenotypes, lcsh:Science, MESH: Health Status, Genetics, Multidisciplinary, Inbreeding Depression, Confounding, Homozygote, RUNS, 631/208/205, 631/208/721, 3. Good health, genomic inbreeding coefficients, MESH: Risk-Taking, 631/208/730, Autozygosit, homozygosity, Erfðarannsóknir, Medical Genetics, genomic inbreeding coefficient, MESH: Homozygote, Offspring, Science, Autozygosity, Blóðsifjar, 610 Medicine & health, Biology, INBREEDING DEPRESSION, HOMOZYGOSITY, FERTILITY, QUANTIFICATION, Physics and Astronomy(all), General Biochemistry, Genetics and Molecular Biology, Article, Association, 03 medical and health sciences, Risk-Taking, 360 Social problems & social services, Journal Article, Humans, ddc:610, Allele, Alleles, Medicinsk genetik, Genetic association study, MESH: Consanguinity, MESH: Body Size, MESH: Humans, Biochemistry, Genetics and Molecular Biology(all), MESH: Alleles, Haplotype, MESH: Fertility, General Chemistry, Brain Disorders, MESH: Inbreeding Depression, 030104 developmental biology, Fertility, Haplotypes, Genetic markers, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 3111 Biomedicine, Genetics and Molecular Biology(all)
Abstract

Publisher's version (útgefin grein)., In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding., This paper is the work of the ROHgen consortium. We thank the Sigma T2D Consortium, whose members are detailed in Supplementary Note 3. We thank the UK Biobank Resource, approved under application 19655; we acknowledge funding from the UK Medical Research Council Human Genetics Unit and MRC Doctoral Training Programme in Precision Medicine. We also thank Neil Robertson, Wellcome Trust Centre for Human Genetics, Oxford, for use of his author details management software, Authorial. Finally, we thank all the participants, researchers and funders of ROHgen cohorts. Cohort-specific acknowledgements are in Supplementary Data 2; personal acknowledgements and disclosures are in Supplementary Note 2. We thank Rachel Edwards for administrative assistance.

Published
2019

40. Improving the prediction of cardiovascular risk with machine-learning and DNA methylation data

Author

Simonetta Guarrera, Paolo Vineis, Carlotta Sacerdote, Giuseppe Matullo, Rosario Tumino, Giovanni Cugliari, Vittorio Krogh, Piero Fariselli, Silvia Benevenuta, and Salvatore Panico

Subjects
0301 basic medicine, Epigenetic biomarkers, 030109 nutrition & dietetics, business.industry, Computer science, Machine learning, computer.software_genre, Random forest, 03 medical and health sciences, 030104 developmental biology, DNA methylation, Computational statistics, Artificial intelligence, business, computer, Reliability (statistics)
Abstract

Classically, the cardiovascular risk of individual is evaluated using phenomenological variables (PV)such as blood pressure, body mass, smoker status, gender, age etc. Here we show that, on prospective study (after 10–15 years)these PV display a poor agreement with case-control samples. We were able to obtain more accurate predictions using both DNA methylation data and PV as input features of a Random Forest model, achieving a ROC-AUC of 0.74. Furthermore, the Random Forest output correlates with the reliability of the predictions producing a ROC-AUC of 0.90 when only the most reliable predictions are taken into consideration.

Published
2019

41. Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9

Author

Chris Finan, Yoav Ben-Shlomo, Eric B. Larson, Tine Jess, Richard W Morris, Daniel I. Chasman, Fernando Pires Hartwig, Catherine Welch, Rodney J. Scott, Helen E. Speedy, Andrzej Pajak, Raha Pazoki, André G. Uitterlinden, Torben Hansen, Marc Sanson, Hakon Hakonarson, Claudia Langenberg, Joey Ward, John Wright, Dorothée Thuillier, Ben Kinnersley, Diederick E. Grobbee, Yvonne T. van der Schouw, Pieter Sonneveld, Michiel L. Bots, Harold Snieder, Karim Labreche, Dan M. Roden, Archie Campbell, Melissa C. Smart, Christine Power, Pim van der Harst, Amélie Bonnefond, Ingrid E. Christophersen, Riyaz S. Patel, Uwe Völker, Stephen Hancock, Niels Grarup, Dennis O. Mook-Kanamori, Mariza de Andrade, Caroline Dale, N. Charlotte Onland-Moret, David R. Crosslin, Meena Kumari, Erik Ingelsson, Michael V. Holmes, Spiros Denaxas, Sudha Seshadri, Kees Hovingh, Marcus Dörr, Paul M. Ridker, Stefan Coassin, Albert Hofman, Andrew N. Nicolaides, Oluf Pedersen, Philippe Froguel, Simonetta Guarrera, Murray H. Brilliant, Sara E. Dobbins, Salim Yusuf, Kari Hemminki, Erik P A Van Iperen, Abbas Dehghan, Jill P. Pell, Alexander Teumer, Peter W. Schofield, Aroon D. Hingorani, Dan Mason, Amand F. Schmidt, Rui Bebiano Da Providencia E Costa, James M. Allan, Leslie A. Lange, Niels Weinhold, Stefan Gustafsson, Jackie F. Price, Mika Kivimäki, Hynek Pikhart, Kirchner H. Lester, Lars Lind, Philip J. Law, Cara L. Carty, David Preiss, Richard S. Houlston, Robin Young, Tom W. Meade, Martin O'Donnell, Alexander P. Reiner, Ni Li, Oscar H. Franco, Zammy Fairhurst-Hunter, Ronan Roussel, Tim Christen, Ilja Demuth, David Carrell, Catherine A. McCarty, Juan P. Casas, Johann Willeit, Peter H. Whincup, Stela McLachlan, Adelaida Sanchez-Galvez, Hartmut Goldschmidt, Guillaume Paré, Harry Hemingway, Anubha Mahajan, Elisabeth Steinhagen-Thiessen, Elizabeth G. Holliday, Giuseppe Matullo, Henry Völzke, Ian Ford, Martin Bobak, Pedro Marques-Vidal, Bertrand Cariou, Bernardo L. Horta, Melissa L. Bondy, Goya Wanamethee, Naveed Sattar, Steve E. Humphries, Marylyn D. Ritchie, Kristina Norman, Carlotta Sacerdote, Giovanni Fiorito, Sebastian E. Baumeister, Amit Sud, Dennis Valentine, Andreas Engert, Juri Demuth, Rupert Faraway, Abdonas Tamosiunas, Andrie G. Panayiotou, Terrie Kitchner, Lars Bertram, Sandosh Padmanabhan, Sofia Malyutina, Anke H. Maitland-van der Zee, Alex J. Cornish, Joshua C. Denny, Jian'an Luan, Robert A. Scott, Daniel I. Swerdlow, John Attia, Karin Willeit, Gareth J. Morgan, Michael Chong, Ruben N. Eppinga, Elina Hyppönen, Ekaterina V. Baranova, Jackie A. Cooper, Ghazaleh Fatemifar, Niek Verweij, Max Moldovan, Brendan J. Keating, M. Abdullah Said, Markus M. Lerch, Christina M. Lill, Markus Hansson, Jemma C. Hopewell, Björn Nilsson, Folkert W. Asselbergs, Ruzena Kubinova, Molly Went, Nicholas J. Wareham, Stefan Kiechl, Yanchun Bao, Allan Linneberg, Matthias Simon, Epidemiology and Data Science, Pulmonology, Paediatric Pulmonology, APH - Personalized Medicine, AII - Inflammatory diseases, AII - Cancer immunology, CCA - Cancer biology and immunology, Ear, Nose and Throat, Schmidt, Amand F, Holmes, Michael V, Preiss, David, Swerdlow, Daniel I, Hypponen, Elina, Dehghan, Abbas, Schmidt, Amand F [0000-0003-1327-0424], Apollo - University of Cambridge Repository, Lifelines Cohort, ICBP Consortium, METASTROKE Consortium of the ISGC, PharmacoTherapy, -Epidemiology and -Economics, Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Schmidt, Amand F. [0000-0003-1327-0424], Epidemiology, and Hematology

Subjects
Oncology, lcsh:Diseases of the circulatory (Cardiovascular) system, Genetic association studies, Proprotein Convertase 9/genetics, Apolipoprotein B, Anticholesteremic Agents/adverse effects, Myocardial Infarction, Blood lipids, Genome-wide association study, 030204 cardiovascular system & hematology, Coronary artery disease, Gastroenterology, Medical and Health Sciences, Stroke/epidemiology, Brain Ischemia, 0302 clinical medicine, Risk Factors, Dyslipidemias/blood, Medicine, LDL-cholesterol, Cardiac and Cardiovascular Systems, 030212 general & internal medicine, Myocardial infarction, Mendelian randomisation, 1102 Cardiorespiratory Medicine and Haematology, Randomized Controlled Trials as Topic, Kardiologi, biology, Anticholesteremic Agents, PCSK9 Inhibitors, Single Nucleotide, 16. Peace & justice, LDL/blood, 3. Good health, Stroke, Cholesterol, Treatment Outcome, Cholesterol, LDL/blood, ICBP Consortium, Phenome-wide association scan, Proprotein Convertase 9, Cardiology and Cardiovascular Medicine, Research Article, medicine.medical_specialty, Serine Proteinase Inhibitors, Down-Regulation, 610 Medicine & health, Single-nucleotide polymorphism, Placebo, Polymorphism, Single Nucleotide, Risk Assessment, 03 medical and health sciences, Internal medicine, Genetic variation, Myocardial Infarction/epidemiology, Humans, Serine Proteinase Inhibitors/adverse effects, Polymorphism, Dyslipidemias, Genetic association, Lifelines Cohort authors, METASTROKE Consortium of the ISGC, business.industry, PCSK9, Cholesterol, LDL, Odds ratio, medicine.disease, Cardiovascular System & Hematology, lcsh:RC666-701, biology.protein, Brain Ischemia/epidemiology, Clinical Medicine, business, Biomarkers, Biomarkers/blood, Genome-Wide Association Study
Abstract

BackgroundWe characterised the phenotypic consequence of genetic variation at the PCSK9 locus and compared findings with recent trials of pharmacological inhibitors of PCSK9.MethodsPublished and individual participant level data (300,000+ participants) were combined to construct a weighted PCSK9 gene-centric score (GS). Fourteen randomized placebo controlled PCSK9 inhibitor trials were included, providing data on 79,578 participants. Results were scaled to a one mmol/L lower LDL-C concentrationResultsThe PCSK9 GS (comprising 4 SNPs) associations with plasma lipid and apolipoprotein levels were consistent in direction with treatment effects. The GS odds ratio (OR) for myocardial infarction (MI) was 0.53 (95%CI 0.42; 0.68), compared to a PCSK9 inhibitor effect of 0.90 (95%CI 0.86; 0.93). For ischemic stroke ORs were 0.84 (95%CI 0.57; 1.22) for the GS, compared to 0.85 (95%CI 0.78; 0.93) in the drug trials. ORs with type 2 diabetes mellitus (T2DM) were 1.29 (95% CI 1.11; 1.50) for the GS, as compared to 1.00 (95%CI 0.96; 1.04) for incident T2DM in PCSK9 inhibitor trials. No genetic associations were observed for cancer, heart failure, atrial fibrillation, chronic obstructive pulmonary disease, or Alzheimer’s disease – outcomes for which large-scale trial data were unavailable.ConclusionsGenetic variation at the PCSK9 locus recapitulates the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and MI. Apparent discordance between genetic associations and trial outcome for T2DM might be explained lack by a of statistical precision, or differences in the nature and duration of genetic versus pharmacological perturbation of PCSK9.FundingThis research was funded by the British Heart Foundation (SP/13/6/30554, RG/10/12/28456, FS/18/23/33512), UCL Hospitals NIHR Biomedical Research Centre, by the Rosetrees and Stoneygate Trusts.Condensed abstractEvidence on the long-term efficacy and safety of therapeutic inhibition of PCSK9 is lacking. To explore potential long-term effects of PCSK9 inhibition, we characterised the phenotypic consequence of LDL-cholesterol lowering variants at the PCSK9 locus. A PCSK9 gene score comprising 4 SNPs recapitulated the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and risk of myocardial infarction, and was associated with an increased risk of type 2 diabetes. No associations with safety outcomes such as cancer, COPD, Alzheimer’s disease or atrial fibrillation were identified. Our findings suggest PCSK9 inhibition may be safe and effective during prolonged use.

Published
2019

42. Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease A Longitudinal Study of 11 461 Participants From Population-Based Cohorts

Author

Symen Ligthart, Luigi Ferrucci, Rosario Tumino, Kerri L. Wiggins, Bruce M. Psaty, Dena G. Hernandez, Philip S. Tsao, Kelly M. Bakulski, Roby Joehanes, Tianxiao Huan, Steven Horvath, Luke C. Pilling, Eric Boerwinkle, Simone Wahl, Annette Peters, Vittorio Krogh, Devin Absher, Myriam Fornage, M. Daniele Fallin, Cavin K. Ward-Caviness, Elena Colicino, Nona Sotoodehnia, Michael M. Mendelson, Lifang Hou, Chunyu Liu, Pantel S. Vokonas, Carlotta Sacerdote, Abbas Dehghan, Andrew P. Feinberg, Jerome I. Rotter, Yun Li, Themistocles L. Assimes, Jennifer A. Brody, Rahul Gondalia, Andrea A. Baccarelli, Christian Gieger, Guosheng Zhang, Jan Bressler, Salvatore Panico, Stefania Bandinelli, Amy R. Vandiver, James S. Floyd, Michael L. Multhaup, Brian H. Chen, Elias Salfati, Giuseppe Matullo, James D. Stewart, Toshiko Tanaka, Joel Schwartz, Daniel Levy, Simonetta Guarrera, Allan C. Just, Andrew B. Singleton, Golareh Agha, Joel N. Hirschhorn, Eric A. Whitsel, Giovanni Fiorito, and Epidemiology

Subjects
Regulation of gene expression, 0303 health sciences, medicine.medical_specialty, business.industry, Genomics, 030204 cardiovascular system & hematology, medicine.disease, Coronary heart disease, Coronary artery disease, 03 medical and health sciences, 0302 clinical medicine, Coronary Artery Disease, Coronary Heart Disease, Epigenetics, Gene Expression Regulation, Physiology (medical), Internal medicine, DNA methylation, medicine, Cardiology, Myocardial infarction, Cardiology and Cardiovascular Medicine, business, 030304 developmental biology
Abstract

Background: DNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts. Methods: Nine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts. Results: Among 11 461 individuals (mean age 64 years, 67% women, 35% African American) free of CHD at baseline, 1895 developed CHD during a mean follow-up of 11.2 years. Methylation levels at 52 CpG (cytosine-phosphate-guanine) sites were associated with incident CHD or myocardial infarction (false discovery rate Conclusion: Methylation of blood-derived DNA is associated with risk of future CHD across diverse populations and may serve as an informative tool for gaining further insight on the development of CHD.

Published
2019

43. Genetics and Epigenetics of Mesothelioma

Author

Marika Sculco, Simonetta Guarrera, Corrado Magnani, Giuseppe Matullo, Elisabetta Casalone, Irma Dianzani, Laura Moro, and Anna Aspesi

Subjects
Genetics, BAP1, Germline mutation, DNA repair, CDKN2A, Point mutation, medicine, Mesothelioma, Epigenetics, Biology, Carcinogenesis, medicine.disease_cause, medicine.disease
Abstract

The definition of the mesothelioma genome is expected to have a great impact toward the development of new drugs and therapeutic approaches with a view to precision medicine. A few studies reported that the malignant pleural mesothelioma (MPM) genomic landscape is characterized by a much greater number of genomic losses than point mutations. Inactivating gene fusions, copy losses, and protein-truncating variants (PTVs) mostly affect tumor suppressor genes, above all BAP1, NF2, CDKN2A, and SETD2. Some of them may be exploited to design novel therapeutic strategies. Germline mutations in some of these genes represent MPM-predisposing risk factors. These mutations require a second hit, i.e., asbestos exposure, to induce carcinogenesis. The most studied of these genes is BAP1. Germline mutations in other tumor suppressor genes, mostly involved in DNA repair, have also been identified in about 10% of MPM patients. These patients are more sensitive to asbestos exposure than those who do not carry such mutations and may benefit of specific treatments. Additionally, epigenetic mechanisms, such as methylation or miRNA alterations, may modify gene expression and drive carcinogenesis. The same abnormalities may be used as disease biomarkers or therapeutic targets.

Published
2019

44. Peripheral Blood DNA Methylation as Potential Biomarker of Malignant Pleural Mesothelioma in Asbestos-Exposed Subjects

Author

Giuseppe Matullo, E. Piccolini, Daniela Ferrante, Giovanni Cugliari, Irma Dianzani, Elisabetta Casalone, Roberta Libener, Corrado Magnani, Anna Aspesi, Marta Betti, Simonetta Guarrera, Clara Viberti, Federica Grosso, Caterina Casadio, Dario Mirabelli, and Alessandra Allione

Subjects
Male, Mesothelioma, 0301 basic medicine, Pulmonary and Respiratory Medicine, Oncology, medicine.medical_specialty, Lung Neoplasms, Pleural Neoplasms, Malignant pleural mesothelioma, medicine.disease_cause, Case-control discrimination, Asbestos, 03 medical and health sciences, 0302 clinical medicine, Occupational Exposure, Internal medicine, Biomarkers, Tumor, medicine, Humans, Prospective cohort study, Aged, Whole blood, Early biomarker, Pleural mesothelioma, business.industry, Mesothelioma, Malignant, DNA, Methylation, DNA Methylation, Prognosis, Peripheral blood, 030104 developmental biology, ROC Curve, Case-Control Studies, 030220 oncology & carcinogenesis, Potential biomarkers, Asbestos exposure, DNA-methylation, DNA methylation, Carcinogens, Female, business, Follow-Up Studies
Abstract

Introduction Malignant pleural mesothelioma (MPM) is an aggressive tumor strongly associated with asbestos exposure. Patients are usually diagnosed when current treatments have limited benefits, highlighting the need for noninvasive early diagnostic tests to monitor asbestos-exposed people. Methods We used a genome-wide methylation array to identify, in asbestos-exposed subjects, novel blood DNA methylation markers of MPM in 163 MPM cases and 137 cancer-free controls (82 MPM cases and 68 controls, training set; replication in 81 MPM cases and 69 controls, test set) sampled from the same areas. Results Evidence of differential methylation between MPM cases and controls was found (more than 800 cytosine-guanine dinucleotide sites, false discovery rate p value (pfdr) Conclusions We identified signatures of differential methylation in DNA from whole blood between asbestos exposed MPM cases and controls. Our results provide the rationale to further investigate, in prospective studies, the potential use of blood DNA methylation profiles for the identification of early changes related to the MPM carcinogenic process.

Published
2019

45. Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease

Author

Golareh, Agha, Michael M, Mendelson, Cavin K, Ward-Caviness, Roby, Joehanes, TianXiao, Huan, Rahul, Gondalia, Elias, Salfati, Jennifer A, Brody, Giovanni, Fiorito, Jan, Bressler, Brian H, Chen, Symen, Ligthart, Simonetta, Guarrera, Elena, Colicino, Allan C, Just, Simone, Wahl, Christian, Gieger, Amy R, Vandiver, Toshiko, Tanaka, Dena G, Hernandez, Luke C, Pilling, Andrew B, Singleton, Carlotta, Sacerdote, Vittorio, Krogh, Salvatore, Panico, Rosario, Tumino, Yun, Li, Guosheng, Zhang, James D, Stewart, James S, Floyd, Kerri L, Wiggins, Jerome I, Rotter, Michael, Multhaup, Kelly, Bakulski, Steven, Horvath, Philip S, Tsao, Devin M, Absher, Pantel, Vokonas, Joel, Hirschhorn, M Daniele, Fallin, Chunyu, Liu, Stefania, Bandinelli, Eric, Boerwinkle, Abbas, Dehghan, Joel D, Schwartz, Bruce M, Psaty, Andrew P, Feinberg, Lifang, Hou, Luigi, Ferrucci, Nona, Sotoodehnia, Giuseppe, Matullo, Annette, Peters, Myriam, Fornage, Themistocles L, Assimes, Eric A, Whitsel, Daniel, Levy, and Andrea A, Baccarelli

Subjects
Risk, Adult, Male, Clinical Sciences, Myocardial Infarction, Coronary Disease, Cardiorespiratory Medicine and Haematology, Cardiovascular, Article, Cohort Studies, Population Groups, Clinical Research, Leukocytes, Genetics, genomics, Humans, Prospective Studies, coronary heart disease, Heart Disease - Coronary Heart Disease, Aged, epigenetics, Incidence, Prevention, Human Genome, gene expression regulation, DNA Methylation, Middle Aged, Prognosis, Atherosclerosis, United States, Europe, Heart Disease, Cardiovascular System & Hematology, coronary artery disease, Public Health and Health Services, CpG Islands, Female, Genome-Wide Association Study
Abstract

BackgroundDNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts.MethodsNine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts.ResultsAmong 11 461 individuals (mean age 64 years, 67% women, 35% African American) free of CHD at baseline, 1895 developed CHD during a mean follow-up of 11.2 years. Methylation levels at 52 CpG (cytosine-phosphate-guanine) sites were associated with incident CHD or myocardial infarction (false discovery rate

Published
2019

46. Association between Beta1-Adrenergic Receptor Polymorphism and Risk of ICD Shock in Heart Failure Patients

Author

Luisa Zanolla, Corrado Vassanelli, Giuseppe Matullo, Luca Tomasi, Simonetta Guarrera, Giovanni Fiorito, Roberto Zanini, Paola Guarise, and Nicola Cicorella

Subjects
medicine.medical_specialty, animal structures, Ejection fraction, Adrenergic receptor, Proportional hazards model, business.industry, Hazard ratio, General Medicine, 030204 cardiovascular system & hematology, medicine.disease, Sudden death, Sudden cardiac death, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Heart failure, medicine, Cardiology, 030212 general & internal medicine, Allele, Cardiology and Cardiovascular Medicine, business
Abstract

BACKGROUND Sympathetic activation in heart failure patients favors the development of ventricular arrhythmias, thus leading to an increased risk of sudden cardiac death. β1 - and β2 -adrenergic receptor polymorphisms have been linked to the risk of sudden death. Implantable cardioverter-defibrillators (ICD) are implanted in a large percentage of heart failure patients, and beyond preventing sudden cardiac death they provide a continuous monitoring of major ventricular arrhythmias and of their own interventions. We investigated whether functionally relevant β1 - and β2 -adrenergic receptor polymorphisms are associated with risk of ICD shocks, as evidenced in ICD memory. METHODS 311 patients with systolic heart failure were enrolled, and number and timing of shocks in ICD memory were recorded. Four selected polymorphisms were determined: β1 -adrenergic receptor polymorphisms Ser(49) Gly and Arg(389) Gly and β2 -adrenergic receptor polymorphisms Arg(16) Gly and Gln(27) Glu. RESULTS Only Ser(49) Gly was significantly correlated with time free from ICD shocks, both considering time to the first event in a Cox model (hazard ratio 2.117), and modeling repeated events with the Andersen-Gill method (hazard ratio 2.088). Gly allele carriers had a higher probability of ICD shock. The relationship remained significant even after adjusting for ejection fraction and beta-blocker dosage (hazard ratio 1.910). CONCLUSIONS Data from our study suggest that the β adrenoreceptor Gly 49 allele of the β1 -adrenergic receptor Ser(49) Gly polymorphisms may increase the risk of ICD shock in patients with heart failure, independent of beta-blocker dosage.

Published
2016

47. DNA Methylation of FKBP5 as Predictor of Overall Survival in Malignant Pleural Mesothelioma

Author

Roberta Libener, Chiara Catalano, Anna Aspesi, Federica Grosso, Dario Mirabelli, Irma Dianzani, Clara Viberti, Giuseppe Matullo, Alessia Russo, Marika Sculco, Corrado Magnani, Elisabetta Casalone, Alessandra Allione, Giovanni Cugliari, Chiara Pirazzini, Simonetta Guarrera, and Daniela Ferrante

Subjects
0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, lymphocyte-to-monocyte ratio, medicine.disease_cause, lcsh:RC254-282, Asbestos, survival analysis, asbestos exposure, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, malignant pleural mesothelioma, Medicine, Mesothelioma, Epigenetics, Survival analysis, DNA methylation, business.industry, dNaM, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, 030104 developmental biology, epigenome-wide analysis, 030220 oncology & carcinogenesis, Cohort, FKBP5, business, Asbestos exposure, Epigenome-wide analysis, Lymphocyte-to-monocyte ratio, Malignant pleural mesothelioma
Abstract

Malignant pleural mesothelioma (MPM) is an aggressive tumor with median survival of 12 months and limited effective treatments. The scope of this study was to study the relationship between blood DNA methylation (DNAm) and overall survival (OS) aiming at a noninvasive prognostic test. We investigated a cohort of 159 incident asbestos exposed MPM cases enrolled in an Italian area with high incidence of mesothelioma. Considering 12 months as a cut-off for OS, epigenome-wide association study (EWAS) revealed statistically significant (p value = 7.7 &times, 10&minus, 9) OS-related differential methylation of a single-CpG (cg03546163), located in the 5&prime, UTR region of the FKBP5 gene. This is an independent marker of prognosis in MPM patients with a better performance than traditional inflammation-based scores such as lymphocyte-to-monocyte ratio (LMR). Cases with DNAm &lt, 0.45 at the cg03546163 had significantly poor survival compared with those showing DNAm &ge, 0.45 (mean: 243 versus 534 days, p value&lt, 0.001). Epigenetic changes at the FKBP5 gene were robustly associated with OS in MPM cases. Our results showed that blood DNA methylation levels could be promising and dynamic prognostic biomarkers in MPM.

Published
2020

48. Author Correction: Lymphoblastoid cell lines from Diamond Blackfan anaemia patients exhibit a full ribosomal stress phenotype that is rescued by gene therapy

Author

Antonia Follenzi, Irma Dianzani, Marcin W. Wlodarski, Marika Sculco, Chiara Actis, Giulia Morleo, Simonetta Guarrera, Claudio Santoro, Ugo Ramenghi, Marta Betti, Steven R. Ellis, Fabrizio Loreni, Anna Aspesi, and Valentina Monteleone

Subjects
0301 basic medicine, Multidisciplinary, Diamond-Blackfan anaemia, Genetic enhancement, lcsh:R, lcsh:Medicine, Ribosomal RNA, Biology, Phenotype, 03 medical and health sciences, 030104 developmental biology, Lymphoblastoid cell, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Cancer research, lcsh:Q, lcsh:Science
Abstract

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Published
2018

49. Epigenome-wide association study of adiposity and future risk of obesity-related diseases

Author

Gianluca Campanella, Rosario Tumino, Marc Chadeau-Hyam, Jos C. S. Kleinjans, Nicolle A. Mode, Robert Murray, Paolo Vineis, Per Lenner, Anne M. May, Theo M. de Kok, Karen A. Lillycrop, H. Bas Bueno-de-Mesquita, Morena Trevisan, Salvatore Panico, Paul Elliott, Silvia Polidoro, Philippe Froguel, Giuseppe Matullo, Soterios A. Kyrtopoulos, Licia Iacoviello, N. Charlotte Onland-Moret, Domenico Palli, Torkjel M. Sandanger, Valentina Fiano, Giovanni Fiorito, Marc J. Gunter, Ingvar A. Bergdahl, Monique Verschuren, Elio Riboli, Simonetta Guarrera, Panagiotis Georgiadis, Vittorio Krogh, Eiliv Lund, Carlotta Sacerdote, Beatrice Melin, Commission of the European Communities, Imperial College Healthcare NHS Trust- BRC Funding, National Institute for Health Research, Medical Research Council (MRC), Campanella, Gianluca, Gunter, Marc J, Polidoro, Silvia, Krogh, Vittorio, Palli, Domenico, Panico, Salvatore, Sacerdote, Carlotta, Tumino, Rosario, Fiorito, Giovanni, Guarrera, Simonetta, Iacoviello, Licia, Bergdahl, Ingvar A, Melin, Beatrice, Lenner, Per, de Kok, Theo M C M, Georgiadis, Panagioti, Kleinjans, Jos C S, Kyrtopoulos, Soterios A, Bueno-de-Mesquita, H Ba, Lillycrop, Karen A, May, Anne M, Onland-Moret, N Charlotte, Murray, Robert, Riboli, Elio, Verschuren, Monique, Lund, Eiliv, Mode, Nicolle, Sandanger, Torkjel M, Fiano, Valentina, Trevisan, Morena, Matullo, Giuseppe, Froguel, Philippe, Elliott, Paul, Vineis, Paolo, Chadeau-Hyam, Marc, Toxicogenomics, RS: FSE MaCSBio, RS: FPN MaCSBio, RS: FHML MaCSBio, RS: MHeNs - R3 - Neuroscience, and RS: GROW - R1 - Prevention

Subjects
0301 basic medicine, Epigenomics, Genetic Markers, Colorectal cancer, Endocrinology, Diabetes and Metabolism, Myocardial Infarction, Medicine (miscellaneous), Genome-wide association study, macromolecular substances, PERIPHERAL-BLOOD, Bioinformatics, 03 medical and health sciences, Endocrinology & Metabolism, 0302 clinical medicine, Endocrinology, Neoplasms, medicine, Humans, CPT1A LOCUS, Obesity, Risk factor, 11 Medical and Health Sciences, Adiposity, INSULIN-RESISTANCE, Nutrition and Dietetics, business.industry, CHOLESTEROL, Cancer, Epigenome, DNA Methylation, medicine.disease, CANCER, GENE, Diabetes and Metabolism, BODY-MASS INDEX, 030104 developmental biology, 030220 oncology & carcinogenesis, HIGH-DENSITY-LIPOPROTEINS, Leukocytes, Mononuclear, 3-BETA-HYDROXYSTEROID-DELTA-24 REDUCTASE, business, Body mass index, 13 Education, Genome-Wide Association Study
Abstract

BackgroundObesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction.MethodsDNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population.ResultsWe identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10−8 to 3.27×10−18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10−7), higher triglyceride levels (P = 5.37×10−9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10−10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P P ConclusionOur results suggest that epigenetic changes, in particular altered DNA methylation patterns, may be an intermediate biomarker at the intersection of obesity and obesity-related diseases, and could offer clues as to underlying biological mechanisms.

Published
2018

50. MMP23B expression and protein levels in blood and urine are associated with bladder cancer

Author

Giuseppe Matullo, Cornelia Di Gaetano, Simonetta Guarrera, Clara Viberti, Barbara Pardini, Alessandra Allione, Marco Oderda, Marco Allasia, Paolo Vineis, Stefano Turini, Giuliana Giribaldi, Carlotta Sacerdote, Francesca Cordero, and Paolo Gontero

Subjects
0301 basic medicine, Adult, Male, Cancer Research, Microarray, Urinary system, Blotting, Western, Urinary Bladder, Enzyme-Linked Immunosorbent Assay, Urine, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, 0302 clinical medicine, Western blot, microRNA, Gene expression, medicine, Biomarkers, Tumor, Humans, Aged, Bladder cancer, medicine.diagnostic_test, business.industry, fungi, General Medicine, Middle Aged, medicine.disease, Matrix Metalloproteinases, MicroRNAs, 030104 developmental biology, Urinary Bladder Neoplasms, 030220 oncology & carcinogenesis, Case-Control Studies, Cancer research, Biomarker (medicine), business, Genome-Wide Association Study
Abstract

Urothelial bladder cancer (UBC) represents a public health problem because of its high incidence/relapse rates. At present, there are no suitable biomarkers for early diagnosis or relapse/progression prognosis. To improve diagnostic accuracy and overcome the disadvantages of current diagnostic strategies, the detection of UBC biomarkers in easily accessible biofluids, such as urine, represents a promising approach compared with painful biopsies. We investigated the levels of MMP23 genes (microarray and qPCR) and protein (western blot and enzyme-linked immunosorbent assay) in a set of samples (blood, plasma and urine) from patients with UBC and controls as biomarkers for this cancer. MMP23B and its pseudogene MMP23A resulted downregulated in blood cells from UBC compared with controls (66 cases, 70 controls; adjusted P-value = 0.02 and 0.03, respectively). In contrast, MMP23B protein levels in plasma (53 UBC, 49 controls) and urine (59 UBC, 57 controls) increased in cases, being statistically significant in urine. MMP23B dosage observed in urine samples was related to both tumor risk classification and grading. As the lack of correlation between mRNA and protein levels could be due to a posttranscriptional regulation mediated by microRNAs (miRNAs), we investigated the expression of urinary miRNAs targeting MMP23B. Five miRNAs resulted differentially expressed between cases and controls. We reported the first evidence of MMP23B secretion in plasma and urine, suggesting a role of this poorly characterized metalloproteinase in UBC as a potential non-invasive biomarker for this cancer. Further analyses are needed to elucidate the mechanism of regulation of MMP23B expression by miRNAs.

Published
2018

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