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2,108 results on '"Kere, Juha"'

1. The DoGA consortium expression atlas of promoters and genes in 100 canine tissues

Author

Hörtenhuber, Matthias, Hytönen, Marjo K., Mukarram, Abdul Kadir, Arumilli, Meharji, Araujo, César L., Quintero, Ileana, Syrjä, Pernilla, Airas, Niina, Kaukonen, Maria, Kyöstilä, Kaisa, Niskanen, Julia, Jokinen, Tarja S., Mottaghitalab, Faezeh, Takan, Işıl, Salokorpi, Noora, Raman, Amitha, Stevens, Irene, Iivanainen, Antti, Yoshihara, Masahito, Gusev, Oleg, Bannasch, Danika, Sukura, Antti, Schoenebeck, Jeffrey J., Ezer, Sini, Katayama, Shintaro, Daub, Carsten O., Kere, Juha, and Lohi, Hannes

Published
2024
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6. Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human

Author

Niskanen, Julia E., Ohlsson, Åsa, Ljungvall, Ingrid, Drögemüller, Michaela, Ernst, Robert F., Dooijes, Dennis, van Deutekom, Hanneke W. M., van Tintelen, J. Peter, Snijders Blok, Christian J. B., van Vugt, Marion, van Setten, Jessica, Asselbergs, Folkert W., Petrič, Aleksandra Domanjko, Salonen, Milla, Hundi, Sruthi, Hörtenhuber, Matthias, Kere, Juha, Pyle, W. Glen, Donner, Jonas, Postma, Alex V., Leeb, Tosso, Andersson, Göran, Hytönen, Marjo K., Häggström, Jens, Wiberg, Maria, Friederich, Jana, Eberhard, Jenny, Harakalova, Magdalena, van Steenbeek, Frank G., Wess, Gerhard, and Lohi, Hannes

Published
2023
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10. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age.

Author

Merid, Simon Kebede, Novoloaca, Alexei, Sharp, Gemma C, Küpers, Leanne K, Kho, Alvin T, Roy, Ritu, Gao, Lu, Annesi-Maesano, Isabella, Jain, Pooja, Plusquin, Michelle, Kogevinas, Manolis, Allard, Catherine, Vehmeijer, Florianne O, Kazmi, Nabila, Salas, Lucas A, Rezwan, Faisal I, Zhang, Hongmei, Sebert, Sylvain, Czamara, Darina, Rifas-Shiman, Sheryl L, Melton, Phillip E, Lawlor, Debbie A, Pershagen, Göran, Breton, Carrie V, Huen, Karen, Baiz, Nour, Gagliardi, Luigi, Nawrot, Tim S, Corpeleijn, Eva, Perron, Patrice, Duijts, Liesbeth, Nohr, Ellen Aagaard, Bustamante, Mariona, Ewart, Susan L, Karmaus, Wilfried, Zhao, Shanshan, Page, Christian M, Herceg, Zdenko, Jarvelin, Marjo-Riitta, Lahti, Jari, Baccarelli, Andrea A, Anderson, Denise, Kachroo, Priyadarshini, Relton, Caroline L, Bergström, Anna, Eskenazi, Brenda, Soomro, Munawar Hussain, Vineis, Paolo, Snieder, Harold, Bouchard, Luigi, Jaddoe, Vincent W, Sørensen, Thorkild IA, Vrijheid, Martine, Arshad, S Hasan, Holloway, John W, Håberg, Siri E, Magnus, Per, Dwyer, Terence, Binder, Elisabeth B, DeMeo, Dawn L, Vonk, Judith M, Newnham, John, Tantisira, Kelan G, Kull, Inger, Wiemels, Joseph L, Heude, Barbara, Sunyer, Jordi, Nystad, Wenche, Munthe-Kaas, Monica C, Räikkönen, Katri, Oken, Emily, Huang, Rae-Chi, Weiss, Scott T, Antó, Josep Maria, Bousquet, Jean, Kumar, Ashish, Söderhäll, Cilla, Almqvist, Catarina, Cardenas, Andres, Gruzieva, Olena, Xu, Cheng-Jian, Reese, Sarah E, Kere, Juha, Brodin, Petter, Solomon, Olivia, Wielscher, Matthias, Holland, Nina, Ghantous, Akram, Hivert, Marie-France, Felix, Janine F, Koppelman, Gerard H, London, Stephanie J, and Melén, Erik

Subjects
Humans, Premature Birth, DNA, DNA Methylation, Fetal Development, Adolescent, Child, Child, Preschool, Infant, Newborn, Infant, Premature, Female, Male, Genetic Loci, Epigenome, Development, Epigenetics, Gestational age, Preterm birth, Transcriptomics, Preschool, Infant, Newborn, Premature, Genetics, Clinical Sciences
Abstract

BackgroundPreterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children.MethodsWe performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung.ResultsWe identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P

Published
2020

11. A putative silencer variant in a spontaneous canine model of retinitis pigmentosa

Author

Kaukonen, Maria, Quintero, Ileana B, Mukarram, Abdul Kadir, Hytönen, Marjo K, Holopainen, Saila, Wickström, Kaisa, Kyöstilä, Kaisa, Arumilli, Meharji, Jalomäki, Sari, Daub, Carsten O, Kere, Juha, and Lohi, Hannes

Subjects
Biological Sciences, Genetics, Rare Diseases, Neurosciences, Biotechnology, Eye Disease and Disorders of Vision, Human Genome, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Eye, Animals, Case-Control Studies, Collagen Type IX, Dog Diseases, Dogs, Endothelin-2, Female, Frameshift Mutation, Genome-Wide Association Study, Haplotypes, Male, Models, Animal, Mutation, Pedigree, Phenotype, Retina, Retinal Degeneration, Retinitis Pigmentosa, DoGA Consortium, Developmental Biology
Abstract

Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30-80% of the RP patients the genetic cause remains unknown. A similar phenotype, progressive retinal atrophy (PRA), affects many dog breeds including the Miniature Schnauzer. We performed clinical, genetic and functional experiments to identify the genetic cause of PRA in the breed. The age of onset and pattern of disease progression suggested that at least two forms of PRA, types 1 and 2 respectively, affect the breed, which was confirmed by genome-wide association study that implicated two distinct genomic loci in chromosomes 15 and X, respectively. Whole-genome sequencing revealed a fully segregating recessive regulatory variant in type 1 PRA. The associated variant has a very recent origin based on haplotype analysis and lies within a regulatory site with the predicted binding site of HAND1::TCF3 transcription factor complex. Luciferase assays suggested that mutated regulatory sequence increases expression. Case-control retinal expression comparison of six best HAND1::TCF3 target genes were analyzed with quantitative reverse-transcriptase PCR assay and indicated overexpression of EDN2 and COL9A2 in the affected retina. Defects in both EDN2 and COL9A2 have been previously associated with retinal degeneration. In summary, our study describes two genetically different forms of PRA and identifies a fully penetrant variant in type 1 form with a possible regulatory effect. This would be among the first reports of a regulatory variant in retinal degeneration in any species, and establishes a new spontaneous dog model to improve our understanding of retinal biology and gene regulation while the affected breed will benefit from a reliable genetic testing.

Published
2020

12. Comprehensive characterization of the embryonic factor LEUTX

Author

Gawriyski, Lisa, Jouhilahti, Eeva-Mari, Yoshihara, Masahito, Fei, Liangru, Weltner, Jere, Airenne, Tomi T., Trokovic, Ras, Bhagat, Shruti, Tervaniemi, Mari H., Murakawa, Yasuhiro, Salokas, Kari, Liu, Xiaonan, Miettinen, Sini, Bürglin, Thomas R., Sahu, Biswajyoti, Otonkoski, Timo, Johnson, Mark S., Katayama, Shintaro, Varjosalo, Markku, and Kere, Juha

Published
2023
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14. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight.

Author

Küpers, Leanne K, Monnereau, Claire, Sharp, Gemma C, Yousefi, Paul, Salas, Lucas A, Ghantous, Akram, Page, Christian M, Reese, Sarah E, Wilcox, Allen J, Czamara, Darina, Starling, Anne P, Novoloaca, Alexei, Lent, Samantha, Roy, Ritu, Hoyo, Cathrine, Breton, Carrie V, Allard, Catherine, Just, Allan C, Bakulski, Kelly M, Holloway, John W, Everson, Todd M, Xu, Cheng-Jian, Huang, Rae-Chi, van der Plaat, Diana A, Wielscher, Matthias, Merid, Simon Kebede, Ullemar, Vilhelmina, Rezwan, Faisal I, Lahti, Jari, van Dongen, Jenny, Langie, Sabine AS, Richardson, Tom G, Magnus, Maria C, Nohr, Ellen A, Xu, Zongli, Duijts, Liesbeth, Zhao, Shanshan, Zhang, Weiming, Plusquin, Michelle, DeMeo, Dawn L, Solomon, Olivia, Heimovaara, Joosje H, Jima, Dereje D, Gao, Lu, Bustamante, Mariona, Perron, Patrice, Wright, Robert O, Hertz-Picciotto, Irva, Zhang, Hongmei, Karagas, Margaret R, Gehring, Ulrike, Marsit, Carmen J, Beilin, Lawrence J, Vonk, Judith M, Jarvelin, Marjo-Riitta, Bergström, Anna, Örtqvist, Anne K, Ewart, Susan, Villa, Pia M, Moore, Sophie E, Willemsen, Gonneke, Standaert, Arnout RL, Håberg, Siri E, Sørensen, Thorkild IA, Taylor, Jack A, Räikkönen, Katri, Yang, Ivana V, Kechris, Katerina, Nawrot, Tim S, Silver, Matt J, Gong, Yun Yun, Richiardi, Lorenzo, Kogevinas, Manolis, Litonjua, Augusto A, Eskenazi, Brenda, Huen, Karen, Mbarek, Hamdi, Maguire, Rachel L, Dwyer, Terence, Vrijheid, Martine, Bouchard, Luigi, Baccarelli, Andrea A, Croen, Lisa A, Karmaus, Wilfried, Anderson, Denise, de Vries, Maaike, Sebert, Sylvain, Kere, Juha, Karlsson, Robert, Arshad, Syed Hasan, Hämäläinen, Esa, Routledge, Michael N, Boomsma, Dorret I, Feinberg, Andrew P, Newschaffer, Craig J, Govarts, Eva, Moisse, Matthieu, Fallin, M Daniele, Melén, Erik, and Prentice, Andrew M

Subjects
Fetus, Humans, Prenatal Exposure Delayed Effects, Birth Weight, Folic Acid, DNA, Body Mass Index, Smoking, DNA Methylation, Epigenesis, Genetic, CpG Islands, Fetal Development, Pregnancy, Genome, Human, Adolescent, Adult, Child, Infant, Newborn, Female, Male, Genome-Wide Association Study, Epigenesis, Genetic, Genome, Human, Infant, Newborn
Abstract

Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (PBonferroni

Published
2019

16. Influence of FLG loss-of-function mutations in host–microbe interactions during atopic skin inflammation

Author

Oláh, Peter, Szlávicz, Eszter, Kuchner, Marcus, Nemmer, Jana, Zeeuwen, Patrick, Lefèvre-Utile, Alain, Fyhrquist, Nanna, Prast-Nielsen, Stefanie, Skoog, Tiina, Serra, Angela, Rodríguez, Elke, Raap, Ulrike, Meller, Stephan, Gyulai, Rolland, Hupé, Philippe, Kere, Juha, Levi-Schaffer, Francesca, Tsoka, Sophia, Alexander, Helen, Nestle, Frank O., Schröder, Jens M., Weidinger, Stephan, van den Bogaard, Ellen, Soumelis, Vassili, Greco, Dario, Barker, Jonathan, Lauerma, Antti, Ranki, Annamari, Andersson, Björn, Alenius, Harri, and Homey, Bernhard

Published
2022
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17. Biomarkers of nanomaterials hazard from multi-layer data

Author

Fortino, Vittorio, Kinaret, Pia Anneli Sofia, Fratello, Michele, Serra, Angela, Saarimäki, Laura Aliisa, Gallud, Audrey, Gupta, Govind, Vales, Gerard, Correia, Manuel, Rasool, Omid, Ytterberg, Jimmy, Monopoli, Marco, Skoog, Tiina, Ritchie, Peter, Moya, Sergio, Vázquez-Campos, Socorro, Handy, Richard, Grafström, Roland, Tran, Lang, Zubarev, Roman, Lahesmaa, Riitta, Dawson, Kenneth, Loeschner, Katrin, Larsen, Erik Husfeldt, Krombach, Fritz, Norppa, Hannu, Kere, Juha, Savolainen, Kai, Alenius, Harri, Fadeel, Bengt, and Greco, Dario

Published
2022
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18. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci.

Author

Khanshour, Anas M, Kou, Ikuyo, Fan, Yanhui, Einarsdottir, Elisabet, Makki, Nadja, Kidane, Yared H, Kere, Juha, Grauers, Anna, Johnson, Todd A, Paria, Nandina, Patel, Chandreshkumar, Singhania, Richa, Kamiya, Nobuhiro, Takeda, Kazuki, Otomo, Nao, Watanabe, Kota, Luk, Keith DK, Cheung, Kenneth MC, Herring, John A, Rios, Jonathan J, Ahituv, Nadav, Gerdhem, Paul, Gurnett, Christina A, Song, You-Qiang, Ikegawa, Shiro, and Wise, Carol A

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Prevention, 2.1 Biological and endogenous factors, Aetiology, Musculoskeletal, ABO Blood-Group System, Adolescent, Cadherins, Child, Ethnicity, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Musculoskeletal Diseases, Polymorphism, Single Nucleotide, SOXD Transcription Factors, Scoliosis, Young Adult, Medical and Health Sciences, Genetics & Heredity
Abstract

Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.

Published
2018

19. Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium

Author

Felix, Janine F, Joubert, Bonnie R, Baccarelli, Andrea A, Sharp, Gemma C, Almqvist, Catarina, Annesi-Maesano, Isabella, Arshad, Hasan, Baïz, Nour, Bakermans-Kranenburg, Marian J, Bakulski, Kelly M, Binder, Elisabeth B, Bouchard, Luigi, Breton, Carrie V, Brunekreef, Bert, Brunst, Kelly J, Burchard, Esteban G, Bustamante, Mariona, Chatzi, Leda, Munthe-Kaas, Monica Cheng, Corpeleijn, Eva, Czamara, Darina, Dabelea, Dana, Smith, George Davey, De Boever, Patrick, Duijts, Liesbeth, Dwyer, Terence, Eng, Celeste, Eskenazi, Brenda, Everson, Todd M, Falahi, Fahimeh, Fallin, M Daniele, Farchi, Sara, Fernandez, Mariana F, Gao, Lu, Gaunt, Tom R, Ghantous, Akram, Gillman, Matthew W, Gonseth, Semira, Grote, Veit, Gruzieva, Olena, Håberg, Siri E, Herceg, Zdenko, Hivert, Marie-France, Holland, Nina, Holloway, John W, Hoyo, Cathrine, Hu, Donglei, Huang, Rae-Chi, Huen, Karen, Järvelin, Marjo-Riitta, Jima, Dereje D, Just, Allan C, Karagas, Margaret R, Karlsson, Robert, Karmaus, Wilfried, Kechris, Katerina J, Kere, Juha, Kogevinas, Manolis, Koletzko, Berthold, Koppelman, Gerard H, Küpers, Leanne K, Ladd-Acosta, Christine, Lahti, Jari, Lambrechts, Nathalie, Langie, Sabine AS, Lie, Rolv T, Liu, Andrew H, Magnus, Maria C, Magnus, Per, Maguire, Rachel L, Marsit, Carmen J, McArdle, Wendy, Melén, Erik, Melton, Phillip, Murphy, Susan K, Nawrot, Tim S, Nisticò, Lorenza, Nohr, Ellen A, Nordlund, Björn, Nystad, Wenche, Oh, Sam S, Oken, Emily, Page, Christian M, Perron, Patrice, Pershagen, Göran, Pizzi, Costanza, Plusquin, Michelle, Raikkonen, Katri, Reese, Sarah E, Reischl, Eva, Richiardi, Lorenzo, Ring, Susan, Roy, Ritu P, Rzehak, Peter, Schoeters, Greet, Schwartz, David A, Sebert, Sylvain, Snieder, Harold, Sørensen, Thorkild IA, and Starling, Anne P

Subjects
Epidemiology, Public Health, Health Sciences, Statistics, Mathematical Sciences, Child Health, Cohort Studies, DNA Methylation, Environmental Pollution, Epigenesis, Genetic, Female, Folic Acid, Humans, Infant, Newborn, Maternal Exposure, Maternal Health, Pregnancy, Prenatal Exposure Delayed Effects, Public Health and Health Services, Public health
Published
2018

20. 49 Early-Onset Common Variable Immunodeficiency in a Patient with Heterozygous Variants in Interferon Response-Associated Genes TRAF3 and IRF4

Author

Le, Kim My, primary, Mamia, Nanni, additional, Kaustio, Meri, additional, Keskitalo, Salla, additional, Kettunen, Kaisa, additional, Kere, Juha, additional, Varjosalo, Markku, additional, Seppanen, Mikko, additional, Martelius, Timi, additional, Saarela, Janna, additional, and Gronholm, Juha, additional

Published
2024
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23. The role of CDHR3 in susceptibility to otitis media

Author

Hirsch, Scott D., Elling, Christina L., Bootpetch, Tori C., Scholes, Melissa A., Hafrén, Lena, Streubel, Sven-Olrik, Pine, Harold S., Wine, Todd M., Szeremeta, Wasyl, Prager, Jeremy D., Einarsdottir, Elisabet, Yousaf, Ayesha, Baschal, Erin E., Rehman, Sakina, Bamshad, Michael J., Nickerson, Deborah A., Riazuddin, Saima, Leal, Suzanne M., Ahmed, Zubair M., Yoon, Patricia J., Kere, Juha, Chan, Kenny H., Mattila, Petri S., Friedman, Norman R., Chonmaitree, Tasnee, Frank, Daniel N., Ryan, Allen F., and Santos-Cortez, Regie Lyn P.

Published
2021
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24. Genome-wide association study reveals new insights into the heritability and genetic correlates of developmental dyslexia

Author

Gialluisi, Alessandro, Andlauer, Till F. M., Mirza-Schreiber, Nazanin, Moll, Kristina, Becker, Jessica, Hoffmann, Per, Ludwig, Kerstin U., Czamara, Darina, Pourcain, Beate St, Honbolygó, Ferenc, Tóth, Dénes, Csépe, Valéria, Huguet, Guillaume, Chaix, Yves, Iannuzzi, Stephanie, Demonet, Jean-Francois, Morris, Andrew P., Hulslander, Jacqueline, Willcutt, Erik G., DeFries, John C., Olson, Richard K., Smith, Shelley D., Pennington, Bruce F., Vaessen, Anniek, Maurer, Urs, Lyytinen, Heikki, Peyrard-Janvid, Myriam, Leppänen, Paavo H. T., Brandeis, Daniel, Bonte, Milene, Stein, John F., Talcott, Joel B., Fauchereau, Fabien, Wilcke, Arndt, Kirsten, Holger, Müller, Bent, Francks, Clyde, Bourgeron, Thomas, Monaco, Anthony P., Ramus, Franck, Landerl, Karin, Kere, Juha, Scerri, Thomas S., Paracchini, Silvia, Fisher, Simon E., Schumacher, Johannes, Nöthen, Markus M., Müller-Myhsok, Bertram, and Schulte-Körne, Gerd

Published
2021
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26. The effect of type 1 diabetes protection and susceptibility associated HLA class II genotypes on DNA methylation in immune cells.

Author

Pahkuri, Sirpa, Katayama, Shintaro, Valta, Milla, Nygård, Lucas, Knip, Mikael, Kere, Juha, Ilonen, Jorma, and Lempainen, Johanna

Subjects
TYPE 1 diabetes, DNA methylation, GENOTYPES, DNA microarrays, EPIGENOMICS, ANTIGEN presentation
Abstract

The HLA region, especially HLA class I and II genes, which encode molecules for antigen presentation to T cells, plays a major role in the predisposition to autoimmune disorders. To clarify the mechanisms behind this association, we examined genome‐wide DNA methylation by microarrays to cover over 850,000 CpG sites in the CD4+ T cells and CD19+ B cells of healthy subjects homozygous either for DRB1*15‐DQA1*01‐DQB1*06:02 (DR2‐DQ6, n = 14), associated with a strongly decreased T1D risk, DRB1*03‐DQA1*05‐DQB1*02 (DR3‐DQ2, n = 19), or DRB1*04:01‐DQA1*03‐DQB1*03:02 (DR4‐DQ8, n = 17), associated with a moderately increased T1D risk. In total, we discovered 14 differentially methylated CpG probes, of which 10 were located in the HLA region and six in the HLA‐DRB1 locus. The main differences were between the protective genotype DR2‐DQ6 and the risk genotypes DR3‐DQ2 and DR4‐DQ8, where the DR2‐DQ6 group was hypomethylated compared to the other groups in all but four of the differentially methylated probes. The differences between the risk genotypes DR3‐DQ2 and DR4‐DQ8 were small. Our results indicate that HLA variants have few systemic effects on methylation and that their effect on autoimmunity is conveyed directly by HLA molecules, possibly by differences in expression levels or function. [ABSTRACT FROM AUTHOR]

Published
2024
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28. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

Author

Joubert, Bonnie R, Felix, Janine F, Yousefi, Paul, Bakulski, Kelly M, Just, Allan C, Breton, Carrie, Reese, Sarah E, Markunas, Christina A, Richmond, Rebecca C, Xu, Cheng-Jian, Küpers, Leanne K, Oh, Sam S, Hoyo, Cathrine, Gruzieva, Olena, Söderhäll, Cilla, Salas, Lucas A, Baïz, Nour, Zhang, Hongmei, Lepeule, Johanna, Ruiz, Carlos, Ligthart, Symen, Wang, Tianyuan, Taylor, Jack A, Duijts, Liesbeth, Sharp, Gemma C, Jankipersadsing, Soesma A, Nilsen, Roy M, Vaez, Ahmad, Fallin, M Daniele, Hu, Donglei, Litonjua, Augusto A, Fuemmeler, Bernard F, Huen, Karen, Kere, Juha, Kull, Inger, Munthe-Kaas, Monica Cheng, Gehring, Ulrike, Bustamante, Mariona, Saurel-Coubizolles, Marie José, Quraishi, Bilal M, Ren, Jie, Tost, Jörg, Gonzalez, Juan R, Peters, Marjolein J, Håberg, Siri E, Xu, Zongli, van Meurs, Joyce B, Gaunt, Tom R, Kerkhof, Marjan, Corpeleijn, Eva, Feinberg, Andrew P, Eng, Celeste, Baccarelli, Andrea A, Neelon, Sara E Benjamin, Bradman, Asa, Merid, Simon Kebede, Bergström, Anna, Herceg, Zdenko, Hernandez-Vargas, Hector, Brunekreef, Bert, Pinart, Mariona, Heude, Barbara, Ewart, Susan, Yao, Jin, Lemonnier, Nathanaël, Franco, Oscar H, Wu, Michael C, Hofman, Albert, McArdle, Wendy, Van der Vlies, Pieter, Falahi, Fahimeh, Gillman, Matthew W, Barcellos, Lisa F, Kumar, Ashish, Wickman, Magnus, Guerra, Stefano, Charles, Marie-Aline, Holloway, John, Auffray, Charles, Tiemeier, Henning W, Smith, George Davey, Postma, Dirkje, Hivert, Marie-France, Eskenazi, Brenda, Vrijheid, Martine, Arshad, Hasan, Antó, Josep M, Dehghan, Abbas, Karmaus, Wilfried, Annesi-Maesano, Isabella, Sunyer, Jordi, Ghantous, Akram, Pershagen, Göran, Holland, Nina, Murphy, Susan K, DeMeo, Dawn L, Burchard, Esteban G, Ladd-Acosta, Christine, Snieder, Harold, and Nystad, Wenche

Subjects
Genetics, Pediatric, Human Genome, Tobacco, Tobacco Smoke and Health, Prevention, Aetiology, 2.1 Biological and endogenous factors, 2.2 Factors relating to the physical environment, Respiratory, Reproductive health and childbirth, Good Health and Well Being, Asthma, Child, Child, Preschool, Chromosome Mapping, Cleft Lip, Cleft Palate, DNA Methylation, Epigenesis, Genetic, Female, Genetic Association Studies, Humans, Infant, Infant, Newborn, Pregnancy, Smoking, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.

Published
2016

32. Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy

Author

Göös, Helka, Fogarty, Christopher L., Sahu, Biswajyoti, Plagnol, Vincent, Rajamäki, Kristiina, Nurmi, Katariina, Liu, Xiaonan, Einarsdottir, Elisabet, Jouppila, Annukka, Pettersson, Tom, Vihinen, Helena, Krjutskov, Kaarel, Saavalainen, Päivi, Järvinen, Asko, Muurinen, Mari, Greco, Dario, Scala, Giovanni, Curtis, James, Nordström, Dan, Flaumenhaft, Robert, Vaarala, Outi, Kovanen, Panu E., Keskitalo, Salla, Ranki, Annamari, Kere, Juha, Lehto, Markku, Notarangelo, Luigi D., Nejentsev, Sergey, Eklund, Kari K., Varjosalo, Markku, Taipale, Jussi, and Seppänen, Mikko R.J.

Published
2019
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33. Epigenome-wide meta-analysis of DNA methylation and childhood asthma

Author

Reese, Sarah E., Xu, Cheng-Jian, den Dekker, Herman T., Lee, Mi Kyeong, Sikdar, Sinjini, Ruiz-Arenas, Carlos, Merid, Simon K., Rezwan, Faisal I., Page, Christian M., Ullemar, Vilhelmina, Melton, Phillip E., Oh, Sam S., Yang, Ivana V., Burrows, Kimberley, Söderhäll, Cilla, Jima, Dereje D., Gao, Lu, Arathimos, Ryan, Küpers, Leanne K., Wielscher, Matthias, Rzehak, Peter, Lahti, Jari, Laprise, Catherine, Madore, Anne-Marie, Ward, James, Bennett, Brian D., Wang, Tianyuan, Bell, Douglas A., Vonk, Judith M., Håberg, Siri E., Zhao, Shanshan, Karlsson, Robert, Hollams, Elysia, Hu, Donglei, Richards, Adam J., Bergström, Anna, Sharp, Gemma C., Felix, Janine F., Bustamante, Mariona, Gruzieva, Olena, Maguire, Rachel L., Gilliland, Frank, Baïz, Nour, Nohr, Ellen A., Corpeleijn, Eva, Sebert, Sylvain, Karmaus, Wilfried, Grote, Veit, Kajantie, Eero, Magnus, Maria C., Örtqvist, Anne K., Eng, Celeste, Liu, Andrew H., Kull, Inger, Jaddoe, Vincent W.V., Sunyer, Jordi, Kere, Juha, Hoyo, Cathrine, Annesi-Maesano, Isabella, Arshad, Syed Hasan, Koletzko, Berthold, Brunekreef, Bert, Binder, Elisabeth B., Räikkönen, Katri, Reischl, Eva, Holloway, John W., Jarvelin, Marjo-Riitta, Snieder, Harold, Kazmi, Nabila, Breton, Carrie V., Murphy, Susan K., Pershagen, Göran, Anto, Josep Maria, Relton, Caroline L., Schwartz, David A., Burchard, Esteban G., Huang, Rae-Chi, Nystad, Wenche, Almqvist, Catarina, Henderson, A. John, Melén, Erik, Duijts, Liesbeth, Koppelman, Gerard H., and London, Stephanie J.

Published
2019
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34. Dominant Mutations in GRHL3 Cause Van der Woude Syndrome and Disrupt Oral Periderm Development

Author

Peyrard-Janvid, Myriam, Leslie, Elizabeth J, Kousa, Youssef A, Smith, Tiffany L, Dunnwald, Martine, Magnusson, Måns, Lentz, Brian A, Unneberg, Per, Fransson, Ingegerd, Koillinen, Hannele K, Rautio, Jorma, Pegelow, Marie, Karsten, Agneta, Basel-Vanagaite, Lina, Gordon, William, Andersen, Bogi, Svensson, Thomas, Murray, Jeffrey C, Cornell, Robert A, Kere, Juha, and Schutte, Brian C

Subjects
Biomedical and Clinical Sciences, Dentistry, Dental/Oral and Craniofacial Disease, Genetics, Pediatric, Rare Diseases, Clinical Research, Biotechnology, Aetiology, 2.1 Biological and endogenous factors, Congenital, Abnormalities, Multiple, Alleles, Animals, Cleft Lip, Cleft Palate, Cysts, DNA-Binding Proteins, Gene Expression Regulation, Developmental, Genotype, Humans, Hybridization, Genetic, Interferon Regulatory Factors, Lip, Mice, Mice, Knockout, Mutation, Missense, Pedigree, Phenotype, Sequence Analysis, DNA, Transcription Factors, Zebrafish, Biological Sciences, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Mutations in interferon regulatory factor 6 (IRF6) account for ∼70% of cases of Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate. In 8 of 45 VWS-affected families lacking a mutation in IRF6, we found coding mutations in grainyhead-like 3 (GRHL3). According to a zebrafish-based assay, the disease-associated GRHL3 mutations abrogated periderm development and were consistent with a dominant-negative effect, in contrast to haploinsufficiency seen in most VWS cases caused by IRF6 mutations. In mouse, all embryos lacking Grhl3 exhibited abnormal oral periderm and 17% developed a cleft palate. Analysis of the oral phenotype of double heterozygote (Irf6(+/-);Grhl3(+/-)) murine embryos failed to detect epistasis between the two genes, suggesting that they function in separate but convergent pathways during palatogenesis. Taken together, our data demonstrated that mutations in two genes, IRF6 and GRHL3, can lead to nearly identical phenotypes of orofacial cleft. They supported the hypotheses that both genes are essential for the presence of a functional oral periderm and that failure of this process contributes to VWS.

Published
2014

35. Annotation of nuclear lncRNAs based on chromatin interactions.

Author

Agrawal, Saumya, Buyan, Andrey, Severin, Jessica, Koido, Masaru, Alam, Tanvir, Abugessaisa, Imad, Chang, Howard Y., Dostie, Josée, Itoh, Masayoshi, Kere, Juha, Kondo, Naoto, Li, Yunjing, Makeev, Vsevolod J., Mendez, Mickaël, Okazaki, Yasushi, Ramilowski, Jordan A., Sigorskikh, Andrey I., Strug, Lisa J., Yagi, Ken, and Yasuzawa, Kayoko

Subjects
RNA-protein interactions, LINCRNA, CHROMATIN, GENE enhancers, WEB portals, HUMAN genome
Abstract

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA. [ABSTRACT FROM AUTHOR]

Published
2024
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37. Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development

Author

Boskovic, Nina, primary, Yazgeldi, Gamze, additional, Ezer, Sini, additional, Tervaniemi, Mari H., additional, Inzunza, Jose, additional, Deligiannis, Spyridon Panagiotis, additional, Yaşar, Barış, additional, Skoog, Tiina, additional, Krjutškov, Kaarel, additional, Katayama, Shintaro, additional, and Kere, Juha, additional

Published
2023
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38. Metabolic and functional changes in transgender individuals following cross-sex hormone treatment: Design and methods of the GEnder Dysphoria Treatment in Sweden (GETS) study

Author

Wiik, Anna, Andersson, Daniel P., Brismar, Torkel B., Chanpen, Setareh, Dhejne, Cecilia, Ekström, Tomas J., Flanagan, John N., Holmberg, Mats, Kere, Juha, Lilja, Mats, Lindholm, Malene E., Lundberg, Tommy R., Maret, Eva, Melin, Michael, Olsson, Sofie M., Rullman, Eric, Wåhlén, Kerstin, Arver, Stefan, and Gustafsson, Thomas

Published
2018
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39. DNA methylation in childhood asthma: an epigenome-wide meta-analysis

Author

Xu, Cheng-Jian, Söderhäll, Cilla, Bustamante, Mariona, Baïz, Nour, Gruzieva, Olena, Gehring, Ulrike, Mason, Dan, Chatzi, Leda, Basterrechea, Mikel, Llop, Sabrina, Torrent, Maties, Forastiere, Francesco, Fantini, Maria Pia, Carlsen, Karin C Lødrup, Haahtela, Tari, Morin, Andréanne, Kerkhof, Marjan, Merid, Simon Kebede, van Rijkom, Bianca, Jankipersadsing, Soesma A, Bonder, Marc Jan, Ballereau, Stephane, Vermeulen, Cornelis J, Aguirre-Gamboa, Raul, de Jongste, Johan C, Smit, Henriette A, Kumar, Ashish, Pershagen, Göran, Guerra, Stefano, Garcia-Aymerich, Judith, Greco, Dario, Reinius, Lovisa, McEachan, Rosemary R C, Azad, Raf, Hovland, Vegard, Mowinckel, Petter, Alenius, Harri, Fyhrquist, Nanna, Lemonnier, Nathanaël, Pellet, Johann, Auffray, Charles, van der Vlies, Pieter, van Diemen, Cleo C, Li, Yang, Wijmenga, Cisca, Netea, Mihai G, Moffatt, Miriam F, Cookson, William O C M, Anto, Josep M, Bousquet, Jean, Laatikainen, Tiina, Laprise, Catherine, Carlsen, Kai-Håkon, Gori, Davide, Porta, Daniela, Iñiguez, Carmen, Bilbao, Jose Ramon, Kogevinas, Manolis, Wright, John, Brunekreef, Bert, Kere, Juha, Nawijn, Martijn C, Annesi-Maesano, Isabella, Sunyer, Jordi, Melén, Erik, and Koppelman, Gerard H

Published
2018
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41. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity

Author

Tsoi, Lam C, Spain, Sarah L, Knight, Jo, Ellinghaus, Eva, Stuart, Philip E, Capon, Francesca, Ding, Jun, Li, Yanming, Tejasvi, Trilokraj, Gudjonsson, Johann E, Kang, Hyun M, Allen, Michael H, McManus, Ross, Novelli, Giuseppe, Samuelsson, Lena, Schalkwijk, Joost, Ståhle, Mona, Burden, A David, Smith, Catherine H, Cork, Michael J, Estivill, Xavier, Bowcock, Anne M, Krueger, Gerald G, Weger, Wolfgang, Worthington, Jane, Tazi-Ahnini, Rachid, Nestle, Frank O, Hayday, Adrian, Hoffmann, Per, Winkelmann, Juliane, Wijmenga, Cisca, Langford, Cordelia, Edkins, Sarah, Andrews, Robert, Blackburn, Hannah, Strange, Amy, Band, Gavin, Pearson, Richard D, Vukcevic, Damjan, Spencer, Chris CA, Deloukas, Panos, Mrowietz, Ulrich, Schreiber, Stefan, Weidinger, Stephan, Koks, Sulev, Kingo, Külli, Esko, Tonu, Metspalu, Andres, Lim, Henry W, Voorhees, John J, Weichenthal, Michael, Wichmann, H Erich, Chandran, Vinod, Rosen, Cheryl F, Rahman, Proton, Gladman, Dafna D, Griffiths, Christopher EM, Reis, Andre, Kere, Juha, Nair, Rajan P, Franke, Andre, Barker, Jonathan NWN, Abecasis, Goncalo R, Elder, James T, and Trembath, Richard C

Subjects
Genetics, Autoimmune Disease, Human Genome, Psoriasis, Aetiology, 2.1 Biological and endogenous factors, Skin, CARD Signaling Adaptor Proteins, Core Binding Factor Alpha 3 Subunit, DEAD Box Protein 58, DEAD-box RNA Helicases, GTPase-Activating Proteins, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Guanylate Cyclase, Humans, Immunity, Innate, Membrane Proteins, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Receptors, Immunologic, STAT3 Transcription Factor, T-Lymphocytes, White People, Collaborative Association Study of Psoriasis, Genetic Analysis of Psoriasis Consortium, Psoriasis Association Genetics Extension, Wellcome Trust Case Control Consortium 2, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.

Published
2012

42. Characterization of a Common Susceptibility Locus for Asthma-Related Traits

Author

Laitinen, Tarja, Polvi, Anne, Rydman, Pia, Vendelin, Johanna, Pulkkinen, Ville, Salmikangas, Paula, Mäkelä, Siru, Rehn, Marko, Pirskanen, Asta, Rautanen, Anna, Zucchelli, Marco, Gullstén, Harriet, Leino, Marina, Alenius, Harri, Petäys, Tuula, Haahtela, Tari, Laitinen, Annika, Laprise, Catherine, Hudson, Thomas J., Laitinen, Lauri A., and Kere, Juha

Published
2004

46. Human Chromosome 7: DNA Sequence and Biology

Author

Scherer, Stephen W., Cheung, Joseph, MacDonald, Jeffrey R., Osborne, Lucy R., Nakabayashi, Kazuhiko, Herbrick, Jo-Anne, Carson, Andrew R., Parker-Katiraee, Layla, Skaug, Jennifer, Khaja, Razi, Zhang, Junjun, Hudek, Alexander K., Li, Martin, Haddad, May, Duggan, Gavin E., Fernandez, Bridget A., Kanematsu, Emiko, Gentles, Simone, Christopoulos, Constantine C., Choufani, Sanaa, Kwasnicka, Dorota, Zheng, Xiangqun H., Lai, Zhongwu, Nusskern, Deborah, Zhang, Qing, Gu, Zhiping, Lu, Fu, Zeesman, Susan, Nowaczyk, Malgorzata J., Teshima, Ikuko, Chitayat, David, Shuman, Cheryl, Weksberg, Rosanna, Zackai, Elaine H., Grebe, Theresa A., Cox, Sarah R., Kirkpatrick, Susan J., Rahman, Nazneen, Friedman, Jan M., Pelicci, Pier Giuseppe, Lo-Coco, Francesco, Belloni, Elena, Shaffer, Lisa G., Pober, Barbara, Morton, Cynthia C., Gusella, James F., Korf, Bruce R., Quade, Bradley J., Ligon, Azra H., Ferguson, Heather, Higgins, Anne W., Leach, Natalia T., Herrick, Steven R., Lemyre, Emmanuelle, Farra, Chantal G., Kim, Hyung-Goo, Summers, Anne M., Gripp, Karen W., Roberts, Wendy, Szatmari, Peter, Grzeschik, Karl-Heinz, Teebi, Ahmed, Minassian, Berge A., Kere, Juha, Armengol, Lluis, Pujana, Miguel Angel, Estivill, Xavier, Wilson, Michael D., Koop, Ben F., Tosi, Sabrina, Moore, Gudrun E., Boright, Andrew P., Zlotorynski, Eitan, Kerem, Batsheva, Kroisel, Peter M., Petek, Erwin, Oscier, David G., Mould, Sarah J., Döhner, Hartmut, Döhner, Konstanze, Rommens, Johanna M., Vincent, John B., Venter, J. Craig, Li, Peter W., Mural, Richard J., Adams, Mark D., and Tsui, Lap-Chee

Published
2003

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