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1. Understanding neurodevelopmental proteasomopathies as new rare disease entities: A review of current concepts, molecular biomarkers, and perspectives

Author

Silvestre Cuinat, Stéphane Bézieau, Wallid Deb, Sandra Mercier, Virginie Vignard, Bertrand Isidor, Sébastien Küry, and Frédéric Ebstein

Subjects
Biomarkers, Loss-of-function variants, Neurodevelopmental disorders, Proteasome, Rare diseases, Therapeutic targets, Medicine (General), R5-920, Genetics, QH426-470
Abstract

The recent advances in high throughput sequencing technology have drastically changed the practice of medical diagnosis, allowing for rapid identification of hundreds of genes causing human diseases. This unprecedented progress has made clear that most forms of intellectual disability that affect more than 3% of individuals worldwide are monogenic diseases. Strikingly, a substantial fraction of the mendelian forms of intellectual disability is associated with genes related to the ubiquitin-proteasome system, a highly conserved pathway made up of approximately 1200 genes involved in the regulation of protein homeostasis. Within this group is currently emerging a new class of neurodevelopmental disorders specifically caused by proteasome pathogenic variants which we propose to designate “neurodevelopmental proteasomopathies”. Besides cognitive impairment, these diseases are typically associated with a series of syndromic clinical manifestations, among which facial dysmorphism, motor delay, and failure to thrive are the most prominent ones. While recent efforts have been made to uncover the effects exerted by proteasome variants on cell and tissue landscapes, the molecular pathogenesis of neurodevelopmental proteasomopathies remains ill-defined. In this review, we discuss the cellular changes typically induced by genomic alterations in proteasome genes and explore their relevance as biomarkers for the diagnosis, management, and potential treatment of these new rare disease entities.

Published
2024
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2. Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer.

Author

Jian Gong, Carolyn M Hutter, Polly A Newcomb, Cornelia M Ulrich, Stephanie A Bien, Peter T Campbell, John A Baron, Sonja I Berndt, Stephane Bezieau, Hermann Brenner, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Mengmeng Du, David Duggan, Jane C Figueiredo, Steven Gallinger, Edward L Giovannucci, Robert W Haile, Tabitha A Harrison, Richard B Hayes, Michael Hoffmeister, John L Hopper, Thomas J Hudson, Jihyoun Jeon, Mark A Jenkins, Jonathan Kocarnik, Sébastien Küry, Loic Le Marchand, Yi Lin, Noralane M Lindor, Reiko Nishihara, Shuji Ogino, John D Potter, Anja Rudolph, Robert E Schoen, Petra Schrotz-King, Daniela Seminara, Martha L Slattery, Stephen N Thibodeau, Mark Thornquist, Reka Toth, Robert Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters, and CCFR and GECCO

Subjects
Genetics, QH426-470
Abstract

Genome-wide association studies (GWAS) have identified many genetic susceptibility loci for colorectal cancer (CRC). However, variants in these loci explain only a small proportion of familial aggregation, and there are likely additional variants that are associated with CRC susceptibility. Genome-wide studies of gene-environment interactions may identify variants that are not detected in GWAS of marginal gene effects. To study this, we conducted a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking using data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Interactions were tested using logistic regression. We identified interaction between CRC risk and alcohol consumption and variants in the 9q22.32/HIATL1 (Pinteraction = 1.76×10-8; permuted p-value 3.51x10-8) region. Compared to non-/occasional drinking light to moderate alcohol consumption was associated with a lower risk of colorectal cancer among individuals with rs9409565 CT genotype (OR, 0.82 [95% CI, 0.74-0.91]; P = 2.1×10-4) and TT genotypes (OR,0.62 [95% CI, 0.51-0.75]; P = 1.3×10-6) but not associated among those with the CC genotype (p = 0.059). No genome-wide statistically significant interactions were observed for smoking. If replicated our suggestive finding of a genome-wide significant interaction between genetic variants and alcohol consumption might contribute to understanding colorectal cancer etiology and identifying subpopulations with differential susceptibility to the effect of alcohol on CRC risk.

Published
2016
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3. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Zhishan Chen, Xingyi Guo, Ran Tao, Jeroen R. Huyghe, Philip J. Law, Ceres Fernandez-Rozadilla, Jie Ping, Guochong Jia, Jirong Long, Chao Li, Quanhu Shen, Yuhan Xie, Maria N. Timofeeva, Minta Thomas, Stephanie L. Schmit, Virginia Díez-Obrero, Matthew Devall, Ferran Moratalla-Navarro, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah E. W. Briggs, Victoria Svinti, Kevin Donnelly, Susan M. Farrington, James Blackmur, Peter G. Vaughan-Shaw, Xiao-Ou Shu, Yingchang Lu, Peter Broderick, James Studd, Tabitha A. Harrison, David V. Conti, Fredrick R. Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John L. Hopper, Mark A. Jenkins, Aung Ko Win, Rish K. Pai, Jane C. Figueiredo, Robert W. Haile, Steven Gallinger, Michael O. Woods, Polly A. Newcomb, David Duggan, Jeremy P. Cheadle, Richard Kaplan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Jukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A. Aaltonen, Harri Rissanen, Eero Pukkala, Johan G. Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Satu Männistö, Demetrius Albanes, Stephanie J. Weinstein, Edward Ruiz-Narvaez, Julie R. Palmer, Daniel D. Buchanan, Elizabeth A. Platz, Kala Visvanathan, Cornelia M. Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter T. Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha L. Slattery, John D. Potter, Kostas K. Tsilidis, Matthias B. Schulze, Marc J. Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, D. Timothy Bishop, Graham G. Giles, Melissa C. Southey, Gregory E. Idos, Kevin J. McDonnell, Zomoroda Abu-Ful, Joel K. Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope O. Keku, Bethany van Guelpen, Thomas J. Hudson, Heather Hampel, Rachel Pearlman, Sonja I. Berndt, Richard B. Hayes, Marie Elena Martinez, Sushma S. Thomas, Paul D. P. Pharoah, Susanna C. Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F. Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T. Chan, Marcia Cruz-Correa, Annika Lindblom, David J. Hunter, Amit D. Joshi, Clemens Schafmayer, Peter C. Scacheri, Anshul Kundaje, Robert E. Schoen, Jochen Hampe, Zsofia K. Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Christopher K. Edlund, W. James Gauderman, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen J. Chanock, Franzel van Duijnhoven, Edith J. M. Feskens, Lori C. Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Barbara Pardini, Liesel M. FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie A. Bien, Charles Kooperberg, Christopher I. Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Loic Le Marchand, Anna H. Wu, Chenxu Qu, Caroline E. McNeil, Gerhard Coetzee, Caroline Hayward, Ian J. Deary, Sarah E. Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Ken S. Lau, Hongyu Zhao, Li Hsu, Qiuyin Cai, Malcolm G. Dunlop, Stephen B. Gruber, Richard S. Houlston, Victor Moreno, Graham Casey, Ulrike Peters, Ian Tomlinson, and Wei Zheng

Subjects
Science
Abstract

Abstract Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.

Published
2024
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4. Exploring the origins of neurodevelopmental proteasomopathies associated with cardiac malformations: are neural crest cells central to certain pathological mechanisms?

Author

Virginie Vignard, Alban-Elouen Baruteau, Bérénice Toutain, Sandra Mercier, Bertrand Isidor, Richard Redon, Jean-Jacques Schott, Sébastien Küry, Stéphane Bézieau, Anne H. Monsoro-Burq, and Frédéric Ebstein

Subjects
neurodevelopmental proteasomopathies, cardiac malformations, craniofacial anomalies, neural crest cells, protein homeostasis, compensatory pathways, Biology (General), QH301-705.5
Abstract

Neurodevelopmental proteasomopathies constitute a recently defined class of rare Mendelian disorders, arising from genomic alterations in proteasome-related genes. These alterations result in the dysfunction of proteasomes, which are multi-subunit protein complexes essential for maintaining cellular protein homeostasis. The clinical phenotype of these diseases manifests as a syndromic association involving impaired neural development and multisystem abnormalities, notably craniofacial anomalies and malformations of the cardiac outflow tract (OFT). These observations suggest that proteasome loss-of-function variants primarily affect specific embryonic cell types which serve as origins for both craniofacial structures and the conotruncal portion of the heart. In this hypothesis article, we propose that neural crest cells (NCCs), a highly multipotent cell population, which generates craniofacial skeleton, mesenchyme as well as the OFT of the heart, in addition to many other derivatives, would exhibit a distinctive vulnerability to protein homeostasis perturbations. Herein, we introduce the diverse cellular compensatory pathways activated in response to protein homeostasis disruption and explore their potential implications for NCC physiology. Altogether, the paper advocates for investigating proteasome biology within NCCs and their early cranial and cardiac derivatives, offering a rationale for future exploration and laying the initial groundwork for therapeutic considerations.

Published
2024
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5. Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancerResearch in context

Author

Nikos Papadimitriou, Andre Kim, Eric S. Kawaguchi, John Morrison, Virginia Diez-Obrero, Demetrius Albanes, Sonja I. Berndt, Stéphane Bézieau, Stephanie A. Bien, D Timothy Bishop, Emmanouil Bouras, Hermann Brenner, Daniel D. Buchanan, Peter T. Campbell, Robert Carreras-Torres, Andrew T. Chan, Jenny Chang-Claude, David V. Conti, Matthew A. Devall, Niki Dimou, David A. Drew, Stephen B. Gruber, Tabitha A. Harrison, Michael Hoffmeister, Jeroen R. Huyghe, Amit D. Joshi, Temitope O. Keku, Anshul Kundaje, Sébastien Küry, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Brigid M. Lynch, Victor Moreno, Christina C. Newton, Mireia Obón-Santacana, Jennifer Ose, Andrew J. Pellatt, Anita R. Peoples, Elizabeth A. Platz, Conghui Qu, Gad Rennert, Edward Ruiz-Narvaez, Anna Shcherbina, Mariana C. Stern, Yu-Ru Su, Duncan C. Thomas, Claire E. Thomas, Yu Tian, Konstantinos K. Tsilidis, Cornelia M. Ulrich, Caroline Y. Um, Kala Visvanathan, Jun Wang, Emily White, Michael O. Woods, Stephanie L. Schmit, Finlay Macrae, John D. Potter, John L. Hopper, Ulrike Peters, Neil Murphy, Li Hsu, Marc J. Gunter, and W. James Gauderman

Subjects
Diet, Fibre, Gene-environment interaction, Colorectal cancer, GWAS, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: Consumption of fibre, fruits and vegetables have been linked with lower colorectal cancer (CRC) risk. A genome-wide gene-environment (G × E) analysis was performed to test whether genetic variants modify these associations. Methods: A pooled sample of 45 studies including up to 69,734 participants (cases: 29,896; controls: 39,838) of European ancestry were included. To identify G × E interactions, we used the traditional 1--degree-of-freedom (DF) G × E test and to improve power a 2-step procedure and a 3DF joint test that investigates the association between a genetic variant and dietary exposure, CRC risk and G × E interaction simultaneously. Findings: The 3-DF joint test revealed two significant loci with p-value

Published
2024
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6. Characterization of genetic variants in the EGLN1/PHD2 gene identified in a European collection of patients with erythrocytosis

Author

Marine Delamare, Amandine Le Roy, Mathilde Pacault, Loïc Schmitt, Céline Garrec, Nada Maaziz, Matti Myllykoski, Antoine Rimbert, Valéna Karaghiannis, Bernard Aral, Mark Catherwood, Fabrice Airaud, Lamisse Mansour-Hendili, David Hoogewijs, Edoardo Peroni, Salam Idriss, Valentine Lesieur, Amandine Caillaud, Karim Si-Tayeb, Caroline Chariau, Anne Gaignerie, Minke Rab, Torsten Haferlach, Manja Meggendorfer, Stéphane Bézieau, Andrea Benetti, Nicole Casadevall, Pierre Hirsch, Christian Rose, Mathieu Wemeau, Frédéric Galacteros, Bruno Cassinat, Beatriz Bellosillo, Celeste Bento, Richard van Wijk, Petro E. Petrides, Maria Luigia Randi, Mary Frances McMullin, Peppi Koivunen, François Girodon, Betty Gardie, and ECYT consortium

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Hereditary erythrocytosis is a rare hematologic disorder characterized by an excess of red blood cell production. Here we describe a European collaborative study involving a collection of 2,160 patients with erythrocytosis sequenced in ten different laboratories. We focused our study on the EGLN1 gene and identified 39 germline missense variants including one gene deletion in 47 probands. EGLN1 encodes the PHD2 prolyl 4-hydroxylase, a major inhibitor of hypoxia-inducible factor. We performed a comprehensive study to evaluate the causal role of the identified PHD2 variants: (i) in silico studies of localization, conservation, and deleterious effects; (ii) analysis of hematologic parameters of carriers identified in the UK Biobank; (iii) functional studies of the protein activity and stability; and (iv) a comprehensive study of PHD2 splicing. Altogether, these studies allowed the classification of 16 pathogenic or likely pathogenic mutants in a total of 48 patients and relatives. The in silico studies extended to the variants described in the literature showed that a minority of PHD2 variants can be classified as pathogenic (36/96), without any differences from the variants of unknown significance regarding the severity of the developed disease (hematologic parameters and complications). Here, we demonstrated the great value of federating laboratories working on such rare disorders in order to implement the criteria required for genetic classification, a strategy that should be extended to all hereditary hematologic diseases.

Published
2023
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7. Comprehensive in silico and functional studies for classification of EPAS1/HIF2A genetic variants identified in patients with erythrocytosis

Author

Valéna Karaghiannis, Darko Maric, Céline Garrec, Nada Maaziz, Alexandre Buffet, Loïc Schmitt, Vincent Antunes, Fabrice Airaud, Bernard Aral, Amandine Le Roy, Sébastien Corbineau, Lamisse Mansour-Hendili, Valentine Lesieur, Antoine Rimbert, Fabien Laporte, Marine Delamare, Minke Rab, Stéphane Bézieau, Bruno Cassinat, Frédéric Galacteros, Anne-Paule Gimenez-Roqueplo, Nelly Burnichon, Holger Cario, Richard van Wijk, Celeste Bento, François Girodon, David Hoogewijs, and Betty Gardie

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Gain-of-function mutations in the EPAS1/HIF2A gene have been identified in patients with hereditary erythrocytosis that can be associated with the development of paraganglioma, pheochromocytoma and somatostatinoma. In the present study, we describe a unique European collection of 41 patients and 28 relatives diagnosed with an erythrocytosis associated with a germline genetic variant in EPAS1. In addition we identified two infants with severe erythrocytosis associated with a mosaic mutation present in less than 2% of the blood, one of whom later developed a paraganglioma. The aim of this study was to determine the causal role of these genetic variants, to establish pathogenicity, and to identify potential candidates eligible for the new hypoxia-inducible factor-2 α (HIF-2α) inhibitor treatment. Pathogenicity was predicted with in silico tools and the impact of 13 HIF-2b variants has been studied by using canonical and real-time reporter luciferase assays. These functional assays consisted of a novel edited vector containing an expanded region of the erythropoietin promoter combined with distal regulatory elements which substantially enhanced the HIF-2α-dependent induction. Altogether, our studies allowed the classification of 11 mutations as pathogenic in 17 patients and 23 relatives. We described four new mutations (D525G, L526F, G527K, A530S) close to the key proline P531, which broadens the spectrum of mutations involved in erythrocytosis. Notably, we identified patients with only erythrocytosis associated with germline mutations A530S and Y532C previously identified at somatic state in tumors, thereby raising the complexity of the genotype/phenotype correlations. Altogether, this study allows accurate clinical follow-up of patients and opens the possibility of benefiting from HIF-2α inhibitor treatment, so far the only targeted treatment in hypoxia-related erythrocytosis disease.

Published
2023
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8. First French study relative to preconception genetic testing: 1500 general population participants’ opinion

Author

Valérie Bonneau, Mathilde Nizon, Xenia Latypova, Aurélie Gaultier, Eugénie Hoarau, Stéphane Bézieau, Guy Minguet, Mauro Turrini, Maud Jourdain, and Bertrand Isidor

Subjects
Preconception genetic testing, Expanded carrier screening, Reproductive medicine, Medicine
Abstract

Abstract Background Until very recently, preconception genetic testing was only conducted in particular communities, ethnic groups or families for which an increased risk of genetic disease was identified. To detect in general population a risk for a couple to have a child affected by a rare, recessive or X-linked, genetic disease, carrier screening is proposed in several countries. We aimed to determine the current public opinion relative to this approach in France, using either a printed or web-based questionnaire. Results Among the 1568 participants, 91% are favorable to preconception genetic tests and 57% declare to be willing to have the screening if the latter is available. A medical prescription by a family doctor or a gynecologist would be the best way to propose the test for 73%, with a reimbursement from the social security insurance. However, 19% declare not to be willing to use the test because of their ethic or moral convictions, and the fear that the outcome would question the pregnancy. Otherwise, most participants consider that the test is a medical progress despite the risk of an increased medicalization of the pregnancy. Conclusion This first study in France highlights a global favorable opinion for the preconception genetic carrier testing under a medical prescription and a reimbursement by social security insurance. Our results emphasize as well the complex concerns underpinned by the use of this screening strategy. Therefore, the ethical issues related to these tests include the risk of eugenic drift mentioned by more than half of the participants.

Published
2021
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9. Adiposity, metabolites, and colorectal cancer risk: Mendelian randomization study

Author

Caroline J. Bull, Joshua A. Bell, Neil Murphy, Eleanor Sanderson, George Davey Smith, Nicholas J. Timpson, Barbara L. Banbury, Demetrius Albanes, Sonja I. Berndt, Stéphane Bézieau, D. Timothy Bishop, Hermann Brenner, Daniel D. Buchanan, Andrea Burnett-Hartman, Graham Casey, Sergi Castellví-Bel, Andrew T. Chan, Jenny Chang-Claude, Amanda J. Cross, Albert de la Chapelle, Jane C. Figueiredo, Steven J. Gallinger, Susan M. Gapstur, Graham G. Giles, Stephen B. Gruber, Andrea Gsur, Jochen Hampe, Heather Hampel, Tabitha A. Harrison, Michael Hoffmeister, Li Hsu, Wen-Yi Huang, Jeroen R. Huyghe, Mark A. Jenkins, Corinne E. Joshu, Temitope O. Keku, Tilman Kühn, Sun-Seog Kweon, Loic Le Marchand, Christopher I. Li, Li Li, Annika Lindblom, Vicente Martín, Anne M. May, Roger L. Milne, Victor Moreno, Polly A. Newcomb, Kenneth Offit, Shuji Ogino, Amanda I. Phipps, Elizabeth A. Platz, John D. Potter, Conghui Qu, J. Ramón Quirós, Gad Rennert, Elio Riboli, Lori C. Sakoda, Clemens Schafmayer, Robert E. Schoen, Martha L. Slattery, Catherine M. Tangen, Kostas K. Tsilidis, Cornelia M. Ulrich, Fränzel J. B. van Duijnhoven, Bethany van Guelpen, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Hansong Wang, Emily White, Alicja Wolk, Michael O. Woods, Anna H. Wu, Peter T. Campbell, Wei Zheng, Ulrike Peters, Emma E. Vincent, and Marc J. Gunter

Subjects
Body mass index, Waist-to-hip ratio, Colorectal cancer, Mendelian randomization, Metabolism, NMR, Medicine
Abstract

Abstract Background Higher adiposity increases the risk of colorectal cancer (CRC), but whether this relationship varies by anatomical sub-site or by sex is unclear. Further, the metabolic alterations mediating the effects of adiposity on CRC are not fully understood. Methods We examined sex- and site-specific associations of adiposity with CRC risk and whether adiposity-associated metabolites explain the associations of adiposity with CRC. Genetic variants from genome-wide association studies of body mass index (BMI) and waist-to-hip ratio (WHR, unadjusted for BMI; N = 806,810), and 123 metabolites from targeted nuclear magnetic resonance metabolomics (N = 24,925), were used as instruments. Sex-combined and sex-specific Mendelian randomization (MR) was conducted for BMI and WHR with CRC risk (58,221 cases and 67,694 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry). Sex-combined MR was conducted for BMI and WHR with metabolites, for metabolites with CRC, and for BMI and WHR with CRC adjusted for metabolite classes in multivariable models. Results In sex-specific MR analyses, higher BMI (per 4.2 kg/m2) was associated with 1.23 (95% confidence interval (CI) = 1.08, 1.38) times higher CRC odds among men (inverse-variance-weighted (IVW) model); among women, higher BMI (per 5.2 kg/m2) was associated with 1.09 (95% CI = 0.97, 1.22) times higher CRC odds. WHR (per 0.07 higher) was more strongly associated with CRC risk among women (IVW OR = 1.25, 95% CI = 1.08, 1.43) than men (IVW OR = 1.05, 95% CI = 0.81, 1.36). BMI or WHR was associated with 104/123 metabolites at false discovery rate-corrected P ≤ 0.05; several metabolites were associated with CRC, but not in directions that were consistent with the mediation of positive adiposity-CRC relations. In multivariable MR analyses, associations of BMI and WHR with CRC were not attenuated following adjustment for representative metabolite classes, e.g., the univariable IVW OR for BMI with CRC was 1.12 (95% CI = 1.00, 1.26), and this became 1.11 (95% CI = 0.99, 1.26) when adjusting for cholesterol in low-density lipoprotein particles. Conclusions Our results suggest that higher BMI more greatly raises CRC risk among men, whereas higher WHR more greatly raises CRC risk among women. Adiposity was associated with numerous metabolic alterations, but none of these explained associations between adiposity and CRC. More detailed metabolomic measures are likely needed to clarify the mechanistic pathways.

Published
2020
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10. Circulating bilirubin levels and risk of colorectal cancer: serological and Mendelian randomization analyses

Author

Nazlisadat Seyed Khoei, Mazda Jenab, Neil Murphy, Barbara L. Banbury, Robert Carreras-Torres, Vivian Viallon, Tilman Kühn, Bas Bueno-de-Mesquita, Krasimira Aleksandrova, Amanda J. Cross, Elisabete Weiderpass, Magdalena Stepien, Andrew Bulmer, Anne Tjønneland, Marie-Christine Boutron-Ruault, Gianluca Severi, Franck Carbonnel, Verena Katzke, Heiner Boeing, Manuela M. Bergmann, Antonia Trichopoulou, Anna Karakatsani, Georgia Martimianaki, Domenico Palli, Giovanna Tagliabue, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote, Guri Skeie, Susana Merino, Catalina Bonet, Miguel Rodríguez-Barranco, Leire Gil, Maria-Dolores Chirlaque, Eva Ardanaz, Robin Myte, Johan Hultdin, Aurora Perez-Cornago, Dagfinn Aune, Konstantinos K. Tsilidis, Demetrius Albanes, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Peter T. Campbell, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Stephen J. Chanock, Michelle Cotterchio, Steven Gallinger, Stephen B. Gruber, Robert W. Haile, Jochen Hampe, Michael Hoffmeister, John L. Hopper, Li Hsu, Jeroen R. Huyghe, Mark A. Jenkins, Amit D. Joshi, Ellen Kampman, Susanna C. Larsson, Loic Le Marchand, Christopher I. Li, Li Li, Annika Lindblom, Noralane M. Lindor, Vicente Martín, Victor Moreno, Polly A. Newcomb, Kenneth Offit, Shuji Ogino, Patrick S. Parfrey, Paul D. P. Pharoah, Gad Rennert, Lori C. Sakoda, Clemens Schafmayer, Stephanie L. Schmit, Robert E. Schoen, Martha L. Slattery, Stephen N. Thibodeau, Cornelia M. Ulrich, Franzel J. B. van Duijnhoven, Korbinian Weigl, Stephanie J. Weinstein, Emily White, Alicja Wolk, Michael O. Woods, Anna H. Wu, Xuehong Zhang, Pietro Ferrari, Gabriele Anton, Annette Peters, Ulrike Peters, Marc J. Gunter, Karl-Heinz Wagner, and Heinz Freisling

Subjects
Bilirubin, Cancer, Colorectal cancer, Anti-oxidants, Mendelian randomization analysis, Medicine
Abstract

Abstract Background Bilirubin, a byproduct of hemoglobin breakdown and purported anti-oxidant, is thought to be cancer preventive. We conducted complementary serological and Mendelian randomization (MR) analyses to investigate whether alterations in circulating levels of bilirubin are associated with risk of colorectal cancer (CRC). We decided a priori to perform analyses separately in men and women based on suggestive evidence that associations may differ by sex. Methods In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition (EPIC), pre-diagnostic unconjugated bilirubin (UCB, the main component of total bilirubin) concentrations were measured by high-performance liquid chromatography in plasma samples of 1386 CRC cases and their individually matched controls. Additionally, 115 single-nucleotide polymorphisms (SNPs) robustly associated (P

Published
2020
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11. Functional informed genome‐wide interaction analysis of body mass index, diabetes and colorectal cancer risk

Author

Zhiyu Xia, Yu‐Ru Su, Paneen Petersen, Lihong Qi, Andre E. Kim, Jane C. Figueiredo, Yi Lin, Hongmei Nan, Lori C. Sakoda, Demetrius Albanes, Sonja I. Berndt, Stéphane Bézieau, Stephanie Bien, Daniel D. Buchanan, Graham Casey, Andrew T. Chan, David V. Conti, David A. Drew, Steven J. Gallinger, W. James Gauderman, Graham G. Giles, Stephen B. Gruber, Marc J. Gunter, Michael Hoffmeister, Mark A. Jenkins, Amit D. Joshi, Loic Le Marchand, Juan P. Lewinger, Li Li, Noralane M. Lindor, Victor Moreno, Neil Murphy, Rami Nassir, Polly A. Newcomb, Shuji Ogino, Gad Rennert, Mingyang Song, Xiaoliang Wang, Alicja Wolk, Michael O. Woods, Hermann Brenner, Emily White, Martha L. Slattery, Edward L. Giovannucci, Jenny Chang‐Claude, Paul D. P. Pharoah, Li Hsu, Peter T. Campbell, and Ulrike Peters

Subjects
BMI, colorectal cancer, diabetes, gene expression, gene‐environmental interaction, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Body mass index (BMI) and diabetes are established risk factors for colorectal cancer (CRC), likely through perturbations in metabolic traits (e.g. insulin resistance and glucose homeostasis). Identification of interactions between variation in genes and these metabolic risk factors may identify novel biologic insights into CRC etiology. Methods To improve statistical power and interpretation for gene‐environment interaction (G × E) testing, we tested genetic variants that regulate expression of a gene together for interaction with BMI (kg/m2) and diabetes on CRC risk among 26 017 cases and 20 692 controls. Each variant was weighted based on PrediXcan analysis of gene expression data from colon tissue generated in the Genotype‐Tissue Expression Project for all genes with heritability ≥1%. We used a mixed‐effects model to jointly measure the G × E interaction in a gene by partitioning the interactions into the predicted gene expression levels (fixed effects), and residual G × E effects (random effects). G × BMI analyses were stratified by sex as BMI‐CRC associations differ by sex. We used false discovery rates to account for multiple comparisons and reported all results with FDR

Published
2020
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12. High-Density of FcγRIIIA+ (CD16+) Tumor-Associated Neutrophils in Metastases Improves the Therapeutic Response of Cetuximab in Metastatic Colorectal Cancer Patients, Independently of the HLA-E/CD94-NKG2A Axis

Author

Marie Denis Musquer, Nicolas Jouand, Morgane Pere, Juliette Eugène Lamer, Stéphane Bézieau, Tamara Matysiak, Roger Faroux, François-Xavier Caroli Bosc, Marie-Christine Rousselet, François Leclair, Jean-François Mosnier, Claire Toquet, Nadine Gervois, and Céline Bossard

Subjects
cetuximab, metastatic colorectal carcinoma, CD16, tumor-associated neutrophils, antibody-dependent cellular cytotoxicity, HLA-E/NKG2A axis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Antibody-dependent cellular cytotoxicity (ADCC) in the anti-tumor effect of cetuximab in metastatic colorectal cancer (mCRC) is only based on the impact of FcγRIIIA (CD16) polymorphisms as predictive of therapeutic response. However, nature, density and therapeutic impact of FcγRIIIA+ (CD16) effector cells in tumor remain poorly documented. Moreover, the inhibition of cetuximab-mediated ADCC induced by NK cells by the engagement of the new inhibitory CD94-NKG2A immune checkpoint has only been demonstrated in vitro. This multicentric study aimed to determine, on paired primary and metastatic tissue samples from a cohort of mCRC patients treated with cetuximab: 1) the nature and density of FcγRIIIA+ (CD16) immune cells, 2) the expression profile of HLA-E/β2m by tumor cells as well as the density of CD94+ immune cells and 3) their impact on both objective response to cetuximab and survival. We demonstrated that FcγRIIIA+ (CD16) intraepithelial immune cells mainly correspond to tumor-associated neutrophils (TAN), and their high density in metastases was significantly associated with a better response to cetuximab, independently of the expression of the CD94/NKG2A inhibitory immune checkpoint. However, HLA-E/β2m, preferentially overexpressed in metastases compared with primary tumors and associated with CD94+ tumor infiltrating lymphocytes (TILs), was associated with a poor overall survival. Altogether, these results strongly support the use of bispecific antibodies directed against both EGFR and FcγRIIIA (CD16) in mCRC patients, to boost cetuximab-mediated ADCC in RAS wild-type mCRC patients. The preferential overexpression of HLA-E/β2m in metastases, associated with CD94+ TILs and responsible for a poor prognosis, provides convincing arguments to inhibit this new immune checkpoint with monalizumab, a humanized anti-NKG2A antibody, in combination with anti- FcγRIIIA/EGFR bispecific antibodies as a promising therapeutic perspective in RAS wild-type mCRC patients.

Published
2021
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13. Diagnosis of exon 12‐positive polycythemia vera rescued by NGS

Author

Antoine Geay, Bernard Aral, Valentin Bourgeois, Pauline Martin, Fabrice Airaud, Céline Garrec, Stéphane Bézieau, Betty Gardie, and François Girodon

Subjects
erythrocytosis, Exon 12, JAK2, next generation sequencing, polycythemia vera, Medicine, Medicine (General), R5-920
Abstract

Abstract A JAK2V617F‐negative polycythemia associated with low serum epo needs to be tested for an exon 12 JAK2 mutation. When negative, due to potential serious complications in PV, a next generation sequencing is necessary to rule out false negative results.

Published
2020
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14. Encephalopathies with KCNC1 variants: genotype‐phenotype‐functional correlations

Author

Jillian M. Cameron, Snezana Maljevic, Umesh Nair, Ye Htet Aung, Benjamin Cogné, Stéphane Bézieau, Edward Blair, Bertrand Isidor, Christiane Zweier, André Reis, Mary Kay Koenig, Timothy Maarup, Dean Sarco, Alexandra Afenjar, A. H. M. Mahbubul Huq, Mary Kukolich, Thierry Billette de Villemeur, Caroline Nava, Bénédicte Héron, Steven Petrou, and Samuel F. Berkovic

Subjects
Encephalopathy, epilepsy, KCNC1, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Objective To analyze clinical phenotypes associated with KCNC1 variants other than the Progressive Myoclonus Epilepsy‐causing variant p.Arg320His, determine the electrophysiological functional impact of identified variants and explore genotype‐phenotype‐physiological correlations. Methods Ten cases with putative pathogenic variants in KCNC1 were studied. Variants had been identified via whole‐exome sequencing or gene panel testing. Clinical phenotypic data were analyzed. To determine functional impact of variants detected in the Kv3.1 channel encoded by KCNC1, Xenopus laevis oocyte expression system and automated two‐electrode voltage clamping were used. Results Six unrelated patients had a Developmental and Epileptic Encephalopathy and a recurrent de novo variant p.Ala421Val (c.1262C > T). Functional analysis of p.Ala421Val revealed loss of function through a significant reduction in whole‐cell current, but no dominant‐negative effect. Three patients had a contrasting phenotype of Developmental Encephalopathy without seizures and different KCNC1 variants, all of which caused loss of function with reduced whole‐cell currents. Evaluation of the variant p.Ala513Val (c.1538C > T) in the tenth case, suggested it was a variant of uncertain significance. Interpretation These are the first reported cases of Developmental and Epileptic Encephalopathy due to KCNC1 mutation. The spectrum of phenotypes associated with KCNC1 is now broadened to include not only a Progressive Myoclonus Epilepsy, but an infantile onset Developmental and Epileptic Encephalopathy, as well as Developmental Encephalopathy without seizures. Loss of function is a key feature, but definitive electrophysiological separation of these phenotypes has not yet emerged.

Published
2019
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15. Hemochromatosis risk genotype is not associated with colorectal cancer or age at its diagnosis

Author

Gail P. Jarvik, Xiaoliang Wang, Pierre Fontanillas, Esther Kim, Sirisak Chanprasert, Adam S. Gordon, Lisa Bastarache, Kris V. Kowdley, Tabitha Harrison, Elisabeth A. Rosenthal, Ian B. Stanaway, Stéphane Bézieau, Stephanie J. Weinstein, Polly A. Newcomb, Graham Casey, Elizabeth A. Platz, Kala Visvanathan, Loic Le Marchand, Cornelia M. Ulrich, Sheetal Hardikar, Christopher I. Li, Franzel J.B. van Duijnhoven, Andrea Gsur, Peter T. Campbell, Victor Moreno, Pavel Vodička, Hermann Brenner, Jenny Chang-Claude, Michael Hoffmeister, Martha L. Slattery, Marc J. Gunter, Elom K. Aglago, Sergi Castellví-Bel, Sun-Seog Kweon, Andrew T. Chan, Li Li, Wei Zheng, D. Timothy Bishop, Graham G. Giles, Gad Rennert, Kenneth Offit, Temitope O. Keku, Michael O. Woods, Jochen Hampe, Bethan Van Guelpen, Steven J. Gallinger, Albert de la Chapelle, Heather Hampel, Sonja I. Berndt, Catherine M. Tangen, Annika Lindblom, Alicja Wolk, Andrea Burnett-Hartman, Anna H. Wu, Emily White, Stephen B. Gruber, Mark A. Jenkins, Joanna Mountain, Ulrike Peters, and David R. Crosslin

Subjects
iron, ferritin, population screening, age of onset, colon cancer, genetic, Genetics, QH426-470
Abstract

Summary: Homozygotes for the higher penetrance hemochromatosis risk allele, HFE c.845G>A (p.Cys282Tyr, or C282Y), have been reported to be at a 2- to 3-fold increased risk for colorectal cancer (CRC). These results have been reported for small sample size studies with no information about age at diagnosis for CRC. An association with age at diagnosis might alter CRC screening recommendations. We analyzed two large European ancestry datasets to assess the association of HFE genotype with CRC risk and age at CRC diagnosis. The first dataset included 59,733 CRC or advanced adenoma cases and 72,351 controls from a CRC epidemiological study consortium. The second dataset included 13,564 self-reported CRC cases and 2,880,218 controls from the personal genetics company, 23andMe. No association of the common hereditary hemochromatosis (HH) risk genotype and CRC was found in either dataset. The odds ratios (ORs) for the association of CRC and HFE C282Y homozygosity were 1.08 (95% confidence interval [CI], 0.91–1.29; p = 0.4) and 1.01 (95% CI, 0.78–1.31, p = 0.9) in the two cohorts, respectively. Age at CRC diagnosis also did not differ by HFE C282Y/C282Y genotype in either dataset. These results indicate no increased CRC risk in individuals with HH genotypes and suggest that persons with HH risk genotypes can follow population screening recommendations for CRC.

Published
2020
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16. Leptin gene variants and colorectal cancer risk: Sex-specific associations.

Author

Kelsey A Chun, Jonathan M Kocarnik, Sheetal S Hardikar, Jamaica R Robinson, Sonja I Berndt, Andrew T Chan, Jane C Figueiredo, Noralane M Lindor, Mingyang Song, Robert E Schoen, Richard B Hayes, John D Potter, Rami Nassir, Stéphane Bézieau, Loic Le Marchand, Martha L Slattery, Emily White, Ulrike Peters, and Polly A Newcomb

Subjects
Medicine, Science
Abstract

BACKGROUND:High levels of serum leptin and low levels of serum adiponectin are strongly correlated with obesity, a well-established risk factor for colorectal cancer (CRC). Growing evidence suggests that dysregulation of leptin and adiponectin levels may play an etiological role in colorectal carcinogenesis. We evaluated 20 candidate variants in 4 genes previously shown to alter serum leptin and adiponectin levels for associations with obesity (BMI>30 kg/m2) and CRC risk. METHODS:We analyzed 6,246 CRC cases and 7,714 population-based controls from 11 studies within the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Associations of each variant with obesity or CRC were evaluated using multivariate logistic regression models stratified by sex and adjusted for age, a study variable, and the first three principal components of genetic ancestry. Gene-specific False Discovery Rate (FDR)-adjusted p-values

Published
2018
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18. Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.

Author

Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu, and GECCO and CCFR

Subjects
Medicine, Science
Abstract

BACKGROUND:The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS:Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects. We investigated whether CRC association p-values were more significant for common variants inside versus outside AREs, or 2) inside colorectal (CR) AREs versus AREs of other tissues and cell-types. We employed an integrative epigenomic RVAM for variants with allele frequency

Published
2017
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19. Differential roles of Hath1, MUC2 and P27Kip1 in relation with gamma-secretase inhibition in human colonic carcinomas: a translational study.

Author

Frédérique Souazé, Chantal Bou-Hanna, Christine Kandel, François Leclair, Julie Devallière, Béatrice Charreau, Stéphane Bézieau, Jean-François Mosnier, and Christian L Laboisse

Subjects
Medicine, Science
Abstract

Hath1, a bHLH transcription factor negatively regulated by the γ-secretase-dependent Notch pathway, is required for intestinal secretory cell differentiation. Our aim was fourfold: 1) determine whether Hath1 is able to alter the phenotype of colon cancer cells that are committed to a differentiated phenotype, 2) determine whether the Hath1-dependent alteration of differentiation is coupled to a restriction of anchorage-dependent growth, 3) decipher the respective roles of three putative tumor suppressor genes Hath1, MUC2 and P27kip1 in this coupling and, 4) examine how our findings translate to primary tumors. Human colon carcinoma cell lines that differentiate along a mucin secreting (MUC2/MUC5AC) and/or enterocytic (DPPIV) lineages were maintained on inserts with or without a γ-secretase inhibitor (DBZ). Then the cells were detached and their ability to survive/proliferate in the absence of substratum was assessed. γ-secretase inhibition led to a Hath1-mediated preferential induction of MUC2 over MUC5AC, without DPPIV modification, in association with a decrease in anchorage-independent growth. While P27kip1 silencing relieved the cells from the Hath1-induced decrease of anchorage-independent growth, MUC2 silencing did not modify this parameter. Hath1 ectopic expression in the Hath1 negative enterocytic Caco2 cells led to a decreased anchorage-independent growth in a P27kip1-independent manner. In cultured primary human colon carcinomas, Hath1 was up-regulated in 7 out of 10 tumors upon DBZ treatment. Parallel MUC2 up-regulation occurred in 4 (4/7) and P27kip1 in only 2 (2/7) tumors. Interestingly, the response patterns of primary tumors to DBZ fitted with the hierarchical model of divergent signalling derived from our findings on cell lines.

Published
2013
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20. Genome-wide search for gene-gene interactions in colorectal cancer.

Author

Shuo Jiao, Li Hsu, Sonja Berndt, Stéphane Bézieau, Hermann Brenner, Daniel Buchanan, Bette J Caan, Peter T Campbell, Christopher S Carlson, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Stephen Chanock, David V Conti, Keith R Curtis, David Duggan, Steven Gallinger, Stephen B Gruber, Tabitha A Harrison, Richard B Hayes, Brian E Henderson, Michael Hoffmeister, John L Hopper, Thomas J Hudson, Carolyn M Hutter, Rebecca D Jackson, Mark A Jenkins, Elizabeth D Kantor, Laurence N Kolonel, Sébastien Küry, Loic Le Marchand, Mathieu Lemire, Polly A Newcomb, John D Potter, Conghui Qu, Stephanie A Rosse, Robert E Schoen, Fred R Schumacher, Daniela Seminara, Martha L Slattery, Cornelia M Ulrich, Brent W Zanke, and Ulrike Peters

Subjects
Medicine, Science
Abstract

Genome-wide association studies (GWAS) have successfully identified a number of single-nucleotide polymorphisms (SNPs) associated with colorectal cancer (CRC) risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG) is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to Interaction (ARDI). With this method, we conducted a genome-wide search to identify SNPs showing evidence for GxG with previously identified CRC susceptibility loci from 14 independent regions. We also conducted a genome-wide search for GxG using the marginal association screening and examining interaction among SNPs that pass the screening threshold (p

Published
2012
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21. Rare pathogenic variants in WNK3 cause X-linked intellectual disability

Author

Sébastien Küry, Jinwei Zhang, Thomas Besnard, Alfonso Caro-Llopis, Xue Zeng, Stephanie M. Robert, Sunday S. Josiah, Emre Kiziltug, Anne-Sophie Denommé-Pichon, Benjamin Cogné, Adam J. Kundishora, Le T. Hao, Hong Li, Roger E. Stevenson, Raymond J. Louie, Wallid Deb, Erin Torti, Virginie Vignard, Kirsty McWalter, F. Lucy Raymond, Farrah Rajabi, Emmanuelle Ranza, Detelina Grozeva, Stephanie A. Coury, Xavier Blanc, Elise Brischoux-Boucher, Boris Keren, Katrin Õunap, Karit Reinson, Pilvi Ilves, Ingrid M. Wentzensen, Eileen E. Barr, Solveig Heide Guihard, Perrine Charles, Eleanor G. Seaby, Kristin G. Monaghan, Marlène Rio, Yolande van Bever, Marjon van Slegtenhorst, Wendy K. Chung, Ashley Wilson, Delphine Quinquis, Flora Bréhéret, Kyle Retterer, Pierre Lindenbaum, Emmanuel Scalais, Lindsay Rhodes, Katrien Stouffs, Elaine M. Pereira, Sara M. Berger, Sarah S. Milla, Ankita B. Jaykumar, Melanie H. Cobb, Shreyas Panchagnula, Phan Q. Duy, Marie Vincent, Sandra Mercier, Brigitte Gilbert-Dussardier, Xavier Le Guillou, Séverine Audebert-Bellanger, Sylvie Odent, Sébastien Schmitt, Pierre Boisseau, Dominique Bonneau, Annick Toutain, Estelle Colin, Laurent Pasquier, Richard Redon, Arjan Bouman, Jill. A. Rosenfeld, Michael J. Friez, Helena Pérez-Peña, Syed Raza Akhtar Rizvi, Shozeb Haider, Stylianos E. Antonarakis, Charles E. Schwartz, Francisco Martínez, Stéphane Bézieau, Kristopher T. Kahle, Bertrand Isidor, Clinical Genetics, Clinical sciences, Medical Genetics, Reproduction and Genetics, Centre hospitalier universitaire de Nantes (CHU Nantes), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), University of Exeter, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The Greenwood Genetic Center, GeneDx [Gaithersburg, MD, USA], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE), Yale School of Medicine [New Haven, Connecticut] (YSM), This work was granted by the French network of University Hospitals HUGO ('Hôpitaux Universitaires du Grand Ouest'), the French Ministry of Health, and and the Health Regional Agencies from Poitou-Charentes (represented by Frédérique Allaire), Bretagne, Pays de la Loire, and Centre-Val de Loire (HUGODIMS, 2013, RC14_0107). W.K.C. was supported by grants from Simons Foundation Autism Research Initiative, United

Subjects
MESH: Symporters, Exome sequencing, Male, KCC2, Mutation, Missense, MESH: Catalytic Domain, Neurodevelopmental disease, Protein Serine-Threonine Kinases, X-linked intellectual disability, MESH: Brain, WNK3, SDG 3 - Good Health and Well-being, Loss of Function Mutation, Catalytic Domain, MESH: Mental Retardation, X-Linked, Humans, Phosphorylation, MESH: Hemizygote, Genetics (clinical), Hemizygote, MESH: Mutation, Missense, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, MESH: Phosphorylation, Symporters, Brain, MESH: Loss of Function Mutation, MESH: Protein Serine-Threonine Kinases, MESH: Male, Mental Retardation, X-Linked, Maternal Inheritance, MESH: Maternal Inheritance
Abstract

PURPOSE: WNK3 kinase (PRKWNK3) has been implicated in the development and function of the brain via its regulation of the cation-chloride cotransporters, but the role of WNK3 in human development is unknown. METHOD: We ascertained exome or genome sequences of individuals with rare familial or sporadic forms of intellectual disability (ID). RESULTS: We identified a total of 6 different maternally-inherited, hemizygous, 3 loss-of-function or 3 pathogenic missense variants (p.Pro204Arg, p.Leu300Ser, p.Glu607Val) in WNK3 in 14 male individuals from 6 unrelated families. Affected individuals had identifier with variable presence of epilepsy and structural brain defects. WNK3 variants cosegregated with the disease in 3 different families with multiple affected individuals. This included 1 large family previously diagnosed with X-linked Prieto syndrome. WNK3 pathogenic missense variants localize to the catalytic domain and impede the inhibitory phosphorylation of the neuronal-specific chloride cotransporter KCC2 at threonine 1007, a site critically regulated during the development of synaptic inhibition. CONCLUSION: Pathogenic WNK3 variants cause a rare form of human X-linked identifier with variable epilepsy and structural brain abnormalities and implicate impaired phospho-regulation of KCC2 as a pathogenic mechanism.

Published
2022

22. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis

Author

Ricardo Moreno Traspas, Tze Shin Teoh, Pui-Mun Wong, Michael Maier, Crystal Y. Chia, Kenneth Lay, Nur Ain Ali, Austin Larson, Fuad Al Mutairi, Nouriya Abbas Al-Sannaa, Eissa Ali Faqeih, Majid Alfadhel, Huma Arshad Cheema, Juliette Dupont, Stéphane Bézieau, Bertrand Isidor, Dorrain Yanwen Low, Yulan Wang, Grace Tan, Poh San Lai, Hugues Piloquet, Madeleine Joubert, Hulya Kayserili, Kimberly A. Kripps, Shareef A. Nahas, Eric P. Wartchow, Mikako Warren, Gandham SriLakshmi Bhavani, Majed Dasouki, Renata Sandoval, Elisa Carvalho, Luiza Ramos, Gilda Porta, Bin Wu, Harsha Prasada Lashkari, Badr AlSaleem, Raeda M. BaAbbad, Anabela Natália Abreu Ferrão, Vasiliki Karageorgou, Natalia Ordonez-Herrera, Suliman Khan, Peter Bauer, Benjamin Cogne, Aida M. Bertoli-Avella, Marie Vincent, Katta Mohan Girisha, Bruno Reversade, Center for Reproductive Medicine, ACS - Heart failure & arrhythmias, and Amsterdam Reproduction & Development

Subjects
Adult, Liver Cirrhosis, Liver, Tumor Suppressor Proteins, Hepatocytes, Genetics, Animals, Humans, RNA, Messenger, Syndrome, Child, Zebrafish
Abstract

Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient’s primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.

Published
2022

23. PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production

Author

Frédéric Ebstein, Sébastien Küry, Victoria Most, Cory Rosenfelt, Marie-Pier Scott-Boyer, Geeske M. van Woerden, Thomas Besnard, Jonas Johannes Papendorf, Maja Studencka-Turski, Tianyun Wang, Tzung-Chien Hsieh, Richard Golnik, Dustin Baldridge, Cara Forster, Charlotte de Konink, Selina M.W. Teurlings, Virginie Vignard, Richard H. van Jaarsveld, Lesley Ades, Benjamin Cogné, Cyril Mignot, Wallid Deb, Marjolijn C.J. Jongmans, F. Sessions Cole, Marie-José H. van den Boogaard, Jennifer A. Wambach, Daniel J. Wegner, Sandra Yang, Vickie Hannig, Jennifer Ann Brault, Neda Zadeh, Bruce Bennetts, Boris Keren, Anne-Claire Gélineau, Zöe Powis, Meghan Towne, Kristine Bachman, Andrea Seeley, Anita E. Beck, Jennifer Morrison, Rachel Westman, Kelly Averill, Theresa Brunet, Judith Haasters, Melissa T. Carter, Matthew Osmond, Patricia G. Wheeler, Francesca Forzano, Shehla Mohammed, Yannis Trakadis, Andrea Accogli, Rachel Harrison, Yiran Guo, Hakon Hakonarson, Sophie Rondeau, Geneviève Baujat, Giulia Barcia, René Günther Feichtinger, Johannes Adalbert Mayr, Martin Preisel, Frédéric Laumonnier, Tilmann Kallinich, Alexej Knaus, Bertrand Isidor, Peter Krawitz, Uwe Völker, Elke Hammer, Arnaud Droit, Evan E. Eichler, Ype Elgersma, Peter W. Hildebrand, François Bolduc, Elke Krüger, Stéphane Bézieau, Clinical Genetics, and Neurosciences

Subjects
General Medicine
Abstract

A critical step in preserving protein homeostasis is the recognition, binding, unfolding, and translocation of protein substrates by six AAA-ATPase proteasome subunits (ATPase-associated with various cellular activities) termed PSMC1-6, which are required for degradation of proteins by 26 S proteasomes. Here, we identified 15 de novo missense variants in the PSMC3 gene encoding the AAA-ATPase proteasome subunit PSMC3/Rpt5 in 23 unrelated heterozygous patients with an autosomal dominant form of neurodevelopmental delay and intellectual disability. Expression of PSMC3 variants in mouse neuronal cultures led to altered dendrite development, and deletion of the PSMC3 fly ortholog Rpt5 impaired reversal learning capabilities in fruit flies. Structural modeling as well as proteomic and transcriptomic analyses of T cells derived from patients with PSMC3 variants implicated the PSMC3 variants in proteasome dysfunction through disruption of substrate translocation, induction of proteotoxic stress, and alterations in proteins controlling developmental and innate immune programs. The proteostatic perturbations in T cells from patients with PSMC3 variants correlated with a dysregulation in type I interferon (IFN) signaling in these T cells, which could be blocked by inhibition of the intracellular stress sensor protein kinase R (PKR). These results suggest that proteotoxic stress activated PKR in patient-derived T cells, resulting in a type I IFN response. The potential relationship among proteosome dysfunction, type I IFN production, and neurodevelopment suggests new directions in our understanding of pathogenesis in some neurodevelopmental disorders.

Published
2023

24. Germline JAK2 E846D Substitution as the Cause of Erythrocytosis?

Author

Nada Maaziz, Céline Garrec, Fabrice Airaud, Victor Bobée, Nathalie Contentin, Emilie Cayssials, Antoine Rimbert, Bernard Aral, Stéphane Bézieau, Betty Gardie, and François Girodon

Subjects
Genetics, erythrocytosis, JAK2 mutation, germline mutation, familial erythrocytosis, Genetics (clinical)
Abstract

The discovery in 2005 of the JAK2 V617F gain-of-function mutation in myeloproliferative neoplasms and more particularly in polycythemia vera has deeply changed the diagnostic and therapeutic approaches to polycythemia. More recently, the use of NGS in routine practice has revealed a large number of variants, although it is not always possible to classify them as pathogenic. This is notably the case for the JAK2 E846D variant for which for which questions remain unanswered. In a large French national cohort of 650 patients with well-characterized erythrocytosis, an isolated germline heterozygous JAK2 E846D substitution was observed in only two cases. For one of the patients, a family study could be performed, without segregation of the variant with the erythrocytosis phenotype. On the other hand, based on the large UK Biobank resource cohort including more than half a million UK participants, the JAK2 E846D variant was found in 760 individuals, associated with a moderate increase in hemoglobin and hematocrit values, but with no significant difference to the mean values of the rest of the studied population. Altogether, our data as well as UK Biobank cohort analyses suggest that the occurrence of an absolute polycythemia cannot be attributed to the sole demonstration of an isolated JAK2 E846D variant. However, it must be accompanied by other stimuli or favoring factors in order to generate absolute erythrocytosis.

Published
2023
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25. Data from Genetic Predictors of Circulating 25-Hydroxyvitamin D and Risk of Colorectal Cancer

Author

Andrew T. Chan, Ulrike Peters, Peter Kraft, Brent W. Zanke, Kana Wu, Emily White, Jean Wactawski-Wende, Martha L. Slattery, Daniela Seminara, Fredrick R. Schumacher, Robert E. Schoen, John D. Potter, Kimmie Ng, Polly A. Newcomb, Hongmei Nan, JoAnn E. Manson, Jing Ma, Mathieu Lemire, Loic Le Marchand, Sébastien Küry, Mark A. Jenkins, Thomas J. Hudson, John L. Hopper, Michael Hoffmeister, Brian Henderson, Aditi Hazra, Richard B. Hayes, Tabitha A. Harrison, Edward L. Giovannucci, Steven Gallinger, Charles S. Fuchs, David Duggan, David V. Conti, Stephen J. Chanock, Jenny Chang-Claude, Graham Casey, Bette J. Caan, Hermann Brenner, Stéphane Bézieau, Sonja I. Berndt, John A. Baron, Carolyn M. Hutter, Conghui Qu, and Linda T. Hiraki

Abstract

Background: Experimental evidence has demonstrated an antineoplastic role for vitamin D in the colon, and higher circulating 25-hydroxyvitamin D [25(OH)D] levels are consistently associated with a lower risk of colorectal cancer. Genome-wide association studies have identified loci associated with levels of circulating 25(OH)D. The identified single-nucleotide polymorphisms (SNPs) from four gene regions collectively explain approximately 5% of the variance in circulating 25(OH)D.Methods: We investigated whether five polymorphisms in GC, CYP2R1, CYP24A1, and DHCR7/NADSYN1, genes previously shown to be associated with circulating 25(OH)D levels, were associated with colorectal cancer risk in 10,061 cases and 12,768 controls drawn from 13 studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR). We conducted a meta-analysis of crude and multivariate-adjusted logistic regression models to calculate odds ratios and associated confidence intervals for SNPs individually, SNPs simultaneously, and for a vitamin D additive genetic risk score (GRS).Results: We did not observe a statistically significant association between the 25(OH)D-associated SNPs and colorectal cancer marginally, conditionally, or as a GRS, or for colon or rectal cancer separately.Conclusions: Our findings do not support an association between SNPs associated with circulating 25(OH)D and risk of colorectal cancer. Additional work is warranted to investigate the complex relationship between 25(OH)D and colorectal cancer risk.Impact: There was no association observed between genetic markers of circulating 25(OH)D and colorectal cancer. These genetic markers account for a small proportion of the variance in 25(OH)D. Cancer Epidemiol Biomarkers Prev; 22(11); 2037–46. ©2013 AACR.

Published
2023

26. Supplementary Data and Supplementary Tables 1 and 2 from Genetic Predictors of Circulating 25-Hydroxyvitamin D and Risk of Colorectal Cancer

Author

Andrew T. Chan, Ulrike Peters, Peter Kraft, Brent W. Zanke, Kana Wu, Emily White, Jean Wactawski-Wende, Martha L. Slattery, Daniela Seminara, Fredrick R. Schumacher, Robert E. Schoen, John D. Potter, Kimmie Ng, Polly A. Newcomb, Hongmei Nan, JoAnn E. Manson, Jing Ma, Mathieu Lemire, Loic Le Marchand, Sébastien Küry, Mark A. Jenkins, Thomas J. Hudson, John L. Hopper, Michael Hoffmeister, Brian Henderson, Aditi Hazra, Richard B. Hayes, Tabitha A. Harrison, Edward L. Giovannucci, Steven Gallinger, Charles S. Fuchs, David Duggan, David V. Conti, Stephen J. Chanock, Jenny Chang-Claude, Graham Casey, Bette J. Caan, Hermann Brenner, Stéphane Bézieau, Sonja I. Berndt, John A. Baron, Carolyn M. Hutter, Conghui Qu, and Linda T. Hiraki

Abstract

Contains more detailed information on the individual cohorts contributing to the study and their genotyping results; Supplemental Tables 1 and 2

Published
2023

27. Supplementary Table 4 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 77K, All GxE interaction results.

Published
2023

28. Supplementary Table 2 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 55K, Study specific definitions of regular aspirin/NSAID use.

Published
2023

29. Supplementary Table 7 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 96K, All GxE interactions stratified by cancer site.

Published
2023

30. Supplementary Figure 1 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 52K, Forest plots for meta-analysis results with GxE interaction p < 0.01

Published
2023

31. Supplementary Table 3 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 67K, Descriptives for smoking, BMI, height, dietary variables, alcohol, sex, and NSAID use.

Published
2023

32. Supplementary Table 6 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 55K, Further information about main finding

Published
2023

33. Supplementary Table 1 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author

Ulrike Peters, Thomas J. Hudson, Andrew T. Chan, Stéphane Bézieau, Li Hsu, John D. Potter, Bette J. Caan, Richard B. Hayes, Sonja I. Berndt, Stephen J. Chanock, Robert E. Schoen, Rebecca D. Jackson, Ross L. Prentice, Andrea Z. LaCroix, Charles Kooperberg, Polly A. Newcomb, Emily White, Cornelia M. Ulrich, Jing Ma, Bernd Frank, Hermann Brenner, Brent W. Zanke, Steven Gallinger, David J. Hunter, Peter Kraft, Aditi Hazra, Edward Giovannucci, Charles S. Fuchs, Sébastien Küry, Michael Hoffmeister, Greg S. Warnick, Deanna L. Stelling, Lin S. Chen, Yan Liu, Tabitha A. Harrison, Shuo Jiao, Jane C. Figueiredo, Jagadish Rangrej, Mathieu Lemire, Hongmei Nan, David Duggan, Yi Lin, Bethann M. Pflugeisen, Martha L. Slattery, Jenny Chang-Claude, and Carolyn M. Hutter

Abstract

PDF file - 168K, SNP details by study.

Published
2023

34. Circulating white blood cell traits and colorectal cancer risk: A Mendelian randomization study

Author

Andrei-Emil Constantinescu, Caroline J Bull, Nicholas Jones, Ruth Mitchell, Kimberley Burrows, Niki Dimou, Stéphane Bézieau, Hermann Brenner, Daniel D Buchanan, Mauro D’Amato, Mark A Jenkins, Victor Moreno, Rish K Pai, Caroline Y Um, Emily White, Neil Murphy, Marc Gunter, Nicholas J Timpson, Jeroen R Huyghe, and Emma E Vincent

Abstract

Observational studies have suggested a protective role for eosinophils in colorectal cancer (CRC) development and implicated neutrophils, but the causal relationships remain unclear. Here, we aimed to estimate the causal effect of circulating white blood cell (WBC) counts (N = ∼550,000) for basophils, eosinophils, monocytes, lymphocytes and neutrophils on CRC risk (N = 52,775 cases and 45,940 controls) using Mendelian randomization (MR). For comparison, we also examined this relationship using individual-level data from UK Biobank (4,043 incident CRC cases and 332,773 controls) in a longitudinal cohort analysis. The inverse-variance weighted (IVW) MR analysis suggested a protective effect of increased basophil count and eosinophil count on CRC risk [OR per 1-SD increase: 0.88, CI(95%): 0.78-0.99,P=0.04; OR: 0.93, CI(95%): 0.88-0.98,P=0.01]. The protective effect of eosinophils remained [OR per 1-SD increase: 0.88, CI(95%): 0.80-0.97,P=0.01] following adjustments for all other WBC subtypes, to account for genetic correlation between the traits, using multivariable MR. A protective effect of increased lymphocyte count on CRC risk was also found [OR: 0.84, CI(95%): 0.76-0.93,P=6.70e-4] following adjustment. Consistent with MR results, a protective effect for eosinophils in the cohort analysis in the fully adjusted model [RR per 1-SD increase: 0.96, CI(95%): 0.93-0.99,P=0.02] and following adjustment for the other WBC subtypes [RR: 0.96, CI(95%): 0.93-0.99,P=0.001] was observed. Our study implicates peripheral blood immune cells, in particular eosinophils and lymphocytes, in CRC development, highlighting a need for mechanistic studies to interrogate these relationships.What is already known of this topicWhile previous observational studies have suggested a protective role for eosinophils in colorectal cancer development and implicated neutrophils, whether changes in the levels of circulating white blood cells causes colorectal cancer has not been explored.What this study addsOur study is the first to use Mendelian randomization (MR) to investigate this relationship. In parallel, for comparison, we also conduct the largest cohort study to date on the topic. We found evidence to suggest that elevated eosinophil and lymphocyte count may have a protective effect on CRC risk, adding new insights into the pathogenesis of CRC.How this study might affect research, practice or policyOur findings will encourage further mechanistic exploration to understand the biological mechanisms underpinning our findings, which may lead to new therapeutic approaches or risk reduction strategies.

Published
2023

35. Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder

Author

Sébastien Küry, Frédéric Ebstein, Alice Mollé, Thomas Besnard, Ming-Kang Lee, Virginie Vignard, Tiphaine Hery, Mathilde Nizon, Grazia M.S. Mancini, Jacques C. Giltay, Benjamin Cogné, Kirsty McWalter, Wallid Deb, Hagar Mor-Shaked, Hong Li, Rhonda E. Schnur, Ingrid M. Wentzensen, Anne-Sophie Denommé-Pichon, Cynthia Fourgeux, Frans W. Verheijen, Eva Faurie, Rachel Schot, Cathy A. Stevens, Daphne J. Smits, Eileen Barr, Ruth Sheffer, Jonathan A. Bernstein, Chandler L. Stimach, Eliana Kovitch, Vandana Shashi, Kelly Schoch, Whitney Smith, Richard H. van Jaarsveld, Anna C.E. Hurst, Kirstin Smith, Evan H. Baugh, Suzanne G. Bohm, Emílie Vyhnálková, Lukáš Ryba, Capucine Delnatte, Juanita Neira, Dominique Bonneau, Annick Toutain, Jill A. Rosenfeld, Séverine Audebert-Bellanger, Brigitte Gilbert-Dussardier, Sylvie Odent, Frédéric Laumonnier, Seth I. Berger, Ann C.M. Smith, Franck Bourdeaut, Marc-Henri Stern, Richard Redon, Elke Krüger, Raphaël Margueron, Stéphane Bézieau, Jeremie Poschmann, Bertrand Isidor, Centre hospitalier universitaire de Nantes (CHU Nantes), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Universität Greifswald - University of Greifswald, Centre de Recherche en Transplantation et Immunologie - Center for Research in Transplantation and Translational Immunology (U1064 Inserm - CR2TI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Erasmus University Medical Center [Rotterdam] (Erasmus MC), University Medical Center [Utrecht], GeneDx [Gaithersburg, MD, USA], Hadassah Hebrew University Medical Center [Jerusalem], Emory University School of Medicine, Emory University [Atlanta, GA], Laboratoire de Biologie Neurovasculaire Intégrée [Angers] (CNRS UMR6214 - INSERM U771), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Tennessee System, Stanford University, Duke University Medical Center, University of Alabama at Birmingham [ Birmingham] (UAB), Columbia University [New York], Charles University [Prague] (CU), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Baylor College of Medicine (BCM), Baylor University, Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Unité neurovasculaire et troubles cognitifs (Neuvacod), Université de Poitiers, CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre de référence Maladies Rares CLAD-Ouest [Rennes], Children's National Medical Center, National Human Genome Research Institute (NHGRI), Institut Curie [Paris], Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Greifswald University Hospital, Research reported in this manuscript was supported by the NIH Common Fund through the Office of Strategic Coordination/Office of the NIH Director under award number U01HG007672 to V.S. Further support was obtained by funding from the German Research Foundation (SFBTR 167 A4, GRK2719 B4) to E.K, and Clinical Genetics

Subjects
Male, Heterozygote, Proteasome Endopeptidase Complex, tumor, Adolescent, T-Lymphocytes, Ubiquitin-Protein Ligases, [SDV]Life Sciences [q-bio], Mutation, Missense, UPS, ubiquitin-proteasome system, chromatin remodeling, Histones, SDG 3 - Good Health and Well-being, Loss of Function Mutation, Report, ubiquitin, Genetics, Humans, cancer, Family, BAP1, Child, deubiquitination, Germ-Line Mutation, Genetics (clinical), [SDV.GEN]Life Sciences [q-bio]/Genetics, neurodevelopment, BRCA1 Protein, Tumor Suppressor Proteins, Ubiquitination, Infant, Chromatin Assembly and Disassembly, BRCA1, Chromatin, Gene Expression Regulation, Neurodevelopmental Disorders, intellectual disability, Child, Preschool, histone 2A, Female, Host Cell Factor C1, Ubiquitin Thiolesterase
Abstract

International audience; Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.

Published
2022

36. Stankiewicz-Isidor syndrome

Author

Ignacio Briceño, Frédéric Ebstein, Alberto Gómez, Heidi Cope, Wallid Deb, Krzysztof Szczaluba, Hutton M. Kearney, Dominique Bonneau, Elke Krüger, Marie Vincent, Jill A. Rosenfeld, Karin E. M. Diderich, Dominique Bourgeois, Kay Metcalfe, Bryce A. Mendelssohn, Magalie Barth, Solène Conrad, Alanna Strong, Patrick R. Blackburn, Amanda Gerard, McKinsey L. Goodenberger, Benjamin Cogné, Geneviève Baujat, Caroline Camby, Thomas Besnard, Natasha L. Rudy, Karin Dahan, Estelle Colin, Carlos A. Bacino, Caleb Bupp, Christel Thauvin-Robinet, Yolande van Bever, Rafał Płoski, Anne de Saint Martin, Johannes A. Mayr, Ingrid Bader, Yong-Hui Jiang, Virginie Vignard, Kathryn Warren, Judith D. Ranells, Yves Alembik, Joanna Kennedy, Stéphane Bézieau, Bertrand Isidor, Anna C.E. Hurst, Amélie Piton, Sébastien Küry, Ange-Line Bruel, PaweƗ Stankiewicz, Ingrid Scurr, Anja Brehm, and Clinical Genetics

Subjects
Genetics, Phenotype, Intellectual Disability, Molecular phenotype, Humans, Language Development Disorders, Haploinsufficiency, Biology, Genetics (clinical), Musculoskeletal Abnormalities
Abstract

Purpose: Haploinsufficiency of PSMD12 has been reported in individuals with neurodevelopmental phenotypes, including developmental delay/intellectual disability (DD/ID), facial dysmorphism, and congenital malformations, defined as Stankiewicz-Isidor syndrome (STISS). Investigations showed that pathogenic variants in PSMD12 perturb intracellular protein homeostasis. Our objective was to further explore the clinical and molecular phenotypic spectrum of STISS. Methods: We report 24 additional unrelated patients with STISS with various truncating single nucleotide variants or copy-number variant deletions involving PSMD12. We explore disease etiology by assessing patient cells and CRISPR/Cas9-engineered cell clones for various cellular pathways and inflammatory status. Results: The expressivity of most clinical features in STISS is highly variable. In addition to previously reported DD/ID, speech delay, cardiac and renal anomalies, we also confirmed preaxial hand abnormalities as a feature of this syndrome. Of note, 2 patients also showed chilblains resembling signs observed in interferonopathy. Remarkably, our data show that STISS patient cells exhibit a profound remodeling of the mTORC1 and mitophagy pathways with an induction of type I interferon-stimulated genes. Conclusion: We refine the phenotype of STISS and show that it can be clinically recognizable and biochemically diagnosed by a type I interferon gene signature.

Published
2022

37. Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response

Author

Robert Carreras-Torres, Andre E. Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A. Bien, Conghui Qu, Jun Wang, Niki Dimou, Elom K. Aglago, Demetrius Albanes, Volker Arndt, James W. Baurley, Sonja I. Berndt, Stéphane Bézieau, D. Timothy Bishop, Emmanouil Bouras, Hermann Brenner, Arif Budiarto, Peter T. Campbell, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Xuechen Chen, David V. Conti, Christopher H. Dampier, Matthew A.M. Devall, David A. Drew, Jane C. Figueiredo, Steven Gallinger, Graham G. Giles, Stephen B. Gruber, Andrea Gsur, Marc J. Gunter, Tabitha A. Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R. Huyghe, Mark A. Jenkins, Kristina M. Jordahl, Eric Kawaguchi, Temitope O. Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L. Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A. Newcomb, Mireia Obón-Santacana, Shuji Ogino, Jennifer Ose, Rish K. Pai, Julie R. Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R. Peoples, Paul D.P. Pharoah, Elizabeth A. Platz, Gad Rennert, Edward Ruiz-Narvaez, Lori C. Sakoda, Peter C. Scacheri, Stephanie L. Schmit, Robert E. Schoen, Anna Shcherbina, Martha L. Slattery, Mariana C. Stern, Yu-Ru Su, Catherine M. Tangen, Duncan C. Thomas, Yu Tian, Konstantinos K. Tsilidis, Cornelia M. Ulrich, Fränzel J.B. van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J. Weinstein, Emily White, Alicja Wolk, Michael O. Woods, Li Hsu, Ulrike Peters, Victor Moreno, and W. James Gauderman

Subjects
Oncology, Nutrition and Disease, Epidemiology, Voeding en Ziekte, Life Science
Abstract

Background:Tobacco smoking is an established risk factor for colorectal cancer. However, genetically defined population subgroups may have increased susceptibility to smoking-related effects on colorectal cancer.Methods:A genome-wide interaction scan was performed including 33,756 colorectal cancer cases and 44,346 controls from three genetic consortia.Results:Evidence of an interaction was observed between smoking status (ever vs. never smokers) and a locus on 3p12.1 (rs9880919, P = 4.58 × 10−8), with higher associated risk in subjects carrying the GG genotype [OR, 1.25; 95% confidence interval (CI), 1.20–1.30] compared with the other genotypes (OR Conclusions:Our study identified novel genetic loci that may modulate the risk for colorectal cancer of smoking status and intensity, linked to tumor suppression and immune response.Impact:These findings can guide potential prevention treatments.

Published
2023

38. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Ceres Fernandez-Rozadilla, Maria Timofeeva, Zhishan Chen, Philip Law, Minta Thomas, Stephanie Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James Studd, Jeroen Huyghe, Tabitha Harrison, David Conti, Christopher Dampier, Mathew Devall, Fredrick Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark Jenkins, Aung Ko Win, Rish Pai, Jane Figueiredo, Robert Haile, Steven Gallinger, Michael Woods, Polly Newcomb, David Duggan, Jeremy Cheadle, Richard Kaplan, Timothy Maughan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie Weinstein, Edward Ruiz-Narvaez, Julie Palmer, Daniel Buchanan, Elizabeth Platz, Kala Visvanathan, Cornelia Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John Potter, Konstantinos Tsilidis, Matthias Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, Timothy Bishop, Graham Giles, Melissa Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany van Guelpen, Thomas Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul Pharoah, Susanna Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly Doheny, Elizabeth Pugh, Tameka Shelford, Andrew Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan Thomas, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen Chanock, Franzel van Duijnhoven, Edith Feskens, Lori Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard Coetzee, Caroline Hayward, Ian Deary, Sarah Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian Tomlinson, Wei Zheng, Malcolm Dunlop, Richard Houlston, and Ulrike Peters

Subjects
Global Nutrition, Wereldvoeding, Nutrition and Disease, Voeding en Ziekte, Genetics, Life Science, Article, VLAG
Abstract

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and East Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions, and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Cross-tissue analyses indicated that over a third of effector genes most likely act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis, and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

Published
2023

39. A de novo pathogenic variant in the MSH6 gene in a 52 years-old woman

Author

Ingrid Ricordeau, Elise Pierre-Noël, Estelle Cauchin, Stéphane Bézieau, Caroline Abadie, Clémence Michon, Fabrice Airaud, Olivier Kerdraon, and Céline Garrec

Subjects
congenital, hereditary, and neonatal diseases and abnormalities, Cancer Research, Biology, MLH1, DNA Mismatch Repair, Germline, Genetics, medicine, Humans, Germ-Line Mutation, Genetics (clinical), Genetic testing, medicine.diagnostic_test, Microsatellite instability, medicine.disease, Colorectal Neoplasms, Hereditary Nonpolyposis, Penetrance, digestive system diseases, Lynch syndrome, MSH6, MutS Homolog 2 Protein, Oncology, MSH2, Female, Microsatellite Instability, MutL Protein Homolog 1
Abstract

Lynch syndrome (LS) is a condition which predisposes individuals primarily to early-onset colorectal and endometrial cancer. LS is characterized by a germline pathogenic variant in one of the MMR (MisMatch Repair) gene, inducing a phenotype of microsatellite instability in the tumor, which may be associated with a loss of expression of MMR proteins detected by standard immunohistochemistry on tumor tissue. Most of the time, LS is inherited from a parent in whom the condition may not be known due to incomplete penetrance, but de novo pathogenic variant is a rare occurrence. Here, we describe the case of a 52-year-old woman with no family history of LS, referred to the genetics department for colorectal cancer at the age of 50. Genetic analysis revealed a de novo germline pathogenic variant in the MSH6 gene. To date, this case is only the second report of a de novo pathogenic variant in the MSH6 gene in Lynch syndrome. De novo mutations have been extensively studied over the past years, but little is known about their origin and mechanism of occurrence in MMR genes. However, knowledge of mutation status allows better cancer risk management for the patient and an appropriate genetic testing and counseling for her family.

Published
2021

40. A new case of Kaufman Oculocerebrofacial syndrome caused by two splicing variants in UBE3B and review of the literature

Author

Loïc Couloigner, Marc Planes, Chandran Ka, Séverine Audebert‐Bellanger, Sylvia Redon, Caroline Benech, Karen Rouault, Sebastien Küry, Sylviane Peudenier, Sandrine Autret, Isabelle Gourlaouen, Dominique Bonneau, Sylvie Odent, Stéphane Bézieau, Brigitte Gilbert‐Dussardier, Annick Toutain, Anne Boland, Jean‐François Deleuze, Cédric Le Marechal, Gérald Le Gac, Claude Ferec, Kevin Uguen, Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Institut du Thorax [Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Recherche en Génomique Humaine (CNRGH), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Genetics, Genetics (clinical)
Abstract

International audience

Published
2022

41. Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

Author

Niki Dimou, Andre E. Kim, Orlagh Flanagan, Neil Murphy, Virginia Diez-Obrero, Anna Shcherbina, Elom K Aglago, Emmanouil Bouras, Peter T Campbell, Graham Casey, Steven Gallinger, Stephen B Gruber, Mark A Jenkins, Yi Lin, Victor Moreno, Edward Ruiz-Narvaez, Mariana C Stern, Yu Tian, Kostas K Tsilidis, Volker Arndt, Elizabeth L Barry, James W Baurley, Sonja I Berndt, Stéphane Bézieau, Stephanie A Bien, D Timothy Bishop, Hermann Brenner, Arif Budiarto, Robert Carreras-Torres, Tjeng Wawan Cenggoro, Andrew T Chan, Jenny Chang-Claude, Stephen J Chanock, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew Devall, David Drew, Jane C Figueiredo, Graham G Giles, Andrea Gsur, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Kristina Jordahl, Eric Kawaguchi, Temitope O Keku, Susanna C Larsson, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John Morrison, Polly A Newcomb, Christina C Newton, Mireia Obon-Santacana, Jennifer Ose, Rish K Pai, Julie R Palmer, Nick Papadimitrou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, John D Potter, Gad Rennert, Peter C Scacheri, Robert E Schoen, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Cornelia Ulrich, Caroline Y Um, Franzel JB van Duijnhoven, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Emily White, Alicja Wolk, Michael O Woods, Conghui Qu, Anshul Kundaje, Li Hsu, W. James Gauderman, Marc J Gunter, and Ulrike Peters

Abstract

Diabetes is an established risk factor for colorectal cancer; however, the mechanisms underlying this relationship are not fully understood and the role of genetic variation is unclear. We used data from 3 genetic consortia (CCFR, CORECT, GECCO; 31,318 colorectal cancer cases/41,499 controls) and undertook genome-wide gene-environment interaction analyses with colorectal cancer risk, including interaction tests of genetics(G)xdiabetes and joint testing of Gxdiabetes, G-colorectal cancer association and/or G-diabetes correlation (2,3-degrees of freedom joint tests; d.f.). Based on the joint tests, variant rs3802177 inSLC30A8(p-value3-d.f.:5.46×10−11; regulates phosphorylation of the insulin receptor and phosphatidylinositol-3 kinase activity) and rs9526201 inLRCH1(p-value2-d.f.:7.84×10−09; regulates T cell migration and Natural Killer Cell cytotoxicity) were associated with colorectal cancer. These results suggest that variation in genes related to insulin signalling and immune function may modify the association of diabetes with colorectal cancer and provide novel insights into the biology underlying the diabetes and colorectal cancer relationship.

Published
2022

42. Novel interstitial 2q12.3q13 microdeletion predisposes to developmental delay and behavioral problems

Author

Minh-Tuan Huynh, Stéphane Bézieau, Madeleine Joubert, Leila Ghesh, Gerard Marion, Claire Beneteau, Khalid Alfallaj, Olivier Pichon, and Kara Ranguin

Subjects
0301 basic medicine, Ectodermal dysplasia, Candidate gene, Microcephaly, Genotype, Endocrinology, Diabetes and Metabolism, Biology, Biochemistry, 03 medical and health sciences, Cellular and Molecular Neuroscience, Endocrinology, 0302 clinical medicine, Pregnancy, Genetics, medicine, Humans, Abnormalities, Multiple, Molecular Biology, Genetics (clinical), Problem Behavior, Comparative Genomic Hybridization, medicine.diagnostic_test, Genomics, Microdeletion syndrome, medicine.disease, Penetrance, Human genetics, Phenotype, 030104 developmental biology, Female, Chromosomes, Human, Pair 3, Chromosome Deletion, 030217 neurology & neurosurgery, Fluorescence in situ hybridization, Comparative genomic hybridization
Abstract

Microarray-based comparative genomic hybridization (aCGH) is being increasingly applied to delineate novel genomic disorders and related syndromes in patients with developmental delay. In this study, detailed clinical and cytogenetic data of three unrelated patients with interstitial 2q12.3q13 microdeletion were described and compared with thirteen 2q12.3q13 microdeletion patients, gathered from the medical literature and public databases. 60 K aCGH analysis revealed three overlapping 2q12.3q13 microdeletions measuring 1.88 Mb in patient 1, 1.25 Mb in patient 2, and 0.41 Mb in patient 3, respectively. Confirmation and segregation studies were performed using fluorescence in situ hybridization (FISH) and quantitative real-time PCR. Variable clinical features of 2q12.3q13 microdeletion including microcephaly, prenatal growth retardation, developmental delay, short stature, behavioral problems, learning difficulties, skeletal anomalies, congenital heart defects, and features of ectodermal dysplasia were observed. The boundaries and sizes of the 2q12.3q13 deletions in the sixteen patients were different, but an overlapping region of 249 kb in 2q12.3 was defined. The SRO (smallest region of overlap) encompasses four genes, including LIMS1, RANBP2, CCDC138, and EDAR. Among these genes, RANBP2 is a strong candidate gene for neurological phenotype and genetic susceptibility to viral infections. To our knowledge, this is the first published report of 2q12.3q13 microdeletion syndrome and our observations strongly suggest that these recurrent CNVs may be a novel risk factor for developmental delay with variable expressivity and incomplete penetrance.

Published
2021

43. Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Ceres Fernandez-Rozadilla, Maria Timofeeva, Zhishan Chen, Philip Law, Minta Thomas, Stephanie Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James Studd, Jeroen Huyghe, Tabitha Harrison, David Conti, Christopher Dampier, Mathew Devall, Fredrick Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark Jenkins, Aung Ko Win, Rish Pai, Jane Figueiredo, Robert Haile, Steven Gallinger, Michael Woods, Polly Newcomb, David Duggan, Jeremy Cheadle, Richard Kaplan, Timothy Maughan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie Weinstein, Edward Ruiz-Narvaez, Julie Palmer, Daniel Buchanan, Elizabeth Platz, Kala Visvanathan, Cornelia Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John Potter, Konstantinos Tsilidis, Matthias Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, Timothy Bishop, Graham Giles, Melissa Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany van Guelpen, Thomas Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul Pharoah, Susanna Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly Doheny, Elizabeth Pugh, Tameka Shelford, Andrew Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan Thomas, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen Chanock, Franzel van Duijnhoven, Edith Feskens, Lori Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard Coetzee, Caroline Hayward, Ian Deary, Sarah Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian Tomlinson, Wei Zheng, Malcolm Dunlop, Richard Houlston, and Ulrike Peters

Subjects
Global Nutrition, Wereldvoeding, Nutrition and Disease, Voeding en Ziekte, Genetics, Life Science, VLAG
Abstract

In the version of this article initially published, the author affiliations incorrectly listed “Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy” as “Candiolo Cancer Institute, Candiolo, Italy.” The change has been made to the HTML and PDF versions of the article.

Published
2023

44. Loss‐of‐function variants in ARHGEF9 are associated with an X‐linked intellectual disability dominant disorder

Author

Laurence Cuisset, Stéphane Bézieau, Flora Breheret, Christel Thauvin-Robinet, Paul Kuentz, Benjamin Cogné, Gaëlle Landeau-Trottier, Boris Keren, Eva Trochu, Leila Ghesh, Mathilde Nizon, Christine Coubes, Thomas Besnard, Cyril Mignot, and Ange-Line Bruel

Subjects
Male, X-linked intellectual disability, media_common.quotation_subject, Nonsense, Mutation, Missense, Biology, 03 medical and health sciences, Genes, X-Linked, X Chromosome Inactivation, Intellectual Disability, Intellectual disability, Genetics, medicine, Humans, Missense mutation, Genetics (clinical), Loss function, 030304 developmental biology, media_common, 0303 health sciences, 030305 genetics & heredity, medicine.disease, Codon, Nonsense, RNA splicing, Female, Rho Guanine Nucleotide Exchange Factors
Abstract

ARHGEF9 defects lead to an X-linked intellectual disability disorder related to inhibitory synaptic dysfunction. This condition is more frequent in males, with a few affected females reported. Up to now, sequence variants and gross deletions have been identified in males, while only chromosomal aberrations have been reported in affected females who showed a skewed pattern of X-chromosome inactivation (XCI), suggesting an X-linked recessive (XLR) disorder. We report three novel loss-of-function (LoF) variants in ARHGEF9: A de novo synonymous variant affecting splicing (NM_015185.2: c.1056G>A, p.(Lys352=)) in one female; a nonsense variant in another female (c.865C>T, p.(Arg289*)), that is, also present as a somatically mosaic variant in her father, and a de novo nonsense variant in a boy (c.899G>A; p.(Trp300*)). Both females showed a random XCI. Thus, we suggest that missense variants are responsible for an XLR disorder affecting males and that LoF variants, mainly occurring de novo, may be responsible for an X-linked dominant disorder affecting males and females.

Published
2021

45. Author Correction: Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility (Nature Genetics, (2022), 54, 3, (232-239), 10.1038/s41588-021-01007-6)

Author

Julien Barc, Barc, J, Tadros, R, Glinge, C, Chiang, D, Jouni, M, Simonet, F, Jurgens, S, Baudic, M, Nicastro, M, Potet, F, Offerhaus, J, Walsh, R, Hoan Choi, S, Verkerk, A, Mizusawa, Y, Anys, S, Minois, D, Arnaud, M, Duchateau, J, Wijeyeratne, Y, Muir, A, Papadakis, M, Castelletti, S, Torchio, M, Gil Ortuño, C, Lacunza, J, Giachino, D, Cerrato, N, Martins, R, Campuzano, O, Van Dooren, S, Thollet, A, Kyndt, F, Mazzanti, A, Clémenty, N, Bisson, A, Corveleyn, A, Stallmeyer, B, Dittmann, S, Saenen, J, Noël, A, Honarbakhsh, S, Rudic, B, Marzak, H, Rowe, M, Federspiel, C, Le Page, S, Placide, L, Milhem, A, Barajas-Martinez, H, Beckmann, B, Krapels, I, Steinfurt, J, Gregers Winkel, B, Jabbari, R, Shoemaker, M, Boukens, B, Škorić-Milosavljević, D, Bikker, H, Manevy, F, Lichtner, P, Ribasés, M, Meitinger, T, Müller-Nurasyid, M, Group, K, Veldink, J, van den Berg, L, Van Damme, P, Cusi, D, Lanzani, C, Rigade, S, Charpentier, E, Baron, E, Bonnaud, S, Lecointe, S, Donnart, A, Le Marec, H, Chatel, S, Karakachoff, M, Bézieau, S, London, B, Tfelt-Hansen, J, Roden, D, Odening, K, Cerrone, M, Chinitz, L, Volders, P, van de Berg, M, Laurent, G, Faivre, L, Antzelevitch, C, Kääb, S, Al Arnaout, A, Dupuis, J, Pasquie, J, Billon, O, Roberts, J, Jesel, L, Borggrefe, M, Lambiase, P, Mansourati, J, Loeys, B, Leenhardt, A, Guicheney, P, Maury, P, Schulze-Bahr, E, Robyns, T, Breckpot, J, Babuty, D, Priori, S, Napolitano, C, Referral Center for inherited cardiac arrhythmia, N, de Asmundis, C, Brugada, P, Brugada, R, Arbelo, E, Brugada, J, Mabo, P, Behar, N, Giustetto, C, Sabater Molina, M, Gimeno, J, Hasdemir, C, Schwartz, P, Crotti, L, Mckeown, P, Sharma, S, Behr, E, Haissaguerre, M, Sacher, F, Rooryck, C, Tan, H, Remme, C, Postema, P, Delmar, M, Ellinor, P, Lubitz, S, Gourraud, J, Tanck, M, L. George Jr., A, Macrae, C, Burridge, P, Dina, C, Probst, V, Wilde, A, Schott, J, Redon &amp, R, Bezzina, C, Julien Barc, Rafik Tadros, Charlotte Glinge, David Y. Chiang, Mariam Jouni, Floriane Simonet, Sean J. Jurgens, Manon Baudic, Michele Nicastro, Franck Potet, Joost A. Offerhaus, Roddy Walsh, Seung Hoan Choi, Arie O. Verkerk, Yuka Mizusawa, Soraya Anys, Damien Minois, Marine Arnaud, Josselin Duchateau, Yanushi D. Wijeyeratne, Alison Muir, Michael Papadakis, Silvia Castelletti, Margherita Torchio, Cristina Gil Ortuño, Javier Lacunza, Daniela F. Giachino, Natascia Cerrato, Raphaël P. Martins, Oscar Campuzano, Sonia Van Dooren, Aurélie Thollet, Florence Kyndt, Andrea Mazzanti, Nicolas Clémenty, Arnaud Bisson, Anniek Corveleyn, Birgit Stallmeyer, Sven Dittmann, Johan Saenen, Antoine Noël, Shohreh Honarbakhsh, Boris Rudic, Halim Marzak, Matthew K. Rowe, Claire Federspiel, Sophie Le Page, Leslie Placide, Antoine Milhem, Hector Barajas-Martinez, Britt-Maria Beckmann, Ingrid P. Krapels, Johannes Steinfurt, Bo Gregers Winkel, Reza Jabbari, Moore B. Shoemaker, Bas J. Boukens, Doris Škorić-Milosavljević, Hennie Bikker, Federico Manevy, Peter Lichtner, Marta Ribasés, Thomas Meitinger, Martina Müller-Nurasyid, KORA-Study Group, Jan H. Veldink, Leonard H. van den Berg, Philip Van Damme, Daniele Cusi, Chiara Lanzani, Sidwell Rigade, Eric Charpentier, Estelle Baron, Stéphanie Bonnaud, Simon Lecointe, Audrey Donnart, Hervé Le Marec, Stéphanie Chatel, Matilde Karakachoff, Stéphane Bézieau, Barry London, Jacob Tfelt-Hansen, Dan Roden, Katja E. Odening, Marina Cerrone, Larry A. Chinitz, Paul G. Volders, Maarten P. van de Berg, Gabriel Laurent, Laurence Faivre, Charles Antzelevitch, Stefan Kääb, Alain Al Arnaout, Jean-Marc Dupuis, Jean-Luc Pasquie, Olivier Billon, Jason D. Roberts, Laurence Jesel, Martin Borggrefe, Pier D. Lambiase, Jacques Mansourati, Bart Loeys, Antoine Leenhardt, Pascale Guicheney, Philippe Maury, Eric Schulze-Bahr, Tomas Robyns, Jeroen Breckpot, Dominique Babuty, Silvia G. Priori, Carlo Napolitano, Nantes Referral Center for inherited cardiac arrhythmia, Carlo de Asmundis, Pedro Brugada, Ramon Brugada, Elena Arbelo, Josep Brugada, Philippe Mabo, Nathalie Behar, Carla Giustetto, Maria Sabater Molina, Juan R. Gimeno, Can Hasdemir, Peter J. Schwartz, Lia Crotti, Pascal P. McKeown, Sanjay Sharma, Elijah R. Behr, Michel Haissaguerre, Frédéric Sacher, Caroline Rooryck, Hanno L. Tan, Carol A. Remme, Pieter G. Postema, Mario Delmar, Patrick T. Ellinor, Steven A. Lubitz, Jean-Baptiste Gourraud, Michael W. Tanck, Alfred L. George Jr., Calum A. MacRae, Paul W. Burridge, Christian Dina, Vincent Probst, Arthur A. Wilde, Jean-Jacques Schott, Richard Redon &, Connie R. Bezzina, Julien Barc, Barc, J, Tadros, R, Glinge, C, Chiang, D, Jouni, M, Simonet, F, Jurgens, S, Baudic, M, Nicastro, M, Potet, F, Offerhaus, J, Walsh, R, Hoan Choi, S, Verkerk, A, Mizusawa, Y, Anys, S, Minois, D, Arnaud, M, Duchateau, J, Wijeyeratne, Y, Muir, A, Papadakis, M, Castelletti, S, Torchio, M, Gil Ortuño, C, Lacunza, J, Giachino, D, Cerrato, N, Martins, R, Campuzano, O, Van Dooren, S, Thollet, A, Kyndt, F, Mazzanti, A, Clémenty, N, Bisson, A, Corveleyn, A, Stallmeyer, B, Dittmann, S, Saenen, J, Noël, A, Honarbakhsh, S, Rudic, B, Marzak, H, Rowe, M, Federspiel, C, Le Page, S, Placide, L, Milhem, A, Barajas-Martinez, H, Beckmann, B, Krapels, I, Steinfurt, J, Gregers Winkel, B, Jabbari, R, Shoemaker, M, Boukens, B, Škorić-Milosavljević, D, Bikker, H, Manevy, F, Lichtner, P, Ribasés, M, Meitinger, T, Müller-Nurasyid, M, Group, K, Veldink, J, van den Berg, L, Van Damme, P, Cusi, D, Lanzani, C, Rigade, S, Charpentier, E, Baron, E, Bonnaud, S, Lecointe, S, Donnart, A, Le Marec, H, Chatel, S, Karakachoff, M, Bézieau, S, London, B, Tfelt-Hansen, J, Roden, D, Odening, K, Cerrone, M, Chinitz, L, Volders, P, van de Berg, M, Laurent, G, Faivre, L, Antzelevitch, C, Kääb, S, Al Arnaout, A, Dupuis, J, Pasquie, J, Billon, O, Roberts, J, Jesel, L, Borggrefe, M, Lambiase, P, Mansourati, J, Loeys, B, Leenhardt, A, Guicheney, P, Maury, P, Schulze-Bahr, E, Robyns, T, Breckpot, J, Babuty, D, Priori, S, Napolitano, C, Referral Center for inherited cardiac arrhythmia, N, de Asmundis, C, Brugada, P, Brugada, R, Arbelo, E, Brugada, J, Mabo, P, Behar, N, Giustetto, C, Sabater Molina, M, Gimeno, J, Hasdemir, C, Schwartz, P, Crotti, L, Mckeown, P, Sharma, S, Behr, E, Haissaguerre, M, Sacher, F, Rooryck, C, Tan, H, Remme, C, Postema, P, Delmar, M, Ellinor, P, Lubitz, S, Gourraud, J, Tanck, M, L. George Jr., A, Macrae, C, Burridge, P, Dina, C, Probst, V, Wilde, A, Schott, J, Redon &amp, R, Bezzina, C, Julien Barc, Rafik Tadros, Charlotte Glinge, David Y. Chiang, Mariam Jouni, Floriane Simonet, Sean J. Jurgens, Manon Baudic, Michele Nicastro, Franck Potet, Joost A. Offerhaus, Roddy Walsh, Seung Hoan Choi, Arie O. Verkerk, Yuka Mizusawa, Soraya Anys, Damien Minois, Marine Arnaud, Josselin Duchateau, Yanushi D. Wijeyeratne, Alison Muir, Michael Papadakis, Silvia Castelletti, Margherita Torchio, Cristina Gil Ortuño, Javier Lacunza, Daniela F. Giachino, Natascia Cerrato, Raphaël P. Martins, Oscar Campuzano, Sonia Van Dooren, Aurélie Thollet, Florence Kyndt, Andrea Mazzanti, Nicolas Clémenty, Arnaud Bisson, Anniek Corveleyn, Birgit Stallmeyer, Sven Dittmann, Johan Saenen, Antoine Noël, Shohreh Honarbakhsh, Boris Rudic, Halim Marzak, Matthew K. Rowe, Claire Federspiel, Sophie Le Page, Leslie Placide, Antoine Milhem, Hector Barajas-Martinez, Britt-Maria Beckmann, Ingrid P. Krapels, Johannes Steinfurt, Bo Gregers Winkel, Reza Jabbari, Moore B. Shoemaker, Bas J. Boukens, Doris Škorić-Milosavljević, Hennie Bikker, Federico Manevy, Peter Lichtner, Marta Ribasés, Thomas Meitinger, Martina Müller-Nurasyid, KORA-Study Group, Jan H. Veldink, Leonard H. van den Berg, Philip Van Damme, Daniele Cusi, Chiara Lanzani, Sidwell Rigade, Eric Charpentier, Estelle Baron, Stéphanie Bonnaud, Simon Lecointe, Audrey Donnart, Hervé Le Marec, Stéphanie Chatel, Matilde Karakachoff, Stéphane Bézieau, Barry London, Jacob Tfelt-Hansen, Dan Roden, Katja E. Odening, Marina Cerrone, Larry A. Chinitz, Paul G. Volders, Maarten P. van de Berg, Gabriel Laurent, Laurence Faivre, Charles Antzelevitch, Stefan Kääb, Alain Al Arnaout, Jean-Marc Dupuis, Jean-Luc Pasquie, Olivier Billon, Jason D. Roberts, Laurence Jesel, Martin Borggrefe, Pier D. Lambiase, Jacques Mansourati, Bart Loeys, Antoine Leenhardt, Pascale Guicheney, Philippe Maury, Eric Schulze-Bahr, Tomas Robyns, Jeroen Breckpot, Dominique Babuty, Silvia G. Priori, Carlo Napolitano, Nantes Referral Center for inherited cardiac arrhythmia, Carlo de Asmundis, Pedro Brugada, Ramon Brugada, Elena Arbelo, Josep Brugada, Philippe Mabo, Nathalie Behar, Carla Giustetto, Maria Sabater Molina, Juan R. Gimeno, Can Hasdemir, Peter J. Schwartz, Lia Crotti, Pascal P. McKeown, Sanjay Sharma, Elijah R. Behr, Michel Haissaguerre, Frédéric Sacher, Caroline Rooryck, Hanno L. Tan, Carol A. Remme, Pieter G. Postema, Mario Delmar, Patrick T. Ellinor, Steven A. Lubitz, Jean-Baptiste Gourraud, Michael W. Tanck, Alfred L. George Jr., Calum A. MacRae, Paul W. Burridge, Christian Dina, Vincent Probst, Arthur A. Wilde, Jean-Jacques Schott, Richard Redon &, and Connie R. Bezzina

Abstract

In the version of this article initially published, Federico Manevy’s name appeared with a middle initial in error. The name has been corrected in the HTML and PDF versions of the article.

Published
2022

46. Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility

Author

Barc, J, Tadros, R, Glinge, C, Chiang, D, Jouni, M, Simonet, F, Jurgens, S, Baudic, M, Nicastro, M, Potet, F, Offerhaus, J, Walsh, R, Hoan Choi, S, Verkerk, A, Mizusawa, Y, Anys, S, Minois, D, Arnaud, M, Duchateau, J, Wijeyeratne, Y, Muir, A, Papadakis, M, Castelletti, S, Torchio, M, Gil Ortuño, C, Lacunza, J, Giachino, D, Cerrato, N, Martins, R, Campuzano, O, Van Dooren, S, Thollet, A, Kyndt, F, Mazzanti, A, Clémenty, N, Bisson, A, Corveleyn, A, Stallmeyer, B, Dittmann, S, Saenen, J, Noël, A, Honarbakhsh, S, Rudic, B, Marzak, H, Rowe, M, Federspiel, C, Le Page, S, Placide, L, Milhem, A, Barajas-Martinez, H, Beckmann, B, Krapels, I, Steinfurt, J, Gregers Winkel, B, Jabbari, R, Shoemaker, M, Boukens, B, Škorić-Milosavljević, D, Bikker, H, Manevy, F, Lichtner, P, Ribasés, M, Meitinger, T, Müller-Nurasyid, M, Group, K, Veldink, J, van den Berg, L, Van Damme, P, Cusi, D, Lanzani, C, Rigade, S, Charpentier, E, Baron, E, Bonnaud, S, Lecointe, S, Donnart, A, Le Marec, H, Chatel, S, Karakachoff, M, Bézieau, S, London, B, Tfelt-Hansen, J, Roden, D, Odening, K, Cerrone, M, Chinitz, L, Volders, P, van de Berg, M, Laurent, G, Faivre, L, Antzelevitch, C, Kääb, S, Al Arnaout, A, Dupuis, J, Pasquie, J, Billon, O, Roberts, J, Jesel, L, Borggrefe, M, Lambiase, P, Mansourati, J, Loeys, B, Leenhardt, A, Guicheney, P, Maury, P, Schulze-Bahr, E, Robyns, T, Breckpot, J, Babuty, D, Priori, S, Napolitano, C, Referral Center for inherited cardiac arrhythmia, N, de Asmundis, C, Brugada, P, Brugada, R, Arbelo, E, Brugada, J, Mabo, P, Behar, N, Giustetto, C, Sabater Molina, M, Gimeno, J, Hasdemir, C, Schwartz, P, Crotti, L, Mckeown, P, Sharma, S, Behr, E, Haissaguerre, M, Sacher, F, Rooryck, C, Tan, H, Remme, C, Postema, P, Delmar, M, Ellinor, P, Lubitz, S, Gourraud, J, Tanck, M, L. George Jr., A, Macrae, C, Burridge, P, Dina, C, Probst, V, Wilde, A, Schott, J, Redon &amp, R, Bezzina, C, Julien Barc, Rafik Tadros, Charlotte Glinge, David Y. Chiang, Mariam Jouni, Floriane Simonet, Sean J. Jurgens, Manon Baudic, Michele Nicastro, Franck Potet, Joost A. Offerhaus, Roddy Walsh, Seung Hoan Choi, Arie O. Verkerk, Yuka Mizusawa, Soraya Anys, Damien Minois, Marine Arnaud, Josselin Duchateau, Yanushi D. Wijeyeratne, Alison Muir, Michael Papadakis, Silvia Castelletti, Margherita Torchio, Cristina Gil Ortuño, Javier Lacunza, Daniela F. Giachino, Natascia Cerrato, Raphaël P. Martins, Oscar Campuzano, Sonia Van Dooren, Aurélie Thollet, Florence Kyndt, Andrea Mazzanti, Nicolas Clémenty, Arnaud Bisson, Anniek Corveleyn, Birgit Stallmeyer, Sven Dittmann, Johan Saenen, Antoine Noël, Shohreh Honarbakhsh, Boris Rudic, Halim Marzak, Matthew K. Rowe, Claire Federspiel, Sophie Le Page, Leslie Placide, Antoine Milhem, Hector Barajas-Martinez, Britt-Maria Beckmann, Ingrid P. Krapels, Johannes Steinfurt, Bo Gregers Winkel, Reza Jabbari, Moore B. Shoemaker, Bas J. Boukens, Doris Škorić-Milosavljević, Hennie Bikker, Federico Manevy, Peter Lichtner, Marta Ribasés, Thomas Meitinger, Martina Müller-Nurasyid, KORA-Study Group, Jan H. Veldink, Leonard H. van den Berg, Philip Van Damme, Daniele Cusi, Chiara Lanzani, Sidwell Rigade, Eric Charpentier, Estelle Baron, Stéphanie Bonnaud, Simon Lecointe, Audrey Donnart, Hervé Le Marec, Stéphanie Chatel, Matilde Karakachoff, Stéphane Bézieau, Barry London, Jacob Tfelt-Hansen, Dan Roden, Katja E. Odening, Marina Cerrone, Larry A. Chinitz, Paul G. Volders, Maarten P. van de Berg, Gabriel Laurent, Laurence Faivre, Charles Antzelevitch, Stefan Kääb, Alain Al Arnaout, Jean-Marc Dupuis, Jean-Luc Pasquie, Olivier Billon, Jason D. Roberts, Laurence Jesel, Martin Borggrefe, Pier D. Lambiase, Jacques Mansourati, Bart Loeys, Antoine Leenhardt, Pascale Guicheney, Philippe Maury, Eric Schulze-Bahr, Tomas Robyns, Jeroen Breckpot, Dominique Babuty, Silvia G. Priori, Carlo Napolitano, Nantes Referral Center for inherited cardiac arrhythmia, Carlo de Asmundis, Pedro Brugada, Ramon Brugada, Elena Arbelo, Josep Brugada, Philippe Mabo, Nathalie Behar, Carla Giustetto, Maria Sabater Molina, Juan R. Gimeno, Can Hasdemir, Peter J. Schwartz, Lia Crotti, Pascal P. McKeown, Sanjay Sharma, Elijah R. Behr, Michel Haissaguerre, Frédéric Sacher, Caroline Rooryck, Hanno L. Tan, Carol A. Remme, Pieter G. Postema, Mario Delmar, Patrick T. Ellinor, Steven A. Lubitz, Jean-Baptiste Gourraud, Michael W. Tanck, Alfred L. George Jr., Calum A. MacRae, Paul W. Burridge, Christian Dina, Vincent Probst, Arthur A. Wilde, Jean-Jacques Schott, Richard Redon &, Connie R. Bezzina, Barc, J, Tadros, R, Glinge, C, Chiang, D, Jouni, M, Simonet, F, Jurgens, S, Baudic, M, Nicastro, M, Potet, F, Offerhaus, J, Walsh, R, Hoan Choi, S, Verkerk, A, Mizusawa, Y, Anys, S, Minois, D, Arnaud, M, Duchateau, J, Wijeyeratne, Y, Muir, A, Papadakis, M, Castelletti, S, Torchio, M, Gil Ortuño, C, Lacunza, J, Giachino, D, Cerrato, N, Martins, R, Campuzano, O, Van Dooren, S, Thollet, A, Kyndt, F, Mazzanti, A, Clémenty, N, Bisson, A, Corveleyn, A, Stallmeyer, B, Dittmann, S, Saenen, J, Noël, A, Honarbakhsh, S, Rudic, B, Marzak, H, Rowe, M, Federspiel, C, Le Page, S, Placide, L, Milhem, A, Barajas-Martinez, H, Beckmann, B, Krapels, I, Steinfurt, J, Gregers Winkel, B, Jabbari, R, Shoemaker, M, Boukens, B, Škorić-Milosavljević, D, Bikker, H, Manevy, F, Lichtner, P, Ribasés, M, Meitinger, T, Müller-Nurasyid, M, Group, K, Veldink, J, van den Berg, L, Van Damme, P, Cusi, D, Lanzani, C, Rigade, S, Charpentier, E, Baron, E, Bonnaud, S, Lecointe, S, Donnart, A, Le Marec, H, Chatel, S, Karakachoff, M, Bézieau, S, London, B, Tfelt-Hansen, J, Roden, D, Odening, K, Cerrone, M, Chinitz, L, Volders, P, van de Berg, M, Laurent, G, Faivre, L, Antzelevitch, C, Kääb, S, Al Arnaout, A, Dupuis, J, Pasquie, J, Billon, O, Roberts, J, Jesel, L, Borggrefe, M, Lambiase, P, Mansourati, J, Loeys, B, Leenhardt, A, Guicheney, P, Maury, P, Schulze-Bahr, E, Robyns, T, Breckpot, J, Babuty, D, Priori, S, Napolitano, C, Referral Center for inherited cardiac arrhythmia, N, de Asmundis, C, Brugada, P, Brugada, R, Arbelo, E, Brugada, J, Mabo, P, Behar, N, Giustetto, C, Sabater Molina, M, Gimeno, J, Hasdemir, C, Schwartz, P, Crotti, L, Mckeown, P, Sharma, S, Behr, E, Haissaguerre, M, Sacher, F, Rooryck, C, Tan, H, Remme, C, Postema, P, Delmar, M, Ellinor, P, Lubitz, S, Gourraud, J, Tanck, M, L. George Jr., A, Macrae, C, Burridge, P, Dina, C, Probst, V, Wilde, A, Schott, J, Redon &amp, R, Bezzina, C, Julien Barc, Rafik Tadros, Charlotte Glinge, David Y. Chiang, Mariam Jouni, Floriane Simonet, Sean J. Jurgens, Manon Baudic, Michele Nicastro, Franck Potet, Joost A. Offerhaus, Roddy Walsh, Seung Hoan Choi, Arie O. Verkerk, Yuka Mizusawa, Soraya Anys, Damien Minois, Marine Arnaud, Josselin Duchateau, Yanushi D. Wijeyeratne, Alison Muir, Michael Papadakis, Silvia Castelletti, Margherita Torchio, Cristina Gil Ortuño, Javier Lacunza, Daniela F. Giachino, Natascia Cerrato, Raphaël P. Martins, Oscar Campuzano, Sonia Van Dooren, Aurélie Thollet, Florence Kyndt, Andrea Mazzanti, Nicolas Clémenty, Arnaud Bisson, Anniek Corveleyn, Birgit Stallmeyer, Sven Dittmann, Johan Saenen, Antoine Noël, Shohreh Honarbakhsh, Boris Rudic, Halim Marzak, Matthew K. Rowe, Claire Federspiel, Sophie Le Page, Leslie Placide, Antoine Milhem, Hector Barajas-Martinez, Britt-Maria Beckmann, Ingrid P. Krapels, Johannes Steinfurt, Bo Gregers Winkel, Reza Jabbari, Moore B. Shoemaker, Bas J. Boukens, Doris Škorić-Milosavljević, Hennie Bikker, Federico Manevy, Peter Lichtner, Marta Ribasés, Thomas Meitinger, Martina Müller-Nurasyid, KORA-Study Group, Jan H. Veldink, Leonard H. van den Berg, Philip Van Damme, Daniele Cusi, Chiara Lanzani, Sidwell Rigade, Eric Charpentier, Estelle Baron, Stéphanie Bonnaud, Simon Lecointe, Audrey Donnart, Hervé Le Marec, Stéphanie Chatel, Matilde Karakachoff, Stéphane Bézieau, Barry London, Jacob Tfelt-Hansen, Dan Roden, Katja E. Odening, Marina Cerrone, Larry A. Chinitz, Paul G. Volders, Maarten P. van de Berg, Gabriel Laurent, Laurence Faivre, Charles Antzelevitch, Stefan Kääb, Alain Al Arnaout, Jean-Marc Dupuis, Jean-Luc Pasquie, Olivier Billon, Jason D. Roberts, Laurence Jesel, Martin Borggrefe, Pier D. Lambiase, Jacques Mansourati, Bart Loeys, Antoine Leenhardt, Pascale Guicheney, Philippe Maury, Eric Schulze-Bahr, Tomas Robyns, Jeroen Breckpot, Dominique Babuty, Silvia G. Priori, Carlo Napolitano, Nantes Referral Center for inherited cardiac arrhythmia, Carlo de Asmundis, Pedro Brugada, Ramon Brugada, Elena Arbelo, Josep Brugada, Philippe Mabo, Nathalie Behar, Carla Giustetto, Maria Sabater Molina, Juan R. Gimeno, Can Hasdemir, Peter J. Schwartz, Lia Crotti, Pascal P. McKeown, Sanjay Sharma, Elijah R. Behr, Michel Haissaguerre, Frédéric Sacher, Caroline Rooryck, Hanno L. Tan, Carol A. Remme, Pieter G. Postema, Mario Delmar, Patrick T. Ellinor, Steven A. Lubitz, Jean-Baptiste Gourraud, Michael W. Tanck, Alfred L. George Jr., Calum A. MacRae, Paul W. Burridge, Christian Dina, Vincent Probst, Arthur A. Wilde, Jean-Jacques Schott, Richard Redon &, and Connie R. Bezzina

Abstract

Brugada syndrome (BrS) is a cardiac arrhythmia disorder associated with sudden death in young adults. With the exception of SCN5A, encoding the cardiac sodium channel NaV1.5, susceptibility genes remain largely unknown. Here we performed a genome-wide association meta-analysis comprising 2,820 unrelated cases with BrS and 10,001 controls, and identified 21 association signals at 12 loci (10 new). Single nucleotide polymorphism (SNP)-heritability estimates indicate a strong polygenic influence. Polygenic risk score analyses based on the 21 susceptibility variants demonstrate varying cumulative contribution of common risk alleles among different patient subgroups, as well as genetic associations with cardiac electrical traits and disorders in the general population. The predominance of cardiac transcription factor loci indicates that transcriptional regulation is a key feature of BrS pathogenesis. Furthermore, functional studies conducted on MAPRE2, encoding the microtubule plus-end binding protein EB2, point to microtubule-related trafficking effects on NaV1.5 expression as a new underlying molecular mechanism. Taken together, these findings broaden our understanding of the genetic architecture of BrS and provide new insights into its molecular underpinnings.

Published
2022

47. THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder

Author

Genetica Klinische Genetica, Martin Broly 1, Bogdan V Polevoda 2, Kamel M Awayda 2, Ning Tong 2, Jenna Lentini 3, Thomas Besnard 4, Wallid Deb 4, Declan O'Rourke 5, Julia Baptista 6, Sian Ellard 6, Mohammed Almannai 7, Mais Hashem 8, Ferdous Abdulwahab 8, Hanan Shamseldin 8, Saeed Al-Tala 9, Fowzan S Alkuraya 10, Alberta Leon 11, Rosa L E van Loon 12, Alessandra Ferlini 13, Mariabeatrice Sanchini 13, Stefania Bigoni 13, Andrea Ciorba 14, Hans van Bokhoven 15, Zafar Iqbal 16, Almundher Al-Maawali 17, Fathiya Al-Murshedi 17, Anuradha Ganesh 18, Watfa Al-Mamari 19, Sze Chern Lim 20, Lynn S Pais 21, Natasha Brown 22, Saima Riazuddin 23, Stéphane Bézieau 4, Dragony Fu 3, Bertrand Isidor 4, Benjamin Cogné 24, Mitchell R O'Connell 25, Genetica Klinische Genetica, and Martin Broly 1, Bogdan V Polevoda 2, Kamel M Awayda 2, Ning Tong 2, Jenna Lentini 3, Thomas Besnard 4, Wallid Deb 4, Declan O'Rourke 5, Julia Baptista 6, Sian Ellard 6, Mohammed Almannai 7, Mais Hashem 8, Ferdous Abdulwahab 8, Hanan Shamseldin 8, Saeed Al-Tala 9, Fowzan S Alkuraya 10, Alberta Leon 11, Rosa L E van Loon 12, Alessandra Ferlini 13, Mariabeatrice Sanchini 13, Stefania Bigoni 13, Andrea Ciorba 14, Hans van Bokhoven 15, Zafar Iqbal 16, Almundher Al-Maawali 17, Fathiya Al-Murshedi 17, Anuradha Ganesh 18, Watfa Al-Mamari 19, Sze Chern Lim 20, Lynn S Pais 21, Natasha Brown 22, Saima Riazuddin 23, Stéphane Bézieau 4, Dragony Fu 3, Bertrand Isidor 4, Benjamin Cogné 24, Mitchell R O'Connell 25

Published
2022

48. Polyglobulie rare par mutation du gène EGLN1 : à propos d’un cas et revue de la littérature

Author

G. Vignon, Stéphane Bézieau, F. Airaud, A. Bonnin, F. Lellouche, P. Mottaz, C. Garrec, François Girodon, J. Labrousse, and B. Gardie

Subjects
0301 basic medicine, Gynecology, 03 medical and health sciences, medicine.medical_specialty, 030104 developmental biology, 0302 clinical medicine, business.industry, Gastroenterology, Internal Medicine, Medicine, Hereditary Erythrocytosis, business, 030215 immunology
Abstract

Resume Introduction Le diagnostic etiologique d’une polyglobulie est souvent simple, l’origine etant le plus souvent acquise. Parfois il faut rechercher des formes rares, hereditaires, l’algorithme decisionnel reposant sur le dosage de l’erythropoietine serique et sur la mesure de la pression en oxygene saturant l’hemoglobine a 50 % (P50). Ces pathologies sont en rapport avec des anomalies du recepteur a l’erythropoietine, des hemoglobines hyperaffines ou a des dysfonctionnements de la voie de regulation du facteur HIF (Hypoxia-Inducible Factor) implique dans la sensibilite renale a l’hypoxie. Observation Nous rapportons le cas d’un patient de 56 ans qui presente une polyglobulie inexpliquee associee a une erythropoietine serique et une P50 normales, chez lequel a ete trouvee la mutation jamais decrite c.400C>T (p.Gln134*) sur l’exon 1 du gene EGLN1 codant pour PHD2, une des molecules impliquee dans la voie de l’hypoxie. Conclusion Les investigations moleculaires et la multiplication des centres experts permettent actuellement de mieux caracteriser certaines polyglobulies rares. Ceci necessite une bonne cooperation entre cliniciens et biologistes, permettant de proposer au cas par cas les explorations les plus pertinentes.

Published
2020

49. Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk

Author

Alicja Wolk, Edward Giovannucci, Li Li, Polly A. Newcomb, Kenneth Offit, Clemens Schafmayer, Vicente Martín, Sergi Castellví-Bel, Daniel D. Buchanan, Mingyang Song, Qianchuan He, Martha L. Slattery, Volker Arndt, Anna H. Wu, Amit Joshi, David A. Drew, D. Timothy Bishop, Annika Lindblom, Temitope O. Keku, Jochen Hampe, Ozan Dikilitas, Douglas A. Corley, John B. Harley, Hakon Hakonarson, Steven Gallinger, Noralane M. Lindor, Ian B. Stanaway, Jeffrey K. Lee, Sonja I. Berndt, Veronika Vymetalkova, Syed H.E. Zaidi, Jessica Minnier, Daniel J. Schaid, Ludmila Vodickova, John D. Potter, Heather Hampel, Christopher I. Li, Frank D. Mentch, Wei-Qi Wei, Cornelia M. Ulrich, Marc J. Gunter, Robert E. Schoen, Catherine M. Tangen, Victor Moreno, Shuji Ogino, Tabitha A. Harrison, Albert de la Chapelle, Pavel Vodicka, Andrew T. Chan, Keith R. Curtis, Elisabeth A. Rosenthal, Jenny Chang-Claude, David C. Muller, Paul D.P. Pharoah, Roger L. Milne, David Duggan, Eric B. Larson, David R. Crosslin, Andrea Gsur, Stéphane Bézieau, Graham G. Giles, Robert J. MacInnis, Bahram Namjou, Christopher H. Dampier, Gail P. Jarvik, Andrea N. Burnett-Hartman, Richard B. Hayes, Fränzel J.B. Van Duijnhoven, Wendy K. Chung, Michael Hoffmeister, Mark A. Jenkins, Mathieu Lemire, Thomas J. Hudson, Elizabeth A. Platz, Neil Murphy, Graham Casey, Michael O. Woods, Aung Ko Win, Flora Qu, Li Hsu, Emily White, Peter T. Campbell, Lori C. Sakoda, Jane C. Figueiredo, Minta Thomas, Jeroen R. Huyghe, Bethany Van Guelpen, Kala Visvanathan, Loic Le Marchand, Corinne E. Joshu, Yu Ru Su, Ulrike Peters, Stephen B. Gruber, Demetrius Albanes, Stephen N. Thibodeau, Antoni Castells, and Hermann Brenner

Subjects
0301 basic medicine, Oncology, medicine.medical_specialty, Linkage disequilibrium, Nutrition and Disease, Population, Genome-wide association study, colorectal cancer, Article, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Voeding en Ziekte, Genetics, Medicine, Family history, education, cancer risk prediction, Genetics (clinical), Genetic association, VLAG, education.field_of_study, business.industry, 030104 developmental biology, machine learning, 030220 oncology & carcinogenesis, Relative risk, Cohort, polygenic risk score, business, Risk assessment
Abstract

Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.

Published
2020

50. SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance

Author

Amélie Cordovado, Martina Schaettin, Médéric Jeanne, Veranika Panasenkava, Anne-Sophie Denommé-Pichon, Boris Keren, Cyril Mignot, Martine Doco-Fenzy, Lance Rodan, Keri Ramsey, Vinodh Narayanan, Julie R Jones, Eloise J Prijoles, Wendy G Mitchell, Jillian R Ozmore, Kali Juliette, Erin Torti, Elizabeth A Normand, Leslie Granger, Andrea K Petersen, Margaret G Au, Juliann P Matheny, Chanika Phornphutkul, Mary-Kathryn Chambers, Joaquín-Alejandro Fernández-Ramos, Eduardo López-Laso, Michael C Kruer, Somayeh Bakhtiari, Marcella Zollino, Manuela Morleo, Giuseppe Marangi, Davide Mei, Tiziana Pisano, Renzo Guerrini, Raymond J Louie, Anna Childers, David B Everman, Betrand Isidor, Séverine Audebert-Bellanger, Sylvie Odent, Dominique Bonneau, Brigitte Gilbert-Dussardier, Richard Redon, Stéphane Bézieau, Frédéric Laumonnier, Esther T Stoeckli, Annick Toutain, Marie-Laure Vuillaume, Jonchère, Laurent, Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universität Zürich [Zürich] = University of Zurich (UZH), FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hémostase et Remodelage Vasculaire Post-Ischémie (HERVI - EA 3801), Université de Reims Champagne-Ardenne (URCA), Boston Children's Hospital, Harvard Medical School [Boston] (HMS), The Translational Genomics Research Institute (TGen), The Greenwood Genetic Center, Keck School of Medicine [Los Angeles], University of Southern California (USC), Dartmouth Hitchcock Medical Center [Lebanon], Gillette Children's Specialty Healthcare [St Paul], GeneDx [Gaithersburg, MD, USA], Randall Children's Hospital [Portland], University of Kentucky (UK), Warren Alpert Medical School of Brown University, Rhode Island Hospital [Providence, RI, États-Unis], Instituto Maimonides de Investigación Biomédica de Cordoba (IMIBIC), Universidad de Córdoba = University of Córdoba [Córdoba]-Hospital Universitario Reina Sofía, Barrow Neurological Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Telethon Institute of Genetics and Medicine = Istituto Telethon di Genetica e Medicina (TIGEM), Università degli Studi di Firenze = University of Florence (UniFI), Centre hospitalier universitaire de Nantes (CHU Nantes), Hôpital Morvan - CHRU de Brest (CHU - BREST ), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Funding for HUGODIMS (Western France exome-based trio approach project to identifygenes involved in intellectual disability) was supported by a grant from the French Ministryof Health and from the Health Regional Agency from Poitou-Charentes [HUGODIMS, 2013,RC14_0107]. [A.C.] is a research student recipient of a grant from the University of Tours., Cordovado, Amélie, Schaettin, Martina, Jeanne, Médéric, Panasenkava, Veranika, Denommé-Pichon, Anne-Sophie, Keren, Bori, Mignot, Cyril, Doco-Fenzy, Martine, Rodan, Lance, Ramsey, Keri, Narayanan, Vinodh, Jones, Julie R, Prijoles, Eloise J, Mitchell, Wendy G, Ozmore, Jillian R, Juliette, Kali, Torti, Erin, Normand, Elizabeth A, Granger, Leslie, Petersen, Andrea K, Au, Margaret G, Matheny, Juliann P, Phornphutkul, Chanika, Chambers, Mary-Kathryn, Fernández-Ramos, Joaquín-Alejandro, López-Laso, Eduardo, Kruer, Michael C, Bakhtiari, Somayeh, Zollino, Marcella, Morleo, Manuela, Marangi, Giuseppe, Mei, Davide, Pisano, Tiziana, Guerrini, Renzo, Louie, Raymond J, Childers, Anna, Everman, David B, Isidor, Betrand, Audebert-Bellanger, Séverine, Odent, Sylvie, Bonneau, Dominique, Gilbert-Dussardier, Brigitte, Redon, Richard, Bézieau, Stéphane, Laumonnier, Frédéric, Stoeckli, Esther T, Toutain, Annick, and Vuillaume, Marie-Laure

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, Epilepsy, Dendritic Spines, [SDV]Life Sciences [q-bio], Intellectual disability, Chick Embryo, Semaphorins, [SDV.GEN] Life Sciences [q-bio]/Genetics, General Medicine, Settore MED/03 - GENETICA MEDICA, Axon Guidance, [SDV] Life Sciences [q-bio], HEK293 Cells, SEMA6B, Intellectual Disability, Genetics, Animals, Humans, Original Article, Molecular Biology, Genetics (clinical)
Abstract

Intellectual disability (ID) is a neurodevelopmental disorder frequently caused by monogenic defects. In this study, we collected 14 SEMA6B heterozygous variants in 16 unrelated patients referred for ID to different centers. Whereas, until now, SEMA6B variants have mainly been reported in patients with progressive myoclonic epilepsy, our study indicates that the clinical spectrum is wider and also includes non-syndromic ID without epilepsy or myoclonus. To assess the pathogenicity of these variants, selected mutated forms of Sema6b were overexpressed in Human Embryonic Kidney 293T (HEK293T) cells and in primary neuronal cultures. shRNAs targeting Sema6b were also used in neuronal cultures to measure the impact of the decreased Sema6b expression on morphogenesis and synaptogenesis. The overexpression of some variants leads to a subcellular mislocalization of SEMA6B protein in HEK293T cells and to a reduced spine density owing to loss of mature spines in neuronal cultures. Sema6b knockdown also impairs spine density and spine maturation. In addition, we conducted in vivo rescue experiments in chicken embryos with the selected mutated forms of Sema6b expressed in commissural neurons after knockdown of endogenous SEMA6B. We observed that expression of these variants in commissural neurons fails to rescue the normal axon pathway. In conclusion, identification of SEMA6B variants in patients presenting with an overlapping phenotype with ID and functional studies highlight the important role of SEMA6B in neuronal development, notably in spine formation and maturation and in axon guidance. This study adds SEMA6B to the list of ID-related genes.

Published
2022

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