Clara Sze-Man Tang1, Peng Li2, Frank Pui-Ling Lai1, Alexander Xi Fu3, Sin-Ting Lau1, Man Ting So2, Kathy Nga-Chu Lui2, Zhixin Li1, Xuehan Zhuang2, Michelle Yu2, Xuelai Liu4, Ngoc D Ngo5, Xiaoping Miao6, Xi Zhang7, Bin Yi7, Shaotao Tang7, Xiaobing Sun8, Furen Zhang9, Hong Liu9, Qiji Liu10, Ruizhong Zhang11, Hualong Wang12, Liuming Huang13, Xiao Dong14, Jinfa Tou15, Kathryn Song-Eng Cheah16, Wanling Yang17, Zhenwei Yuan18, Kevin Yuk-Lap Yip3, Pak-Chung Sham19, Paul Kwang-Hang Tam2, Maria-Mercè Garcia-Barcelo20, Elly Sau-Wai Ngan21. 1. Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China; Dr Li Dak-Sum Research Centre, The University of Hong Kong, Pokfulam, Hong Kong, China. 2. Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. 3. Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China. 4. Hebei Medical University Second Hospital, Shijiazhuang, Hebei, China. 5. National Hospital of Pediatrics, Ha Noi, Viet Nam. 6. Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. 7. Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. 8. Department of Paediatric Surgery, Shandong Medical University, Shandong, China. 9. Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China. 10. The Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China. 11. Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China. 12. Changchun Children's Hospital, Changchun, Jilin, China. 13. Bayi Children's Hospital, General Hospital of Beijing Military Region, Beijing, China. 14. Shenzhen Children's Hospital, Shenzhen, Guangdong, China. 15. Zhejiang Children's Hospital, Hangzhou, Zhejiang, China. 16. School of Biological Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. 17. Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. 18. Department of Paediatric Surgery, Shengjing Hospital, China Medical University, Shenyang, China. 19. Department of Psychiatry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China; Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. 20. Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. Electronic address: mmgarcia@hku.hk. 21. Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China. Electronic address: engan@hku.hk.
Abstract
BACKGROUND & AIMS: Hirschsprung disease, or congenital aganglionosis, is believed to be oligogenic-that is, caused by multiple genetic factors. We performed whole-genome sequence analyses of patients with Hirschsprung disease to identify genetic factors that contribute to disease development and analyzed the functional effects of these variants. METHODS: We performed whole-genome sequence analyses of 443 patients with short-segment disease, recruited from hospitals in China and Vietnam, and 493 ethnically matched individuals without Hirschsprung disease (controls). We performed genome-wide association analyses and gene-based rare-variant burden tests to identify rare and common disease-associated variants and study their interactions. We obtained induced pluripotent stem cell (iPSC) lines from 4 patients with Hirschsprung disease and 2 control individuals, and we used these to generate enteric neural crest cells for transcriptomic analyses. We assessed the neuronal lineage differentiation capability of iPSC-derived enteric neural crest cells using an in vitro differentiation assay. RESULTS: We identified 4 susceptibility loci, including 1 in the phospholipase D1 gene (PLD1) (P = 7.4 × 10-7). The patients had a significant excess of rare protein-altering variants in genes previously associated with Hirschsprung disease and in the β-secretase 2 gene (BACE2) (P = 2.9 × 10-6). The epistatic effects of common and rare variants across these loci provided a sensitized background that increased risk for the disease. In studies of the iPSCs, we observed common and distinct pathways associated with variants in RET that affect risk. In functional assays, we found variants in BACE2 to protect enteric neurons from apoptosis. We propose that alterations in BACE1 signaling via amyloid β precursor protein and BACE2 contribute to pathogenesis of Hirschsprung disease. CONCLUSIONS: In whole-genome sequence analyses of patients with Hirschsprung disease, we identified rare and common variants associated with disease risk. Using iPSC cells, we discovered some functional effects of these variants.
BACKGROUND & AIMS:Hirschsprung disease, or congenital aganglionosis, is believed to be oligogenic-that is, caused by multiple genetic factors. We performed whole-genome sequence analyses of patients with Hirschsprung disease to identify genetic factors that contribute to disease development and analyzed the functional effects of these variants. METHODS: We performed whole-genome sequence analyses of 443 patients with short-segment disease, recruited from hospitals in China and Vietnam, and 493 ethnically matched individuals without Hirschsprung disease (controls). We performed genome-wide association analyses and gene-based rare-variant burden tests to identify rare and common disease-associated variants and study their interactions. We obtained induced pluripotent stem cell (iPSC) lines from 4 patients with Hirschsprung disease and 2 control individuals, and we used these to generate enteric neural crest cells for transcriptomic analyses. We assessed the neuronal lineage differentiation capability of iPSC-derived enteric neural crest cells using an in vitro differentiation assay. RESULTS: We identified 4 susceptibility loci, including 1 in the phospholipase D1 gene (PLD1) (P = 7.4 × 10-7). The patients had a significant excess of rare protein-altering variants in genes previously associated with Hirschsprung disease and in the β-secretase 2 gene (BACE2) (P = 2.9 × 10-6). The epistatic effects of common and rare variants across these loci provided a sensitized background that increased risk for the disease. In studies of the iPSCs, we observed common and distinct pathways associated with variants in RET that affect risk. In functional assays, we found variants in BACE2 to protect enteric neurons from apoptosis. We propose that alterations in BACE1 signaling via amyloid β precursor protein and BACE2 contribute to pathogenesis of Hirschsprung disease. CONCLUSIONS: In whole-genome sequence analyses of patients with Hirschsprung disease, we identified rare and common variants associated with disease risk. Using iPSC cells, we discovered some functional effects of these variants.
Authors: Thuy-Linh Le; Louise Galmiche; Jonathan Levy; Pim Suwannarat; Debby Mei Hellebrekers; Khomgrit Morarach; Franck Boismoreau; Tom Ej Theunissen; Mathilde Lefebvre; Anna Pelet; Jelena Martinovic; Antoinette Gelot; Fabien Guimiot; Amanda Calleroz; Cyril Gitiaux; Marie Hully; Olivier Goulet; Christophe Chardot; Severine Drunat; Yline Capri; Christine Bole-Feysot; Patrick Nitschké; Sandra Whalen; Linda Mouthon; Holly E Babcock; Robert Hofstra; Irenaeus Fm de Coo; Anne-Claude Tabet; Thierry J Molina; Boris Keren; Alice Brooks; Hubert Jm Smeets; Ulrika Marklund; Christopher T Gordon; Stanislas Lyonnet; Jeanne Amiel; Nadège Bondurand Journal: J Clin Invest Date: 2021-03-15 Impact factor: 14.808
Authors: Ellen M Schill; Christina M Wright; Alisha Jamil; Jonathan M LaCombe; Randall J Roper; Robert O Heuckeroth Journal: JCI Insight Date: 2019-04-18
Authors: Alexander Xi Fu; Kathy Nga-Chu Lui; Clara Sze-Man Tang; Ray Kit Ng; Frank Pui-Ling Lai; Sin-Ting Lau; Zhixin Li; Maria-Mercè Garcia-Barcelo; Pak-Chung Sham; Paul Kwong-Hang Tam; Elly Sau-Wai Ngan; Kevin Y Yip Journal: Genome Res Date: 2020-09-18 Impact factor: 9.043
Authors: Tanja Mederer; Stefanie Schmitteckert; Julia Volz; Cristina Martínez; Ralph Röth; Thomas Thumberger; Volker Eckstein; Jutta Scheuerer; Cornelia Thöni; Felix Lasitschka; Leonie Carstensen; Patrick Günther; Stefan Holland-Cunz; Robert Hofstra; Erwin Brosens; Jill A Rosenfeld; Christian P Schaaf; Duco Schriemer; Isabella Ceccherini; Marta Rusmini; Joseph Tilghman; Berta Luzón-Toro; Ana Torroglosa; Salud Borrego; Clara Sze-Man Tang; Mercè Garcia-Barceló; Paul Tam; Nagarajan Paramasivam; Melanie Bewerunge-Hudler; Carolina De La Torre; Norbert Gretz; Gudrun A Rappold; Philipp Romero; Beate Niesler Journal: PLoS Genet Date: 2020-11-05 Impact factor: 5.917