Xujie Zhao1, Maoxiang Qian2, Charnise Goodings1, Yang Zhang3, Wenjian Yang1, Ping Wang4, Beisi Xu5, Cheng Tian1, Ching-Hon Pui6, Stephen P Hunger7, Elizabeth A Raetz8, Meenakshi Devidas9, Mary V Relling1, Mignon L Loh10, Daniel Savic1, Chunliang Li3, Jun J Yang1,6. 1. Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA. 2. Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China. 3. Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. 4. Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. 5. Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA. 6. Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA. 7. Department of Pediatrics and The Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. 8. Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA. 9. Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA. 10. Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Abstract
BACKGROUND: There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-cell ALL leukemogenesis remain largely unknown. METHODS: We performed targeted sequencing of ARID5B in germline DNA of 5008 children with ALL. Variants were evaluated for association with ALL susceptibility using 3644 patients from the UK10K cohort as non-ALL controls, under an additive model. Cis-regulatory elements in ARID5B were systematically identified using dCas9-KRAB-mediated enhancer interference system enhancer screen in ALL cells. Disruption of transcription factor binding by ARID5B variant was predicted informatically and then confirmed using chromatin immunoprecipitation and coimmunoprecipitation. ARID5B variant association with hematological traits was examined using UK Biobank dataset. All statistical tests were 2-sided. RESULTS: We identified 54 common variants in ARID5B statistically significantly associated with leukemia risk, all of which were noncoding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P = 5.57 × 10-45) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n = 349 861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P = 8.6 × 10-22 and 2.1 × 10-18, respectively). CONCLUSIONS: Our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.
BACKGROUND: There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-cell ALL leukemogenesis remain largely unknown. METHODS: We performed targeted sequencing of ARID5B in germline DNA of 5008 children with ALL. Variants were evaluated for association with ALL susceptibility using 3644 patients from the UK10K cohort as non-ALL controls, under an additive model. Cis-regulatory elements in ARID5B were systematically identified using dCas9-KRAB-mediated enhancer interference system enhancer screen in ALL cells. Disruption of transcription factor binding by ARID5B variant was predicted informatically and then confirmed using chromatin immunoprecipitation and coimmunoprecipitation. ARID5B variant association with hematological traits was examined using UK Biobank dataset. All statistical tests were 2-sided. RESULTS: We identified 54 common variants in ARID5B statistically significantly associated with leukemia risk, all of which were noncoding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P = 5.57 × 10-45) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n = 349 861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P = 8.6 × 10-22 and 2.1 × 10-18, respectively). CONCLUSIONS: Our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.
Authors: Denes Hnisz; Brian J Abraham; Tong Ihn Lee; Ashley Lau; Violaine Saint-André; Alla A Sigova; Heather A Hoke; Richard A Young Journal: Cell Date: 2013-10-10 Impact factor: 41.582
Authors: Heng Xu; Cheng Cheng; Meenakshi Devidas; Deqing Pei; Yiping Fan; Wenjian Yang; Geoff Neale; Paul Scheet; Esteban G Burchard; Dara G Torgerson; Celeste Eng; Michael Dean; Frederico Antillon; Naomi J Winick; Paul L Martin; Cheryl L Willman; Bruce M Camitta; Gregory H Reaman; William L Carroll; Mignon Loh; William E Evans; Ching-Hon Pui; Stephen P Hunger; Mary V Relling; Jun J Yang Journal: J Clin Oncol Date: 2012-01-30 Impact factor: 44.544
Authors: C H Pui; H H Mahmoud; G K Rivera; M L Hancock; J T Sandlund; F G Behm; D R Head; M V Relling; R C Ribeiro; J E Rubnitz; L E Kun; W E Evans Journal: Blood Date: 1998-07-15 Impact factor: 22.113
Authors: Lisa R Treviño; Wenjian Yang; Deborah French; Stephen P Hunger; William L Carroll; Meenakshi Devidas; Cheryl Willman; Geoffrey Neale; James Downing; Susana C Raimondi; Ching-Hon Pui; William E Evans; Mary V Relling Journal: Nat Genet Date: 2009-08-16 Impact factor: 38.330
Authors: Virginia Perez-Andreu; Kathryn G Roberts; Richard C Harvey; Wenjian Yang; Cheng Cheng; Deqing Pei; Heng Xu; Julie Gastier-Foster; Shuyu E; Joshua Yew-Suang Lim; I-Ming Chen; Yiping Fan; Meenakshi Devidas; Michael J Borowitz; Colton Smith; Geoffrey Neale; Esteban G Burchard; Dara G Torgerson; Federico Antillon Klussmann; Cesar Rolando Najera Villagran; Naomi J Winick; Bruce M Camitta; Elizabeth Raetz; Brent Wood; Feng Yue; William L Carroll; Eric Larsen; W Paul Bowman; Mignon L Loh; Michael Dean; Deepa Bhojwani; Ching-Hon Pui; William E Evans; Mary V Relling; Stephen P Hunger; Cheryl L Willman; Charles G Mullighan; Jun J Yang Journal: Nat Genet Date: 2013-10-20 Impact factor: 38.330
Authors: Yaron Tomer; Alia Hasham; Terry F Davies; Mihaela Stefan; Erlinda Concepcion; Mehdi Keddache; David A Greenberg Journal: J Clin Endocrinol Metab Date: 2012-11-01 Impact factor: 5.958
Authors: Ching-Hon Pui; Dario Campana; Deqing Pei; W Paul Bowman; John T Sandlund; Sue C Kaste; Raul C Ribeiro; Jeffrey E Rubnitz; Susana C Raimondi; Mihaela Onciu; Elaine Coustan-Smith; Larry E Kun; Sima Jeha; Cheng Cheng; Scott C Howard; Vickey Simmons; Amy Bayles; Monika L Metzger; James M Boyett; Wing Leung; Rupert Handgretinger; James R Downing; William E Evans; Mary V Relling Journal: N Engl J Med Date: 2009-06-25 Impact factor: 91.245