Oral Presentation 28th Lorne Cancer Conference 2016

Point mutations in promoter 1B of APC in a syndrome of gastric adenocarcinoma and proximal polyposis of the stomach (#15)

Jun Li 1 , Sue Healey 1 , Jonathan Beesley 1 , Susan L Woods 2 , Xiaoqing Chen 1 , Jason S Lee 1 , Haran Sivakumaran 1 , Nicci Wayte 1 , Katia Nones 1 , Joshua J Waterfall 3 , John Pearson 1 4 , Anne-Marie Patch 1 , Janine Senz 5 , Pardeep Kaurah 6 , Robertson Mackenzie 7 , Alireza Heravi-Moussavi 8 , Samantha Hansford 5 , Amanda B Spurdle 1 , Peter T Simpson 9 10 , Leonard da Silva 9 10 , Sunil R Lakhani 9 10 11 , Andrew D Clouston 12 13 , Mark Bettington 10 12 14 , Rita A Busuttil 15 16 , Alex Boussioutas 15 16 17 , Geoffrey J Faulkner 18 , Evangelos Bellos 4 19 , Lachlan Coin 4 , Kevin Rioux 20 , Oliver F Bathe 21 , Xiaogang Wen 22 23 , Hilary C Martin 24 , Deborah W Neklason 25 , Sean R Davis 3 , Robert L Walker 3 , Kathleen A Calzone 3 , Theo Heller 26 , Christopher Koh 26 , Marbin Pineda 3 , Udo Rudloff 27 , Martha Quezado 28 , Pavel N Pichurin 29 , Peter J Hulick 30 , Scott M Weissman 31 , Anna Newlin 30 , Wendy S Rubenstein 32 , Jone E Sampson 33 , Kelly Hamman 33 , David Goldgar 34 , Nicola Poplawski 35 36 , Kerry Phillips 35 36 , Lyn Schofield 37 , Jacqueline Armstrong 35 , Cathy Kiraly-Borri 37 , Graeme K Suthers 36 , David G Huntsman 7 38 , Fatima Carneiro 23 39 , Noralane M Lindor 40 , Stacey L Edwards 1 , Juliet D French 1 , Nicola Waddell 1 4 , Paul S Meltzer 3 , Daniel L Worthley 2 , Kasmintan A Schrader 6 7 , Georgia Chenevix-Trench 1
  1. Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD, Australia
  2. School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA, Australia
  3. Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethseda, MD, USA
  4. Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
  5. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
  6. Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
  7. Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
  8. Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
  9. UQ Centre for Clinical Research, The University of Queensland , Brisbane, QLD, Australia
  10. School of Medicine, The University of Queensland, Brisbane, QLD, Australia
  11. Anatomical Pathology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
  12. Envoi Specialist Pathologists, Kelvin Grove, QLD, Australia
  13. Centre for Liver Disease Research, University of Queensland, Woolloongabba, QLD, Australia
  14. The Conjoint Gastroenterology Laboratory, QIMR Berghofer, Herston, QLD, Australia
  15. Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
  16. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
  17. Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
  18. Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
  19. Department of Epidemiology and Biostatistics, Imperial College London, London, UK
  20. Department of Medicine, Department of Microbiology , University of Calgary, Calgary, AB, Canada
  21. Departments of Surgery and Oncology, University of Calgary, Calgary, AB, Canada
  22. Centro Hospitalar Vila Nova de Gaia, Espinho, Portugal
  23. Institute of Molecular Pathology and Immunology of the University of Porto , Porto, Portugal
  24. Wellcome Trust Centre for Human Genetics, Oxford, UK
  25. Department of Internal Medicine, Huntsman Cancer Institute at University of Utah, Salt Lake City, UT, USA
  26. Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease , Bethseda, MD, USA
  27. Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethseda, MD, USA
  28. Laboratory of Pathology, National Cancer Institute, Bethseda, MD, USA
  29. Department of Medical Genetics, Mayo Clinic, Rochester, MN, Australia
  30. Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
  31. GeneDx, Gaithersberg, MD, USA
  32. National Center for Biotechnology Information/National Library of Medicine/National Institutes of Health, Bethseda, MD, USA
  33. Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
  34. Department of Dermatology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
  35. Adult Genetics Unit, SA Pathology at the Women’s and Children’s Hospital, North Adelaide, SA, Australia
  36. Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
  37. Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
  38. Department of Pathology and Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
  39. Medical Faculty of the University of Porto/Centro Hospitalar São João, Porto, Portugal
  40. Department of Medical Genetics, Mayo Clinic College of Medicine, Scottsdale, AZ, USA
Gastricadenocarcinoma andproximalpolyposis of thestomach (GAPPS) is an autosomal dominant cancer predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. Using a large Australian pedigree, we mapped the disease linked genetic region to an interval of 46Mb at 5q22 that contains 51 genes.   Extensive whole exome and whole genome sequencing using HiSeq failed to identify any novel or rare coding mutations, or obvious regulatory mutations, in the linkage region. Whole genome copy number analysis showed loss of heterozygosity (LOH) only on 5q in fundic gland polyps from affected individuals. The minimal common region of loss overlapped the linkage region by 12 Mb, centered aroundAPC.Sanger sequencing revealed novel point mutations in the APC promoter 1B that co-segregated perfectly with disease in six families, including five smaller GAPPS families from North America. All three mutations cluster within a Yin Yang 1 (YY1) transcription factor binding site that was occupied by YY1 in gastric and colorectal cancer cell lines by chromatin immunoprecipitation. The presence of these mutations reduced YY1 binding in vitro as predicted. Furthermore, luciferase assays showed that all three mutations abrogated activity of theAPC1B promoter in gastric and colorectal cancer cell lines, suggesting that YY1 normally acts as an activator of this promoter. We observed allelic imbalance of APC in blood in carriers, suggesting that the presence of these mutations leads to decreased allele specific expression in vivo. Whole genome sequencing of fundic gland polyps without 5q LOH identified somatic truncating mutations inAPC.  In summary, we have shown that GAPPS is caused by specific point mutations in the YY1 binding site in the 1B promoter ofAPC. A second “hit” by LOH or somatic mutation involvingAPC is common in the fundic gland polyps from affected individuals.