Doctoral Programme in Biomedicine (DPBM) Genetic modifiers of CHEK2-associated and familial breast cancer Taru A. Muranen Department of Obstetrics and Gynecology Helsinki University Hospital Faculty of Medicine University of Helsinki Helsinki, Finland Academic Dissertation To be discussed, with permission of the Faculty of Medicine, University of Helsinki, in Biomedicum 1, Lecture Hall 2, Haartmaninkatu 8, Helsinki on 2 November 2018, at 12 noon. Helsinki 2018 Supervised by: Adjunct Professor Heli Nevanlinna, PhD Department of Obstetrics and Gynecology Helsinki University Hospital and University of Helsinki, Finland Associate Professor Dario Greco, PhD Faculty of Medicine and Life Sciences Institute of Biosciences and Medical Technology University of Tampere, Finland Reviewed by: Adjunct Professor Minna Tanner, MD, PhD Faculty of Medicine and Life Sciences University of Tampere, Finland Professor Matti Nykter, PhD Faculty of Medicine and Life Sciences University of Tampere, Finland Official Opponent: Associate Professor Ingrid Hedenfalk, PhD Division of Oncology and Pathology Department of Clinical Sciences Lund University, Sweden Cover image: Three versions of the same pedigree overlaid: one colored by disease status (on the bottom), one colored by genotype of a moderate penetrance mutation (middle), and one colored by polygenic risk score (on the top). Dissertationes Scholae Doctoralis Ad Sanitatem Investigandam Universitatis Helsinkiensis ISBN 978-951-51-4503-1 (Paperback) ISBN 978-951-51-4504-8 (PDF) ISSN 2342-3161 (print) ISSN 2342-317X (online) Unigrafia Helsinki 2018 2 Itseoppinut on ainoa oppinut. Muut ovat opetettuja. Erno Paasilinna Ursalle, Elselle, Eerolle ja Urholle 3 Table of Contents Table of Contents .................................................................................................................................... 4 Abstract .................................................................................................................................................. 7 List of Original Publications .................................................................................................................... 9 Abbreviations ........................................................................................................................................ 10 Gene and protein names......................................................................................................................... 11 1 Introduction .................................................................................................................................. 12 2 Review of the Literature ................................................................................................................ 13 2.1 General cancer characteristics .............................................................................................. 13 2.1.1 Cancer progression ......................................................................................................... 13 2.1.2 Cancer genes .................................................................................................................. 15 2.2 Breast cancer ...................................................................................................................... 16 2.2.1 Mammary gland ............................................................................................................. 17 2.2.2 Breast cancer risk factors ................................................................................................ 20 2.2.3 Breast cancer subtypes .................................................................................................... 20 2.2.4 Origin of breast cancer.................................................................................................... 22 2.3 Breast cancer treatment ....................................................................................................... 23 2.3.1 Adjuvant endocrine therapy ............................................................................................ 23 2.3.2 Other targeted biological therapies .................................................................................. 23 2.3.3 Adjuvant chemotherapy .................................................................................................. 24 2.4 Genetic predisposition to breast cancer ................................................................................ 25 2.4.1 Breast cancer heritability ................................................................................................ 25 2.4.2 High-risk genes .............................................................................................................. 28 2.4.3 Moderate-risk genes ....................................................................................................... 29 2.4.4 The Breast cancer pathway ............................................................................................. 29 2.4.5 Common predisposing variants ....................................................................................... 31 2.5 CHEK2............................................................................................................................... 31 2.5.1 CHEK2 protein function ................................................................................................. 31 2.5.2 CHEK2 mutations .......................................................................................................... 32 2.5.3 CHEK2 and breast cancer risk......................................................................................... 33 2.5.4 CHEK2 in breast tumors ................................................................................................. 34 3 Aims of the Study ......................................................................................................................... 35 4 Materials and Methods .................................................................................................................. 36 4 4.1 Study subjects and data sources ........................................................................................... 36 4.1.1 Breast tumors (I, II) ........................................................................................................ 36 4.1.2 Study subjects from the Breast Cancer Association Consortium (II, III) ............................ 36 4.1.3 Study subjects of the Helsinki breast cancer study (IV) .................................................... 37 4.2 Methods.............................................................................................................................. 37 4.2.1 Microarray data processing and analyses (I, II) ................................................................ 37 4.2.2 Permutation analysis (I: unpublished data)....................................................................... 39 4.2.3 Survival analyses (II) ...................................................................................................... 40 4.2.4 Tumor pathology analyses (II) ........................................................................................ 40 4.2.5 The Polygenic risk score (III, IV) .................................................................................... 40 4.2.6 Risk association analyses (III, IV) ................................................................................... 40 4.2.7 Feature selection (III: unpublished data) .......................................................................... 40 4.2.8 In silico functional analysis (III: unpublished data) .......................................................... 41 4.3 Ethics statement .................................................................................................................. 41 5 Results .......................................................................................................................................... 42 5.1 c.1100delC and p.(I157T) carrier tumors (I, II) ..................................................................... 42 5.1.1 c.1100delC-associated copy number aberrations (I) ......................................................... 42 5.1.2 c.1100delC-associated differences in gene expression (I and unpublished data) ................ 42 5.1.3 Combined analysis of aCGH and GEX data (I and unpublished data) ............................... 43 5.1.4 p.(I157T)-associated gene expression (II) ........................................................................ 45 5.1.5 Clinico-pathological characteristics (II) ........................................................................... 45 5.2 p.(I157T) or c.1100delC carrier survival (II) ........................................................................ 45 5.3 Genetic modifiers of c.1100delC-associated breast cancer risk (III)....................................... 45 5.3.1 Synergistic risk effect of common variants for c.1100delC carriers (III)............................ 45 5.3.2 The sparse model (III: unpublished data) ......................................................................... 46 5.3.3 In silico functional characterization (III: unpublished data) .............................................. 46 5.4 Risk modifiers in breast cancer families (IV) ........................................................................ 47 6 Discussion ...................................................................................................................................