title: Examining the Relationship between Pre-Malignant Breast Lesions, Carcinogenesis and Tumor Evolution in the Mammary Epithelium Using an Agent-Based Model.
abstract: BACKGROUND
  Breast cancer, the product of numerous rare mutational events that occur over an extended time period, presents numerous challenges to investigators interested in studying the transformation from normal breast epithelium to malignancy using traditional laboratory methods, particularly with respect to characterizing transitional and pre-malignant states. Dynamic computational modeling can provide insight into these pathophysiological dynamics, and as such we use a previously validated agent-based computational model of the mammary epithelium (the DEABM) to investigate the probabilistic mechanisms by which normal populations of ductal cells could transform into states replicating features of both pre-malignant breast lesions and a diverse set of breast cancer subtypes.
  
  
  METHODS
  The DEABM consists of simulated cellular populations governed by algorithms based on accepted and previously published cellular mechanisms. Cells respond to hormones, undergo mitosis, apoptosis and cellular differentiation. Heritable mutations to 12 genes prominently implicated in breast cancer are acquired via a probabilistic mechanism. 3000 simulations of the 40-year period of menstrual cycling were run in wild-type (WT) and BRCA1-mutated groups. Simulations were analyzed by development of hyperplastic states, incidence of malignancy, hormone receptor and HER-2 status, frequency of mutation to particular genes, and whether mutations were early events in carcinogenesis.
  
  
  RESULTS
  Cancer incidence in WT (2.6%) and BRCA1-mutated (45.9%) populations closely matched published epidemiologic rates. Hormone receptor expression profiles in both WT and BRCA groups also closely matched epidemiologic data. Hyperplastic populations carried more mutations than normal populations and mutations were similar to early mutations found in ER+ tumors (telomerase, E-cadherin, TGFB, RUNX3, p < .01). ER- tumors carried significantly more mutations and carried more early mutations in BRCA1, c-MYC and genes associated with epithelial-mesenchymal transition.
  
  
  CONCLUSIONS
  The DEABM generates diverse tumors that express tumor markers consistent with epidemiologic data. The DEABM also generates non-invasive, hyperplastic populations, analogous to atypia or ductal carcinoma in situ (DCIS), via mutations to genes known to be present in hyperplastic lesions and as early mutations in breast cancers. The results demonstrate that agent-based models are well-suited to studying tumor evolution through stages of carcinogenesis and have the potential to be used to develop prevention and treatment strategies.
authors.affiliation: Pritzker School of Medicine, University of Chicago, 924 East 57th Street #104, Chicago, Illinois, 60637, United States of America.
authors.forename: Joaquin
authors.initials: J
authors.lastname: Chapa
authors.affiliation: Department of Surgery, University of Chicago, 5841 S. Maryland Ave, Chicago, Illinois, 60637, United States of America.
authors.forename: Gary
authors.initials: G
authors.lastname: An
authors.affiliation: Department of Surgery, Northwestern University, Robert H. Lurie Comprehensive Cancer Center, 303 E Superior Street, Lurie, 4-105, Chicago, Illinois, 60611, United States of America.
authors.forename: Swati A
authors.initials: SA
authors.lastname: Kulkarni
mesh_terms: D001943:Breast Neoplasms / Q000453:epidemiology / Q000473:pathology*; D063646:Carcinogenesis / Q000473:pathology*; D019070:Cell Lineage; D004249:DNA Damage; D004260:DNA Repair; D004848:Epithelium / Q000473:pathology*; D005260:Female; D006801:Humans; D006965:Hyperplasia; D015994:Incidence; D042361:Mammary Glands, Human / Q000473:pathology*; D009154:Mutation; D011960:Receptors, Estrogen / Q000378:metabolism; D015398:Signal Transduction; D013597:Systems Analysis
chemical_list: D011960:Receptors, Estrogen