title: Transitions at CpG dinucleotides, geographic clustering of TP53 mutations and food availability patterns in colorectal cancer.
abstract: BACKGROUND
  Colorectal cancer is mainly attributed to diet, but the role exerted by foods remains unclear because involved factors are extremely complex. Geography substantially impacts on foods. Correlations between international variation in colorectal cancer-associated mutation patterns and food availabilities could highlight the influence of foods on colorectal mutagenesis.
  
  
  METHODS
  To test such hypothesis, we applied techniques based on hierarchical clustering, feature extraction and selection, and statistical pattern recognition to the analysis of 2,572 colorectal cancer-associated TP53 mutations from 12 countries/geographic areas. For food availabilities, we relied on data extracted from the Food Balance Sheets of the Food and Agriculture Organization of the United Nations. Dendrograms for mutation sites, mutation types and food patterns were constructed through Ward's hierarchical clustering algorithm and their stability was assessed evaluating silhouette values. Feature selection used entropy-based measures for similarity between clusterings, combined with principal component analysis by exhaustive and heuristic approaches.
  
  
  CONCLUSIONS
  Mutations clustered in two major geographic groups, one including only Western countries, the other Asia and parts of Europe. This was determined by variation in the frequency of transitions at CpGs, the most common mutation type. Higher frequencies of transitions at CpGs in the cluster that included only Western countries mainly reflected higher frequencies of mutations at CpG codons 175, 248 and 273, the three major TP53 hotspots. Pearson's correlation scores, computed between the principal components of the datamatrices for mutation types, food availability and mutation sites, demonstrated statistically significant correlations between transitions at CpGs and both mutation sites and availabilities of meat, milk, sweeteners and animal fats, the energy-dense foods at the basis of "Western" diets. This is best explainable by differential exposure to nitrosative DNA damage due to foods that promote metabolic stress and chronic inflammation.
authors.affiliation: Department of Oncology and Neurosciences, G d'Annunzio University, and Center of Excellence on Aging (CeSI), G d'Annunzio University Foundation, Chieti, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Verginelli
authors.forename: Faraz
authors.initials: F
authors.lastname: Bishehsari
authors.forename: Francesco
authors.initials: F
authors.lastname: Napolitano
authors.forename: Mahboobeh
authors.initials: M
authors.lastname: Mahdavinia
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cama
authors.forename: Reza
authors.initials: R
authors.lastname: Malekzadeh
authors.forename: Gennaro
authors.initials: G
authors.lastname: Miele
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Raiconi
authors.forename: Roberto
authors.initials: R
authors.lastname: Tagliaferri
authors.forename: Renato
authors.initials: R
authors.lastname: Mariani-Costantini
mesh_terms: D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000453:epidemiology / Q000235:genetics*; D018899:CpG Islands; D005523:Food Supply; D016158:Genes, p53; D005843:Geography; D006801:Humans; D009154:Mutation