Novel computer driven scanning and image processing methodology demonstrated that genetic inheritance of risk for colorectal cancer in familial polyposis (FAP) and hereditary non-polyposis colon cancer (HNPCC) families is associated with highly pleiotropic affects on patterns of gene expression in the flat colonic mucosa. Among a panel of cloned sequences identified which characterize genetic risk, one is the mitochondrial (mt) encoded gene for the third subunit of mt cytochrome oxidase (COXIII). Expression was decreased in both progression of, and genetic risk for, colonic tumors in vivo, and metabolizable, unbranched, short-chain fatty acids (SCFAs) elevated these depressed levels of mtCOXIII expression, as well as mtCOXI, in colonic carcinoma cells in culture and also elevated mtCOX enzymatic activity, while leaving unaffected nuclear encoded subunits of COX. These changes may underlie the documented alterations in mitochondria structure and function in transformed colonic epithelial cells. Since SCFAs produced by fermentation of fiber by colonic microflora are the principle energy source for colonic epithelial cells, and since SCFAs also induce colonic epithelial cell differentiation both in vitro and in vivo, this suggests a mechanistic link between the molecular events in inherited risk and a dietary factor (fiber) which may modulate risk. To understand this relationship between diet and genetic risk, we will: l) determine SCFA affects on expression of genes on the mtDNA H and L strands in colonic carcinoma, adenoma and normal epithelial cells; 2) utilize a unique Utah kindred K353, in which gene carriers have variable penetrance of a mutation at the FAP locus on chromosome 5q21, to determine the relationship between the number of tumors which form and mt gene expression, and the impact of fiber intake in these patients on these two parameters; 3) determine mechanisms by which SCFAs elevate mt gene expression, including: the rate constants for mtRNA synthesis and degredation; structural alterations in the H and L strand bipartite promotors in tumors and tissue at risk; alterations in function and covalent modification of the major mt transcription factor mtTF1; and alterations in the mtTF1 nuclear encoded sequence in colonic tumors.