High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection.

Researchers in several laboratories have reported a high frequency of homoplasmic mitochondrial DNA (mtDNA) mutations in human tumors. This observation has been interpreted to reflect a replicative advantage for mutated mtDNA copies, a growth advantage for a cell containing certain mtDNA mutations, and/or tumorigenic properties of mtDNA mutations. We consider another possibility-that the observed homoplasmy arose entirely by chance in tumor progenitor cells, without any physiological advantage or tumorigenic requirement. Through extensive computer modeling, we demonstrate that there is sufficient opportunity for a tumor progenitor cell to achieve homoplasmy through unbiased mtDNA replication and sorting during cell division. To test our model in vivo, we analyzed mtDNA homoplasmy in healthy human epithelial tissues and discovered that the model correctly predicts the considerable observed frequency of homoplasmic cells. Based on the available data on mitochondrial mutant fractions and cell division kinetics, we show that the predicted frequency of homoplasmy in tumor progenitor cells in the absence of selection is similar to the reported frequency of homoplasmic mutations in tumors. Although a role for other mechanisms is not excluded, random processes are sufficient to explain the incidence of homoplasmic mtDNA mutations in human tumors.

Single nucleotide polymorphism spectra in newborns and centenarians: identification of genes coding for rise of mortal disease.

Some single-nucleotide polymorphisms (SNPs) increase the risk of mortal disease. Identifying these SNPs and the genes in which they reside is an important area in human genomics. Such qualitative observations are important in themselves. However, an accurate assessment of the numerical distribution and age-dependent decline of SNPs in the population would permit calculation of the rises represented by each SNP. Such analyses have not been attempted because of a lack of an efficient and cost-effective method to detect multiple SNPs in a large number of individuals and a large number of genes. Here, we suggest the use of an analytical procedure that can scan for SNPs in 100-bp DNA sequences from as many as 10000 donors' blood cell samples, or 20000 alleles, simultaneously. Our suggestion is based on technology developed for studies of somatic mutations in human tissue DNA for point mutations at frequencies equal to or greater than 10(-6). In a simplified version of this technology, any SNP arising at frequencies at or above 5x10(-4) would be identified with useful precision. A gene would be represented by 10 or more sections of 100bp. This strategy includes splice-site mutations that represent a significant fraction of gene inactivating point mutations and would not be observed in strategies using cDNA. To illustrate the logic of the suggested approach, we use American mortality records to calculate the expected decrease in SNPs coding for premature mortality in newborns and centenarians. We consider several elementary cases: SNPs in one gene only, any of several genes, or all of several genes that create a risk of death by pancreatic cancer. The fraction of expressed polymorphisms affecting mortality should be simultaneously increased in probands and decreased in the aged relative to newborns. Silent polymorphisms in the same gene would remain unchanged in all three groups and serve as internal standards. A key point is that scanning a gene, in which loss of gene function creates the risk of mortality is expected to reveal not one, but multiple SNPs, which decline with age, as carriers die earlier in life than non-carriers. Several SNPs in a scanned gene would suggest that the decreasing SNP was genetically linked to a different polymorphism that creates the disease risk.

Population risk and physiological rate parameters for colon cancer. The union of an explicit model for carcinogenesis with the public health records of the United States.

The relationship between the molecular mechanisms of mutagenesis and the actual processes by which most people get cancer is still poorly understood. One missing link is a physiologically based but quantitative model uniting the processes of mutation, cell growth and turnover. Any useful model must also account for human heterogeneity for inherited traits and environmental experiences. Such a coherent algebraic model for the age-specific incidence of cancer has been developing over the past 50 years. This development has been spurred primarily by the efforts of Nordling [N.O. Nordling, A new theory on the cancer-inducing mechanism, Br. J. Cancer 7 (1953) 68-72], Armitage and Doll [P. Armitage, R. Doll, The age distribution of cancer and a multi-stage theory of carcinogenesis, Br. J. Cancer 8 (1) (1954) 1-12; P. Armitage, R. Doll, A two-stage theory of carcinogenesis in relation to the age distribution of human cancer, Br. J. Cancer 9 (2) (1957) 161-169], and Moolgavkar and Knudson [S.H. Moolgavkar, A.G. Knudson Jr., Mutation and cancer: a model for human carcinogenesis. JNCI 66 (6) (1981) 1037-1052], whose work defined two rate-limiting stages identified with initiation and promotion stages in experimental carcinogenesis. Unfinished in these efforts was an accounting of population heterogeneity and a complete description of growth and genetic change during the growth of adenomas. In an attempt to complete a unified model, we present herein the first means to explicitly compute the essential parameters of the two-stage initiation-promotion model using colon cancer as an example. With public records from the 1930s to the present day, we first calculate the fraction at primary risk for each birth year cohort and note historical changes. We then calculate the product of rates for n initiation-mutations, the product of rates for m promotion-mutations and the average growth rate of the intermediate adenomatous colonies from which colon carcinomas arise. We find that the population fraction at primary risk for colon cancer risk was historically invariant at about 42% for the birth year cohorts from 1860 through 1930. This was true for each of the four cohorts we examined (European- and African-Americans of each gender). Additionally, the data indicate an historical increase in the initiation-mutation rates for the male cohorts and the promotion-mutation rates for the female cohorts. Interestingly, the calculated rates for initiation-mutations are in accord with mutation rates derived from observations of mutations in peripheral blood cells drawn from persons of different ages. Adenoma growth rates differed significantly between genders but were essentially historically invariant. In its present form, the model has also allowed us to calculate the rate of loss of heterozygosity (LOH) or loss of genomic imprinting (LOI) in adenomas to result in the high LOH/LOI fractions in tumors. But it has not allowed us to specify the number of events m required during promotion.

Mutation, cell kinetics, and subpopulations at risk for colon cancer in the United States.

We have extended the algebraic models for cancer initiation and progression developed by Nordling, Armitage-Doll and Knudson-Moolgavkar to include the effect of cell turnover rate in normal tissue, stochastic growth of preneoplastic adenomas, and the general case wherein a subfraction of the population is at risk. We have also gathered the mortality data available for the United States from 1900 to 1991 and categorically organized them by birth year cohorts and age specific death rates for ages 0 to 104 in 5-year groupings. Using these data, we first explored the quantitative nature of the biases of underreporting or misdiagnosis as historical age-dependent functions. Then we used the extended algebraic model to calculate the parameters of subpopulation fraction at risk, mutation rates and adenoma growth rates. We observe that death rates for all cancers are low in childhood and early adulthood, rise in middle age in an approximately linear manner, reach a maximum in old age, and even after correction for reporting bias, decrease markedly in extreme old age. We represent this behavior as the natural result of a continuous process of cell division, death and mutation within a subpopulation at risk. This population at risk within any birth cohort is defined by the product of a constant inherited risk factor multiplied by a historically valuable environmental risk factor. Our formulation permits explicit calculation of the fraction at risk of death from any cancer as a historical function. With regard to the algebraic description of the process of carcinogenesis, we use Nordling's concept that n genetic events in a cell population of constant cell number are required to initiate a colony capable of net cell growth or 'adenoma.' We adopt and extend Moolgavkar's use of the 'Gambler's Ruin' stochastic process to describe the probability of adenoma survival and the canonical expectation that a surviving adenoma will soon contain many initiated cells by virtue of stochastic distribution of surviving cells. We consider that within the growing adenoma, it is necessary for a cell to acquire m additional mutations in order to attain the carcinoma phenotype of cell growth rapid enough to kill in a short time. This would be irrespective of the need for any additional genetic events that may define the subsequent phenotypes of large lethal tumors, as these would be automatically acquired and be physiologically selected in any rapidly growing cell mass. It is evident that the steps of initiation and progression are dependent on both the rates of genetic change per cell division and the cell kinetic rates of division and death. We have chosen to first examine colon cancer because the rates of cell division in normal colonic epithelium, dysplastic adenomas and small carcinomas have been directly observed as reported herein. For colon cancer, we calculate that about 65% of the US population is at risk for both males and females, and that this fraction has been constant for the earliest recorded birth cohorts of the mid-19th century to the beginning of the 20th century. The changes that have been observed in colon cancer mortality rates appear to arise from historical changes in death rates by unknown 'other causes of death', which share both genetic and environmental risk factors with colon cancer and explicitly include undiagnosed deaths by colon cancer. Considering all possible values of n and m, we find the case of n=2 and m=1 to give the best concordance with present knowledge of mutations in the colon by the loss of two alleles of the APC gene and the observation that for m=1, a rate of genetic change approximately equal to that calculated for initiation mutation rates is obtained. Our estimates for the rate of initiation and progression mutation rates show no significant historical shifts and are approximately 1-2x10-7 events per cell division. (ABSTRACT TRUNCATED)